@article{Figueiredo2009, author = "de Figueiredo, Amanda Faria and Hasmik Mkrtchyan and Thomas Liehr and Eliane Maria Soares Ventura and de Jesus Marques-Salles, Terezinha and Neide Santos and Raul Corr{\^e}a Ribeiro and Eliana Abdelhay and Maria Luiza Macedo Silva", abstract = "Hyperdiploidy is rarely observed in childhood acute myeloid leukemia (AML). Described here is the case of a 2(1/2)-year-old girl with AML-M5 and 51 chromosomes characterized by double tetrasomy of chromosomes 8 and 21 and also a neocentric derivative chromosome neo(1)(qter-->q23 approximately 24::q23 approximately 24-->q43-->neo-->q43-->qter). Little is known about the prognostic significance of these chromosomal abnormalities in childhood AML. In the actual case, complete remission was achieved after chemotherapy, which continued for 7 months. No acquired neocentric chromosome 1 has been described previously, even though neocentromere formation has been reported for other chromosomes in neoplasms.", journal = "Cancer Genet Cytogenet", keywords = "Isis, mBAND, Child, Preschool; Chromosome Aberrations; Chromosomes, Human, Pair 21; Chromosomes, Human, Pair 8; Female; Humans; In Situ Hybridization, Fluorescence; Karyotyping; Leukemia, Myelogenous, Chronic, BCR-ABL Positive, genetics", month = "Sep", number = "2", pages = "123--126", title = "A case of childhood acute myeloid leukemia AML (M5) with a neocentric chromosome neo(1)(qter-->q23 approximately 24::q23 approximately 24-->q43-->neo-->q43-->qter) and tetrasomy of chromosomes 8 and 21.", url = "http://dx.doi.org/10.1016/j.cancergencyto.2009.05.001", volume = "193", year = "2009", } @article{00168, author = "M. Volleth and K.-G. Heller and R.A. Pfeiffer and H. Hameister", journal = "Chromosome Research", keywords = "Isis", pages = "477- 497", title = "A comparative ZOO-FISH analysis in bats elucidates the phylogenetic relationships between Megachiroptera and five microchiroptera families", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12489830{\&}dopt=Abstract", volume = "10", year = "2002", } @article{00173, author = "A. Heller and H. Starke and V. Trifonov and N. Rubtsov and U. Wedding and I. Loncarevic and C. Bleck and U. Claussen and T. Liehr", journal = "Int. J. Oncol.", keywords = "Isis mBAND", pages = "1179- 1181", title = "A complex translocation event between the two homologues of chromosomes 5 leading to a del(5)(q21q33) as a sole aberration in a case clinically diagnosed as CML: characterization of the aberration by multicolor banding", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12011996{\&}dopt=Abstract", volume = "20", year = "2002", } @article{00231, author = "M. K{\"u}hne and E. Riballo and N. Rief and K. Rothkamm and P.A. Jeggo and M. L{\"o}brich", journal = "Cancer Research", keywords = "Isis", pages = "500- 508", title = "A double-strand break repair defect in ATM-deficient cells contributes to radiosensitivity.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=14744762", volume = "64", year = "2004", } @article{00235, author = "N. Makretsov and M. He and M. Hayes and S. Chia and D.E. Horsman and P.H.B. Sorensen and D.G. Huntsman", journal = "Genes Chromosomes {\&} Cancer", keywords = "Isis", pages = "152- 157", title = "A fluorescence in situ hybridization study of ETV6-NTRK3 fusion gene in secretory breast carcinoma.", url = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed{\&}Cmd=ShowDetailView{\&}TermToSearch=15101049{\&}ordinalpos=8{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Res", volume = "40", year = "2004", } @article{00043, author = "O. Bartsch and G.K. Hinkel and M.B. Petersen and U. K{\"o}nig and M. Bugge and M. Mikkelsen and D. Avramopoulos and M. Morris and S.E. Antonarakis", journal = "Human Genetics", pages = "669- 675", title = "A large family with subtelomeric translocation t(18/21)(q23/q22.1) and molecular breakpoint in the Down syndrome critical region", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9341890{\&}dopt=Abstract", volume = "100", year = "1997", } @article{00140, author = "A. Bleichert and W. Fiedler and U. Clausen and G. Ernst and I.F. LonCarevic and A. Heller and T. Liehr and C. Kunert and von Eggeling, F.", journal = "International Journal of Molecular Medicine", keywords = "Isis", pages = "591- 595", title = "A long distance-PCR derived FISH probe detects a deletion between p15 and p16 in CML and T-ALL patients", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11351270{\&}dopt=Abstract", volume = "7", year = "2001", } @article{00044, author = "V.I. Bashkirov and H. Scherthan and J.A. Solinger and J.-M. Buerstedde and W.-D. Heyer", journal = "J Cell Biol", pages = "761- 773", title = "A mouse cytoplasmic exoribonuclease (mXRN1p) with preference for G4 tetraplex substrates", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9049243{\&}dopt=Abstract", volume = "136", year = "1997", } @article{00221, author = "J. Seidel and A. Heller and G. Senger and H. Starke and I. Chudoba and C. Kelbova and H. T{\"o}nnies and H. Neitzel and C. Haase and V. Beensen and F. Zintl and U. Claussen and T. Liehr", journal = "Eur J Pediatr", keywords = "Isis mFISH mBAND CGH Ikaros", pages = "582- 588", title = "A multiple translocation event in a patient with hexadactyly, facial dysmorphism, mental retardation and behaviour disorder characterised comprehensively by molecular cytogenetics. Case report and review of the literature.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12819962{\&}dopt=Abstract", volume = "162", year = "2003", } @article{JesusMarques-Salles2009, author = "de Jesus Marques-Salles, Terezinha and Thomas Liehr and Hasmik Mkrtchyan and Susana C Raimondi and de Souza, Mariana Tavares and de Figueiredo, Amanda Faria and Soraia Rouxinol and Fernanda C Jordy Macedo and Eliana Abdelhay and Neide Santos and Maria Luiza Macedo Silva", abstract = "Infants diagnosed with acute myelogenous leukemia (AML) are likely to have subtypes M4 or M5 characterized by 11q23 abnormalities like a t(9;11)(p22;q23). Detection of all possible types of chromosomal abnormalities, including mixed lineage leukemia (MLL) gene rearrangements at 11q23, is of importance for the identification of biological subgroups, which might differ in drug resistance and/or clinical outcome. Here, we report the clinical, conventional banding and molecular cytogenetics data of a 6-month-old boy with an AML-M5 presenting with a unique cryptic rearrangement involving the MLL gene: a three-way t(9;19;11)(p11.2;p13.1;q23).", journal = "Cancer Genet Cytogenet", keywords = "Isis, Chromosomes, Human, Pair 11, genetics; Chromosomes, Human, Pair 19, genetics; Chromosomes, Human, Pair 9, genetics; Humans; In Situ Hybridization, Fluorescence; Infant; Karyotyping; Leukemia, Myeloid, Acute, genetics; Male; Myeloid-Lymphoid Leukemia", month = "Feb", number = "1", pages = "59--62", title = "A new chromosomal three-way rearrangement involving MLL masked by a t(9;19)(p11;p13) in an infant with acute myeloid leukemia.", url = "http://dx.doi.org/10.1016/j.cancergencyto.2008.10.009", volume = "189", year = "2009", } @article{00151, author = "A. Nietzel and M. Rocchi and H. Starke and A. Heller and W. Fiedler and I. Wlodarska and I.F. Loncarevic and V. Beensen and U. Claussen and T. Liehr", journal = "Hum. Genet.", keywords = "Isis mFISH", pages = "199- 204", title = "A new multicolor-FISH approach for the characterization of marker chromosomes: centromere-specific multicolor-FISH (cenM-FISH)", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11354630{\&}dopt=Abstract", volume = "108", year = "2001", } @article{00305, author = "A. Kowalska and E. Bozsaky and T. Ramsauer and D. Rieder and G. Bindea and T. L{\"o}rch and Z. Trajanosky and P.F. Ambros", journal = "Chromosome Res.", keywords = "Isis Warp", pages = "327- 339", title = "A new platform linking chromosomal and sequence information.", url = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed{\&}Cmd=ShowDetailView{\&}TermToSearch=17406992{\&}ordinalpos=1{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Res", volume = "15", year = "2007", } @article{00070, author = "V.A. Botchkarev and P. Welker and K.M. Albers and N.V. Botchkareva and M. Metz and G.R. Lewin and S. Bulfone-Paus and E.M.J. Peters and G. Lindner and R. Paus", journal = "Am. J. Pathol.", keywords = "Isis", pages = "785- 799", title = "A new role for neurotrophin-3. Involvement in the regulation of hair follicle regression (catagen).", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=9736028{\&}query_hl=12{\&}itool=pubmed_docsum", volume = "153", year = "1998", } @article{Simkova2008, author = "Hana Simkov{\'a} and Jan Saf{\'a}r and Pavla Such{\'a}nkov{\'a} and Pavl{\'i}na Kov{\'a}rov{\'a} and Jan Bartos and Marie Kubal{\'a}kov{\'a} and Jaroslav Janda and Jarmila C{\'i}hal{\'i}kov{\'a} and Rohit Mago and Tamas Lelley and Jaroslav Dolezel", abstract = "BACKGROUND: Genomics of rye (Secale cereale L.) is impeded by its large nuclear genome (1C approximately 7,900 Mbp) with prevalence of DNA repeats (> 90\%). An attractive possibility is to dissect the genome to small parts after flow sorting particular chromosomes and chromosome arms. To test this approach, we have chosen 1RS chromosome arm, which represents only 5.6\% of the total rye genome. The 1RS arm is an attractive target as it carries many important genes and because it became part of the wheat gene pool as the 1BL.1RS translocation. RESULTS: We demonstrate that it is possible to sort 1RS arm from wheat-rye ditelosomic addition line. Using this approach, we isolated over 10 million of 1RS arms using flow sorting and used their DNA to construct a 1RS-specific BAC library, which comprises 103,680 clones with average insert size of 73 kb. The library comprises two sublibraries constructed using HindIII and EcoRI and provides a deep coverage of about 14-fold of the 1RS arm (442 Mbp). We present preliminary results obtained during positional cloning of the stem rust resistance gene SrR, which confirm a potential of the library to speed up isolation of agronomically important genes by map-based cloning. CONCLUSION: We present a strategy that enables sorting short arms of several chromosomes of rye. Using flow-sorted chromosomes, we have constructed a deep coverage BAC library specific for the short arm of chromosome 1R (1RS). This is the first subgenomic BAC library available for rye and we demonstrate its potential for positional gene cloning. We expect that the library will facilitate development of a physical contig map of 1RS and comparative genomics of the homoeologous chromosome group 1 of wheat, barley and rye.", journal = "BMC Genomics", keywords = "Chromosomes;Plant;Plant Diseases;Isis", pages = "237", title = "A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS).", url = "http://dx.doi.org/10.1186/1471-2164-9-237", volume = "9", year = "2008", } @article{00017, author = "H. Steilen-Gimbel and K. Remberger and N. Graf and W.-I. Streudel and K.D. Zang and W. Henn", journal = "Human Genetics", keywords = "Isis CGH", pages = "87- 90", title = "A novel site of DNA amplification on the chromosome 1p32-33 in a rhabdomyosarcoma revealed by comparative genome hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8557268{\&}dopt=Abstract", volume = "97", year = "1996", } @article{00220, author = "J. Cermak and K. Michalova and J. Brezinova and Z. Zemanova", journal = "Leukemia Research", keywords = "Isis mFISH mBAND", pages = "221- 229", title = "A prognostic impact of separation of refractory cytopenia with multilineage dysplasia and 5q-syndrome from refractory anemia in primary myelodysplastic syndrome.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=12537974", volume = "27", year = "2003", } @article{00012, author = "T. Liehr and H. Grehl and B. Rautenstrauss", journal = "TIG", keywords = "Isis", pages = "505- 505", title = "A rapid method for FISH analysis on interphase nuclei extracted from cryofixed tissues", volume = "12", year = "1996", } @article{Doherty2011, author = "Ann T Doherty and Julie Hayes and Mick Fellows and Sarah Kirk and Mike O'Donovan", abstract = "A semi-automated scoring system has been developed to provide rapid, accurate assessment of micronuclei in preparations of mononuclear mouse lymphoma L5178Y cells. Following exposure to a range of test agents, flat, single-cell preparations were produced from exponentially growing cultures by cytocentrifugation. Following staining with 4'-6-diamidino-2-phenylindole (DAPI), cells were scanned by use of the MicroNuc module of Metafer 4 v 3.4.102, after modifying the classifier developed for selecting micronuclei in binucleate cells to increase its sensitivity. The image gallery of all cells was then sorted to bring aberrant cells to the top of the gallery to assess visually the numbers of cells with micronuclei, as distinct from other debris. Slide quality was shown to be paramount in obtaining accurate results from an automated scan and the data obtained compared very well with the incidence of micronuclei scored conventionally by microscopy. Compared with manual scoring the time saving is considerable, as more than 2000 images are captured in approximately 2min, with subsequent visual assessment of aberrant cells in the image gallery taking about 1-2min/slide. By scanning all aberrant cells, the system also captures additional information on necrotic, apoptotic and fragmented cells. Although optimised for mouse lymphoma cells, it should be simple to adapt the method for any cell type growing in suspension.", journal = "Mutat Res", keywords = "Metafer MNScore", month = "Nov", number = "1", pages = "36--41", title = "A rapid, semi-automated method for scoring micronuclei in mononucleated mouse lymphoma cells.", url = "http://dx.doi.org/10.1016/j.mrgentox.2011.08.002", volume = "726", year = "2011", } @article{Rocha2011, author = "Cristiano Krings Rocha and Inka Praulich and Iris Gehrke and Michael Hallek and Karl-Anton Kreuzer", abstract = "ABSTRACT: The chromosomal translocation (11;14)(q13;q32) rearranging the locus for cyclin D1 (CCND1) to that of the immunoglobulin heavy chain (IGH) can be found in virtually all cases of mantle cell lymphoma (MCL), while other CCND1 translocations are extremely rare. As CCND1 overexpression and activation is a hallmark of MCL it is regarded as a central biological mechanism in the development and maintenance of this disease.Here we present a patient initially diagnosed with chronic lymphocytic leukemia (CLL) where chromosome banding analysis revealed, among other aberrations, a translocation (11;22)(q13;q11.2). We show by fluorescence in situ hybridization (FISH) analysis that on chromosome 22 the immunoglobulin light chain lambda (IGL) is involved in this cytogenetic aberration. Additionally, we demonstrate the resulting overexpression of CCND1 on the RNA and protein level, thereby consolidating the new diagnosis of a MCL-like B-cell neoplasia. Summing up, we described a rare case of t(11;22)(q13;q11.2) in a MCL-like neoplasia and showed that this aberration leads to an overexpression of CCND1 which is regarded as a key biological feature in MCL. This case underlines the importance of cytogenetic analyses especially in atypical cases of B cell lymphomas.", journal = "Mol Cytogenet", keywords = "XL Isis mFISH", number = "1", pages = "8", title = "A rare case of t(11;22) in a mantle cell lymphoma like B-cell neoplasia resulting in a fusion of IGL and CCND1: case report.", url = "http://dx.doi.org/10.1186/1755-8166-4-8", volume = "4", year = "2011", } @article{00216, author = "J. Ad{\'e}laide and H.-E. Huang and A. Murati and A.E. Alsop and B. Orsetti and M.-J. Mozziconacci and C. Popovici and C. Ginestier and A. Letessier and C. Basset and C. Courtay-Cahen and J. Jacquemier and C. Theillet and D. Birnbaum and P.A.W. Edwards and M. Chaffanet", journal = "Genes Chromosomes Cancer", keywords = "Isis mFISH", pages = "333- 345", title = "A recurrent translocation breakpoint in breast and pancreatic cancer cell lines targets the Neuregulin/NRG I gene", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12800145{\&}dopt=Abstract", volume = "37", year = "2003", } @article{00051, author = "H. Kehrer-Sawatzki and T. Schwickardt and G. Assum and M. Rocchi and W. Krone", journal = "Human Genetics", pages = "595- 600", title = "A third neurofibromatosis type 1 (NF1) pseudogene at chromosome 15q11.2", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9341878{\&}dopt=Abstract", volume = "100", year = "1997", } @article{Lapointe2007, author = "Jacques Lapointe and Young H. Kim and Melinda A. Miller and Chunde Li and Gulsah Kaygusuz and {van de Rijn}, Matt and David G. Huntsman and James D. Brooks and Jonathan R. Pollack", journal = "Mod Pathol", keywords = "Isis", month = "Apr", number = "4", pages = "467--473", title = "A variant TMPRSS2 isoform and ERG fusion product in prostate cancer with implications for molecular diagnosis.", url = "http://dx.doi.org/10.1038/modpathol.3800759", volume = "20", year = "2007", } @article{Carver2009, author = "BS Carver and J Tran and A Gopalan and Z Chen and S Shaikh and A Carracedo and A Alimonti and C Nardella and S Varmeh and PT Scardino and C Cordon-Cardo and W Gerald and PP Pandolfi", abstract = "Chromosomal translocations involving the ERG locus are frequent events in human prostate cancer pathogenesis; however, the biological role of aberrant ERG expression is controversial. Here we show that aberrant expression of ERG is a progression event in prostate tumorigenesis. We find that prostate cancer specimens containing the TMPRSS2-ERG rearrangement are significantly enriched for loss of the tumor suppressor PTEN. In concordance with these findings, transgenic overexpression of ERG in mouse prostate tissue promotes marked acceleration and progression of high-grade prostatic intraepithelial neoplasia (HGPIN) to prostatic adenocarcinoma in a Pten heterozygous background. In vitro overexpression of ERG promotes cell migration, a property necessary for tumorigenesis, without affecting proliferation. ADAMTS1 and CXCR4, two candidate genes strongly associated with cell migration, were upregulated in the presence of ERG overexpression. Thus, ERG has a distinct role in prostate cancer progression and cooperates with PTEN haploinsufficiency to promote progression of HGPIN to invasive adenocarcinoma.", journal = "Nat Genet", keywords = "Metafer MetaCyte TMA", number = "5", pages = "619-24", title = "Aberrant ERG expression cooperates with loss of PTEN to promote cancer progression in the prostate", url = "http://dx.doi.org/10.1038/ng.370", volume = "41", year = "2009", } @article{00055, author = "T. Liehr and H. Grehl and B. Rautenstrauss", journal = "Acta Neuropathol", pages = "514- 516", title = "Accumulation of peripherial mylin protein 22 (PMP22) in onion bulbs of nerves biopsied from patients with different subtypes of Charcot-Marie-Tooth disease type 1", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9386787{\&}dopt=Abstract", volume = "94", year = "1997", } @article{Steidl2005, author = "C Steidl and R Steffens and W Gassmann and B Hildebrandt and R Hilgers and U Germing and L Tr{\"u}mper and D Haase", journal = "Leuk Res", keywords = "Metafer MSearch", number = "9", pages = "987-93", title = "Adequate cytogenetic examination in myelodysplastic syndromes: analysis of 529 patients", url = "http://dx.doi.org/10.1016/j.leukres.2005.01.019", volume = "29", year = "2005", } @article{Granic2010b, author = "Antoneta Granic and Jaya Padmanabhan and Michelle Norden and Huntington Potter", abstract = "Both sporadic and familial Alzheimer's disease (AD) patients exhibit increased chromosome aneuploidy, particularly trisomy 21, in neurons and other cells. Significantly, trisomy 21/Down syndrome patients develop early onset AD pathology. We investigated the mechanism underlying mosaic chromosome aneuploidy in AD and report that FAD mutations in the Alzheimer Amyloid Precursor Protein gene, APP, induce chromosome mis-segregation and aneuploidy in transgenic mice and in transfected cells. Furthermore, adding synthetic Abeta peptide, the pathogenic product of APP, to cultured cells causes rapid and robust chromosome mis-segregation leading to aneuploid, including trisomy 21, daughters, which is prevented by LiCl addition or Ca(2+) chelation and is replicated in tau KO cells, implicating GSK-3beta, calpain, and Tau-dependent microtubule transport in the aneugenic activity of Abeta. Furthermore, APP KO cells are resistant to the aneugenic activity of Abeta, as they have been shown previously to be resistant to Abeta-induced tau phosphorylation and cell toxicity. These results indicate that Abeta-induced microtubule dysfunction leads to aneuploid neurons and may thereby contribute to the pathogenesis of AD.", journal = "Mol Biol Cell", keywords = "Metafer MSearch Isis", month = "Feb", number = "4", pages = "511--520", title = "Alzheimer Abeta peptide induces chromosome mis-segregation and aneuploidy, including trisomy 21: requirement for tau and APP.", url = "http://dx.doi.org/10.1091/mbc.E09-10-0850", volume = "21", year = "2010", } @article{00200, author = "C. Schoch and S. Schnittger and M. Klaus and W. Kern and W. Hiddemann and T. Haferlach", journal = "Blood", keywords = "Isis", pages = "2395- 2402", title = "AML with 11q23/MLL abnormalities as defined by the WHO classification: incidence, partner chromosomes, FAB subtype, age distribution, and prognostic impact in an unselected series of 1897 cytogenetically analyzed AMl cases.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=12805060{\&}query_hl=2", volume = "102", year = "2003", } @article{00045, author = "E.D. Coene and V. Schelfhout and R.A. Winkler and A.-M. Schelfhout and N. Van Roy and M. Grooteclaes and F. Speleman and C.R. De Potter", journal = "Virchows Arch", pages = "365- 372", title = "Amplification units and translocation at chromosome 17q and c-erbB-2 overexpression in the pathogenesis of breast cancer", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9174626{\&}dopt=Abstract", volume = "430", year = "1997", } @article{00259, author = "D. Varga and T. Johannes and S. Jainta and S. Schuster and U. Schwarz-Boeger and M. Kiechle and B.P. Garcia and W. Vogel", journal = "Mutagenesis", keywords = "Metafer MSearch MicroNuclei", pages = "391- 397", title = "An automated scoring procedure for the micronucleus test by image analysis", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15388812", volume = "19", year = "2004", } @article{Uldrijan2007, author = "Stjepan Uldrijan and Willem-Jan Pannekoek and Karen H Vousden", abstract = "MDM2 (HDM2) is a ubiquitin ligase that can target the p53 tumor suppressor protein for degradation. The RING domain is essential for the E3 activity of MDM2, and we show here that the extreme C-terminal tail of MDM2 is also critical for efficient E3 activity. Loss of E3 function in MDM2 mutants deleted of the C-terminal tail correlated with a failure of these mutants to oligomerize with MDM2, or with the related protein MDMX (HDMX). However, MDM2 containing point mutations within the C-terminus that inactivated E3 function retained the ability to oligomerize with the wild-type MDM2 RING domain and MDMX, and our results indicate that oligomers containing both wild-type MDM2 and a C-terminal mutant protein retain E3 function both in auto-degradation and degradation of p53. Interestingly, the E3 activity of C-terminal point mutants of MDM2 can also be supported by interaction with wild-type MDMX, suggesting that MDMX can directly contribute to E3 function.", journal = "EMBO J", keywords = "Isis", month = "Jan", number = "1", pages = "102--112", title = "An essential function of the extreme C-terminus of MDM2 can be provided by MDMX.", url = "http://dx.doi.org/10.1038/sj.emboj.7601469", volume = "26", year = "2007", } @article{00131, author = "C. Helmken and A. Wetter and S. Rudnik-Sch{\"o}neborn and T. Liehr and K. Zerres and B. Wirth", journal = "European Journal of Human Genetics", pages = "493- 499", title = "An Essential SMN Interacting Protein (SIP1) is not involved in the Phenotypic Variability of Spinal Muscular Atrophy (SMA)", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10909848{\&}dopt=Abstract", volume = "8", year = "2000", } @article{May2008, author = "Philippa C May and Caroline Mackie Ogilvie and Shehla Mohammed and Zoe Docherty and Richard Peter Hall", abstract = "Karyotyping is currently the "gold standard" test for the detection of human chromosome abnormalities. Over the past 40 years, changes in techniques have improved the band definition of chromosomes; however, very little has changed with respect to improvements through automation. In this study, we compare chromosome analysis by traditional microscopy with semi-automatic karyotyping using robotic equipment from MetaSystems (Altlussheim, Germany). Analysis using MetaSystems was significantly quicker than using the microscope with an average reduction in analysis time of 26.5 minutes; for the average analyst, this equates to a reduction of 27 percent. Analysis checking times using MetaSystems showed even greater improvement with an average reduction in checking time of 11.4 minutes; for the average checker, this equates to a reduction of 48 percent. The MetaSystems semi-automatic karyotyping equipment offers increased throughput of cases for karyotype analysis while maintaining accuracy.", journal = "J Assoc Genet Technol", keywords = "Metafer MSearch Ikaros AutoCapt", number = "4", pages = "177--187", title = "An Evaluation of the Effectiveness of a Semi-automatic Metaphase Locating and On-screen Karyotyping System.", url = "http://www.agt-info.org/pdfs/AGT%20Journal%204th%20Qtr%2008%20final%20galley.pdf", volume = "34", year = "2008", } @article{Moralli2011, author = "Daniela Moralli and Mohammed Yusuf and Mohammad A Mandegar and Suhail Khoja and Zoia L Monaco and Emanuela V Volpi", abstract = "Prolonged in vitro culture of human embryonic stem (hES) cells can result in chromosomal abnormalities believed to confer a selective advantage. This potential occurrence has crucial implications for the appropriate use of hES cells for research and therapeutic purposes. In view of this, time-point karyotypic evaluation to assess genetic stability is recommended as a necessary control test to be carried out during extensive 'passaging'. Standard techniques currently used for the cytogenetic assessment of ES cells include G-banding and/or Fluorescence in situ Hybridization (FISH)-based protocols for karyotype analysis, including M-FISH and SKY. Critical for both banding and FISH techniques are the number and quality of metaphase spreads available for analysis at the microscope. Protocols for chromosome preparation from hES and human induced pluripotent stem (hiPS) cells published so far appear to differ considerably from one laboratory to another. Here we present an optimized technique, in which both the number and the quality of chromosome metaphase spreads were substantially improved when compared to current standard techniques for chromosome preparations. We believe our protocol represents a significant advancement in this line of work, and has the required attributes of simplicity and consistency to be widely accepted as a reference method for high quality, fast chromosomal analysis of human ES and iPS cells.", journal = "Stem Cell Rev", keywords = "24XCyte Probes", month = "Jun", number = "2", pages = "471--477", title = "An improved technique for chromosomal analysis of human ES and iPS cells.", url = "http://dx.doi.org/10.1007/s12015-010-9224-4", volume = "7", year = "2011", } @article{00064, author = "N. Van Roy and G. Laureys and M. Van Gele and G. Opdenakker and R. Miura and van der Drift, P. and A. Chan and R. Versteeg and F. Speleman", journal = "Eur J Cancer", pages = "1974- 1978", title = "Analysis of 1/17 Translocation Breakpoints in Neuroblastoma: Implications for Mapping of Neuroblastoma Genes", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9516836{\&}dopt=Abstract", volume = "33", year = "1997", } @article{00304, author = "L. Babicka and S. Ransdorfova and J. Brezinova and Z. Zemanova and L. Sindelarova and M. Siskova and J. Maaloufova and J. Cermak and K. Michalova", journal = "Leukemia Research", keywords = "Isis mFISH", pages = "39- 47", title = "Analysis of complex chromosomal rearrangements in adult patients with MDS and AML by multicolor FISH.", url = "http://www.ncbi.nlm.nih.gov/pubmed/16687173?ordinalpos=5{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDoc", volume = "31", year = "2007", } @article{00306, author = "R. Stevens and I. Almanaseer and M. Gonzalez and D. Caglar and R.A. Knudson and R.P. Ketterling and D.S. Schrock and T.A. Seemayer and J.A. Bridge", journal = "J Molecular Diagn", keywords = "MetaCyte (AutoVysion)", pages = "144- 150", title = "Analysis of HER2 gene amplification using an automated fluorescence in situ hybridization signal enumeration system.", url = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed{\&}Cmd=ShowDetailView{\&}TermToSearch=17384205{\&}ordinalpos=9{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Res", volume = "9", year = "2007", } @article{00309, author = "R. Stevens and I. Almanaseer and M. Gonzalez and D. Caglar and R.A. Knudson and R.P. Ketterling and D.S. Schrock and T.A. Seemayer and J.A. Bridge", journal = "Journal of Molecular Diagnostics", keywords = "Metafer MetaCyte AutoVysion", pages = "144- 150", title = "Analysis of HER2 gene amplification using an automated fluorescence in situ hybridization signal enumeration system.", url = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed{\&}Cmd=ShowDetailView{\&}TermToSearch=17384205{\&}ordinalpos=1{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Res", volume = "9", year = "2007", } @article{00107, author = "C. Johannes and I. Chudoba and G. Obe", journal = "Chromosome Res", keywords = "Isis mBAND", pages = "625- 633", title = "Analysis of X-ray-induced aberrations in human chromosome 5 using high-resolution multicolor banding FISH (mBAND)", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10628663{\&}dopt=Abstract", volume = "7", year = "1999", } @article{00149, author = "P. Duesberg and R. Stindl and R. Li and R. Hehlmann and D. Rasnick", journal = "Current Science", keywords = "Isis mFISH", pages = "490- 500", title = "Aneuploidy versus gene mutation as cause of cancer", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=10725343{\&}query_hl=5{\&}itool=pubmed_docsum", volume = "81", year = "2001", } @article{00285, author = "E. Zamorano-Ponce and C. Morales and D. Ramos and C. Sep{\'u}lveda and S. Cares and P. Rivera and J. Fern{\'a}ndez and M.A. Carballo", journal = "Mutation Research", keywords = "CometImager", pages = "145- 150", title = "Anti-genotoxic effect of Aloysia triphylla infusion against acrylamide-induced DNA damage as shown by the comet assay technique.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=16413820{\&}query_hl=3{\&}itool=pubmed_docsum", volume = "603", year = "2006", } @article{Vree2009, author = "de Vree, Paula Jp and Marleen Eh Simon and van Dooren, Marieke F and Gerda Ht Stoevelaar and Jos{\'e} Tw Hilkmann and Michel A Rongen and Gido Cm Huijbregts and Annemieke Jmh Verkerk and Pino J Poddighe", abstract = "ABSTRACT: BACKGROUND: Complex chromosomal rearrangements (CCR) are rare cytogenetic findings that are difficult to karyotype by conventional cytogenetic analysis partially because of the relative low resolution of this technique. High resolution genotyping is necessary in order to identify cryptic imbalances, for instance near the multiple breakpoints, to explain the abnormal phenotype in these patients. We applied several molecular techniques to elucidate the complexity of the CCRs of two adult patients with abnormal phenotypes. RESULTS: Multicolour fluorescence in situ hybridization (M-FISH) showed that in patient 1 the chromosomes 1, 10, 15 and 18 were involved in the rearrangement whereas for patient 2 the chromosomes 5, 9, 11 and 13 were involved. A 250 k Nsp1 SNP-array analysis uncovered a deletion in chromosome region 10p13 for patient 1, harbouring 17 genes, while patient 2 showed no pathogenic gains or losses. Additional FISH analysis with locus specific BAC-probes was performed, leading to the identification of cryptic interstitial structural rearrangements in both patients. CONCLUSION: Application of M-FISH and SNP-array analysis to apparently balanced CCRs is useful to delineate the complex chromosomal rearrangement in detail. However, it does not always identify cryptic imbalances as an explanation for the abnormal phenotype in patients with a CCR.", journal = "Mol Cytogenet", keywords = "Ikaros Isis mFISH ", pages = "15", title = "Application of molecular cytogenetic techniques to clarify apparently balanced complex chromosomal rearrangements in two patients with an abnormal phenotype: case report.", url = "http://dx.doi.org/10.1186/1755-8166-2-15", volume = "2", year = "2009", } @article{00087, author = "A. Herry and C. Berthou and M.-C. L{\'e}glise and J.-F. Abgrall and P. Morice and M. Lessard", journal = "H{\'e}matologie", pages = "67- 73", title = "Apport de la FISH dans l'{\'e}tude des remaniements acquis des chromosomes 5 et 7", volume = "4", year = "1998", } @article{00290, author = "O.P.F. Clausen and H.C.D. Aass and M. Beigi and K.J. Purdie and C.M. Proby and V.L. Brown and M. Mattingsdahl and F. Micci and S. K{\o}lvraa and L. Bolund and P.M. De Angelis", journal = "J Invest Dermatol", keywords = "Isis CGH", pages = "2308- 2315", title = "Are keratoacanthomas variants of squamous cell carcinomas? A comparison of chromosomal aberrations by comparative genomic hybridization.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=16728973{\&}query_hl=17{\&}itool=pubmed_docsum", volume = "126", year = "2006", } @article{00276, author = "U. Wick and E. Gebhart", journal = "Int J Radiat Biol", keywords = "Isis Telomere", pages = "1707- 1713", title = "Are telomeres a specific target for mutagenic attack by cytostatics in neoplastic cells?", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=15870889{\&}query_hl=5{\&}itool=pubmed_docsum", volume = "26", year = "2005", } @article{00100, author = "H. Scherthan and R. Eils and E. Trelles-Sticken and S. Dietzel and T. Cremer and H. Walt and A. Jauch", journal = "Journal of Cell Science", pages = "2337- 2351", title = "Aspects of tree4-dimensional chromosome reorganization during the onset of human male meiotic prophase", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9683629{\&}dopt=Abstract", volume = "111", year = "1998", } @article{00097, author = "B. Rautenstrauss and C. Fuchs and A. Ekici and E. Nelis and C. Van Broeckhoven and T. Liehr", journal = "Genet Analysis: Biomolec Engineer", pages = "103- 104", title = "Assay of transfection rate in insect cells on a single cell level", volume = "14", year = "1998", } @article{Markunas2008, author = "Christina A. Markunas and David M. Umbach and Zongli Xu and Jack A. Taylor", abstract = "Nonsynonymous SNPs (nsSNPs) in DNA repair genes may be important determinants of DNA damage and cancer risk. We applied a set of screening criteria to a large number of nsSNPs and selected a subset of SNPs that were likely candidates for phenotypic effects on DNA double-strand break repair (DSBR). In order to induce and follow DSBR, we exposed panels of cell lines to gamma irradiation and followed the formation and disappearance of gammaH2A.X foci over time. All panels of cell lines showed significant increases in number, intensity, and area of foci at both the 1-hour and 3-hour time points. Twenty four hours following exposure, the number of foci returned to preexposure levels in all cell lines, whereas the size and intensity of foci remained significantly elevated. We saw no significant difference in gammaH2A.X foci between controls and any of the panels of cell lines representing the different nsSNPs.", journal = "J Cancer Epidemiol", keywords = "Foci, Metafer, MetaCyte, H2AX", pages = "387423", title = "Assessing Candidate Gene nsSNPs for Phenotypic Differences in Double-Strand Break Repair Using Radiation-Induced gammaH2A.X Foci.", url = "http://dx.doi.org/10.1155/2008/387423", volume = "2008", year = "2008", } @article{00307, author = "M. Ruchirawat and D. Settachan and P. Navasumrit and J. Tuntawiroon and H. Autrup", journal = "Toxicol Lett", keywords = "Metafer CometScan", pages = "200- 209", title = "Assessment of potential cancer risk in children exposed to urban air pollution in Bangkok, Thailand.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=17157453{\&}query_hl=23{\&}itool=pubmed_docsum", volume = "168", year = "2007", } @article{00072, author = "S. Scohy and P. Van Vooren and C. Spzirer and J. Szpirer", journal = "Cytogenet Cell Genet", keywords = "Isis", pages = "273- 274", title = "Assignement of Sp to the rat chromosome band 7q36 (Sp1), 10q31 (r) q32.1 (Sp2), 3q24(r) q31(Sp3), and 6q33 (Sp4) and of the SP2 gene to the human band 17q21.3 (r) q22 by in situ hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9730617{\&}dopt=Abstract", volume = "81", year = "1998", } @article{00092, author = "J.-F. Laes and P. Van Vooren and J. Szpirer and C. Szpirer", journal = "Cytogent Cell Genet", pages = "290- 291", title = "Assignement of the cyclin-dependent kinase inhibitor genes Cdkn2a and Cdkn2b to rat chromosome bands 5q32 (r) q34 and 5q31(r) q33 respectively by flourescence in situ hybridization using small PCR-generated probes", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9730623{\&}dopt=Abstract", volume = "81", year = "1998", } @article{00073, author = "T. Van Reeth and P. Van Vooren and C. Szpirer and J. Szpirer", journal = "Cytogenet Cell Genet", keywords = "Isis", pages = "174- 175", title = "Assignment of the hepatocyte nuclear factor 3 genes to rat chromosome band 6q23(r) q24 (alpha: Hnf3a), 3q41 (beta: Hnf3b) and 1q21(r) q22 (gamma: Hnf3g) by insitu hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9730593{\&}dopt=Abstract", volume = "81", year = "1998", } @article{00031, author = "E. Pr{\"o}ls and T. Liehr and R. Rinke and B. Rautenstrauss", journal = "Cytogenet Cell Genet", keywords = "Isis", pages = "149- 150", title = "Assignment of the microvascular endothelial differentiation gene 1 (MDG1) to human chromosome band 14q24.2 (r) q24.3 by flourescence in situ hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9533036{\&}dopt=Abstract", volume = "79", year = "1997", } @article{00164, author = "H. Scherthan and I. Sch{\"o}nborn", journal = "Chromosome Res", keywords = "Isis", pages = "273- 382", title = "Asynchronous chromosome pairing in male meiosis of the rat (Rattus norvegicus)", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11419792{\&}dopt=Abstract", volume = "9", year = "2001", } @article{00287, author = "A.L. Bredemeyer and G.G. Sharma and C.-Y. Huang and B.A. Helmink and L.M. Walker and K.C. Khor and B. Nuskey and K.E. Sullivan and T.K. Pandita and C.H. Bassing and B.P. Sleckman", journal = "Nature", keywords = "Isis", pages = "466- 470", title = "ATM stabilizes DNA double-strand-break complexes during V(D)J recombination.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=16799570{\&}query_hl=3{\&}itool=pubmed_docsum", volume = "442", year = "2006", } @article{00192, author = "S. Sauter and von Beust, G. and P. Burfeind and A. Weise and H. Starke and T. Liehr and B. Zoll", journal = "Am J Med Genet", keywords = "Ikaros Isis mBAND", pages = "533- 536", title = "Autistic disorder and chromosomal mosaicism 46,XY[123]/46,XY,del(20)(pter->p12.2)[10]", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12884434{\&}dopt=Abstract", volume = "120", year = "2003", } @article{Stang2010, author = "A. Stang and M. Brend'amour and C. Schunck and I. Witte", abstract = "Recently a high-throughput version of the comet assay was developed using a special 96-well multichamber plate (MCP) [1]. In this version, the electrophoresis is performed directly on the MCP, which makes transferring of cells to microscope slides unnecessary. In order to facilitate the scoring procedure we adapted an automated slide-scanning system (Metafer MetaCyte with CometScan) to enable unattended analysis of comets on the MCP. The results of the system were compared with the data obtained with two interactive comet-assay analysis systems. For induction of DNA damage in human fibroblasts methylmethane sulfonate (MMS) or H(2)O(2) was used. The three systems revealed similar, concentration-dependent results for all parameters tested: tail moment (tm), \% DNA-in-tail and olive tail moment. Near the detection limit of 5-6\% DNA-in-tail a significant difference with the untreated control was obtained by use of four parallel samples (p=0.01). With the newly developed automated analysis system, the evaluation of either 50 or 100 comets yielded similar standard errors for either treatment with MMS or H(2)O(2), thus showing that the method is suitable to reveal the crucial low-dose effects with high precision. The results also show that the time needed for automated evaluation of comets on the MCP was reduced by a factor of 10 when compared with the time required for interactive evaluation. In summary, the high-throughput version of the comet assay combined with the automated evaluating system increased the output by a factor up to 180 compared with the standard method.", journal = "Mutat Res", keywords = "Metafer CometScan", month = "Mar", title = "Automated analysis of DNA damage in the high-throughput version of the comet assay.", url = "http://dx.doi.org/10.1016/j.mrgentox.2010.02.014", year = "2010", } @article{Schunck2011, author = "Christian Schunck and Eiman Mohammad", abstract = "The HER2/neu gene (also known as ERBB2) is located on chromosome 17 (q11.2-q12) and encodes a glycoprotein known to be a member of the epidermal growth factor receptor family. Clinically, the determination of its amplification status is of utmost importance, as 10-35\% of invasive human breast carcinomas come along with HER2/neu overexpression, and treatment has to be adjusted accordingly. Here a method to analyze HER2 FISH samples with digital microscopy, using the slide scanning -platform Metafer PV (MetaSystems, Altlussheim, Germany), is presented. Metafer PV is a system for the automation of HER2/neu FISH assay analysis of samples hybridized with the Abbott(™) PathVysion(®) probe kit.", journal = "Methods Mol Biol", keywords = "Metafer MetaCyte Metafer-PV Her2 PathVysion", pages = "91--103", title = "Automated Analysis of FISH-Stained HER2/neu Samples with Metafer.", url = "http://www.ncbi.nlm.nih.gov/pubmed/21370008", volume = "724", year = "2011", } @article{00297, author = "K.K. Reichard and B.K. Hall and A. Corn and M.K. Foucar and J. Hozier", journal = "Modern Pathology", keywords = "Metafer MetaCyte", pages = "1027- 1033", title = "Automated analysis of fluorescence in situ hybridization on fixed, paraffin-embedded whole tissue sections in B-cell lymphoma.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=16680153{\&}query_hl=1{\&}itool=pubmed_docsum", volume = "19", year = "2006", } @article{Gaiser2010, author = "Timo Gaiser and Lissa Berroa-Garcia and Ralf Kemmerling and Aparajita Dutta and Thomas Ried and Kerstin Heselmeyer-Haddad", abstract = "The simultaneous detection of protein expression and gene copy number changes in patient samples, like paraffin-embedded tissue sections, is challenging since the procedures of immunohistochemistry (IHC) and Fluorescence in situ Hybridization (FISH) negatively influence each other which often results in suboptimal staining.Therefore, we developed a novel automated algorithm based on relocation which allows subsequent detection of protein content and gene copy number changes within the same cell.Paraffin-embedded tissue sections of colorectal cancers were stained for CD133 expression. IHC images were acquired and image coordinates recorded. Slides were subsequently hybridized with fluorescently labeled DNA probes. FISH images were taken at the previously recorded positions allowing for direct comparison of protein expression and gene copy number signals within the same cells/tissue areas. Relocation, acquisition of the IHC and FISH images, and enumeration of FISH signals in the immunophenotyped tumour areas were done in an automated fashion.Automated FISH analysis was performed on 13 different colon cancer samples that had been stained for CD133; each sample was scored for MYC, ZNF217 and Chromosome 6 in CD133 positive and negative glands. From the 13 cases four (31\%) showed amplification for the MYC oncogene and seven of 13 (54\%) cases were amplified for ZNF217. There was no significant difference between CD133 positive tumour and CD133 negative tumour cells.The technique and algorithm presented here enables an easy and reproducible combination of IHC and FISH based on a novel automated algorithm using relocation and automated spot counting.", journal = "Anal Cell Pathol (Amst)", keywords = "Metafer MetaCyte", number = "2", pages = "105--112", title = "Automated analysis of protein expression and gene amplification within the same cells of paraffin-embedded tumour tissue.", url = "http://dx.doi.org/10.3233/ACP-CLO-2010-0532", volume = "33", year = "2010", } @article{Verbeek2008, author = "F. Verbeek and G. Koppen and B. Schaeken and L. Verschaeve", abstract = "Food irradiation is the process of exposing food to ionising radiation in order to disinfect, sanitise, sterilise and preserve food or to provide insect disinfestation. Irradiated food should be adequately labelled according to international and national guidelines. In many countries, there are furthermore restrictions to the product-specific maximal dose that can be administered. Therefore, there is a need for methods that allow detection of irradiated food, as well as for methods that provide a reliable dose estimate. In recent years, the comet assay was proposed as a simple, rapid and inexpensive method to fulfil these goals, but further research is required to explore the full potential of this method. In this paper we describe the use of an automated image analysing system to measure DNA comets which allow the discrimination between irradiated and non-irradiated food as well as the set-up of standard dose-response curves, and hence a sufficiently accurate dose estimation.", journal = "Radiat Prot Dosimetry", keywords = "Metafer MetaCyte CometScan", number = "4", pages = "421--426", title = "Automated detection of irradiated food with the comet assay.", url = "http://dx.doi.org/10.1093/rpd/ncm433", volume = "128", year = "2008", } @article{00310, author = "F. Verbeek and G. Koppen and B. Schaeken and L. Verschaeve", journal = "Radiation Protection Dosimetry", keywords = "Metafer MetaCyte CometScan", pages = "1- 6", title = "Automated detection of irradiated food with the Comet assay.", url = "http://www.ncbi.nlm.nih.gov/pubmed/17921509?ordinalpos=1{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", year = "2007", } @article{00325, author = "J. Erlecke and I. Hartmann and M. Hoffmann and T. Kroll and H. Starke and A. Heller and A. Gloria and H.G. Sayer and T. Johannes and U. Claussen and T. Liehr and I.F. Loncarevic", abstract = "A new chimerism analysis based on automated interphase fluorescence in situ hybridization (FISH) evaluation was established to detect residual cells after allogene sex-mismatched bone marrow or blood stem-cell transplantation.Cells of 58 patients were characterized as disease-associated due to presence of a bcr/abl-gene-fusion or a trisomy 8 and/or a simultaneous hybridization of gonosome-specific centromeric probes. The automatic slide scanning platform Metafer with its module MetaCyte was used to analyse 3,000 cells per sample. RESULTS: Overall 454 assays of 58 patients were analyzed. 13 of 58 patients showed residual recipient cells at one stage of more than 4% and 12 of 58 showed residual recipient cells less than 4%, respectively. As to be expected, patients of the latter group were associated with a higher survival rate (48 vs. 34 month). In only two of seven patients with disease-marker positive residual cells between 0.1-1.3% a relapse was observed. Besides, disease-marker negative residual cells were found in two patients without relapse at a rate of 2.8% and 3.3%, respectively. CONCLUSION: The definite origin and meaning of disease-marker negative residual cells is still unclear. Overall, with the presented automatic chimerism analysis of interphase FISH slides, a sensitive method for detection of disease-marker positive residual cells is on hand. ", journal = "Molecular Cytogenetics", keywords = "Metafer MetaCyte", pages = "0- 0", title = "Automated detection of residual cells after sex-mismatched stem-cell transplantation - evidence for presence of disease-marker negative residual cells.", url = "http://www.ncbi.nlm.nih.gov/pubmed/19480690?ordinalpos=1{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDoc", volume = "2", year = "2009", } @article{Alpar2007, author = "Don{\'a}t Alp{\'a}r and B{\'e}la Kajt{\'a}r and M{\'a}ria Kneif and P{\'a}l J{\'a}ks{\'o} and Ren{\'a}ta L{\'a}szl{\'o} and L{\'a}szl{\'o} Kereskai and L{\'a}szl{\'o} Pajor", abstract = "Among the various methods available for analyzing minimal residual disease, a new procedure for the cell-based approaches using consecutive phenotypic and genotypic analysis as revealed by immunofluorescent labeling and subsequent fluorescent in situ hybridization (FISH) has been developed. We are introducing a fluorescent microscopy-based technique by which not only cellular targets and immunological marker positivity, but also the FISH pattern was identified by automated scanning. For the latter one translocation-specific FISH pattern recognition was accomplished by using an automated scanning mode for the 3D determination of valid distances between FISH signals, to define the cutoff value for the shortest green-red spot distance differentiating positive cells from negative ones. The procedure was tested with CD10(+) acute lymphoblastic leukemia cell line harboring the t(12;21)(p13;q22) resulting in the ETV6/RUNX1 rearrangement (formerly TEL/AML1), as well as peripheral blood lymphocytes of healthy individuals. Using the combined, automated method, a sensitivity of 98.67\% and a specificity of 99.97\% were obtained. The mean false positivity + 2 standard deviations cutoff level (0.09\%) allows detection of leukemic cells with high accuracy, even a bit below the tumor load dilution of 10(-3), a value reported to be critical in clinical decision making.", journal = "Cancer Genet Cytogenet", keywords = "Metafer, RCDetect, MetaCyte", month = "Feb", number = "1", pages = "23--30", title = "Automated detection of residual leukemic cells by consecutive immunolabeling for CD10 and fluorescence in situ hybridization for ETV6/RUNX1 rearrangement in childhood acute lymphoblastic leukemia.", url = "http://dx.doi.org/10.1016/j.cancergencyto.2006.09.007", volume = "173", year = "2007", } @article{00318, author = "D. Alp{\'a}r and J. Hermesz and L. P{\'o}t{\'o} and R. L{\'a}szl{\'o} and L. Kereskai and P. J{\'a}ks{\'o} and G. Pajor and L. Pajor and B. Kajt{\'a}r", journal = "Cytometry", keywords = "Metafer MetaCyte", pages = "651- 657", title = "Automated FISH analysis using dual-fusion and break-apart probes on paraffin-embedded tissue sections.", url = "http://www.ncbi.nlm.nih.gov/pubmed/18393324?ordinalpos=1{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", volume = "73", year = "2008", } @article{00252, author = "A. Plesch", journal = "E.C.A. Newsletter", keywords = "Metafer MetaCyte", pages = "26- 26", title = "Automated FISH analysis: state of the art", volume = "13", year = "2004", } @article{00296, author = "B. Kajt{\'a}r and G. M{\'e}hes and T. L{\"o}rch and L. De{\'a}k and M. Kneifn{\'e} and D. Alp{\'a}r and L. Pajor", journal = "International Society for Analytical Cytology", keywords = "Metafer MetaCyte", pages = "506- 514", title = "Automated fluorescent in situ hybridization (FISH) analysis of t(9;22)(q34;q11) in interphase nuclei.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=Abstract{\&}list_uids=16646048{\&}query_hl=1{\&}itool=pubmed_docsum", volume = "69", year = "2006", } @article{00319, author = "A.T. Blandin and D. M{\"u}hlematter and S. Bougeon and C. Gogniat and S. Porter and V. Beyer and V. Parlier and J.S. Beckmann and van Melle, G. and M. Jotterand", journal = "Cancer Genet Cytogenet", keywords = "Metafer MetaCyte", pages = "69- 77", title = "Automated four-color interphase fluorescence in situ hybridization approach for the simultaneous detection of specific aneuploidies of diagnostic and prognostic significance in high hyperdiploid acute lymphoblastic leukemia.", url = "http://www.ncbi.nlm.nih.gov/pubmed/18940469?ordinalpos=4{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDoc", volume = "186", year = "2008", } @article{00311, author = "A. Maes and E. Den Hond and L. Verschaeve", journal = "Microscopy and Analysis", keywords = "Metafer MSearch MicroNuclei", pages = "7- 9", title = "Automated image analysis of micronuclei in binucleated human lymphocytes.", url = "http://www.microscopy-analysis.com/cgi-bin/item.cgi?ap=1{\&}id=457", volume = "21", year = "2007", } @article{00006, author = "R. Huber and U. Kulka and T. L{\"o}rch and H. Braselmann and M. Bauchinger", journal = "Mutation Research", keywords = "Metafer MSearch", pages = "97- 102", title = "Automated metaphase finding: an assessment of the efficiency of the METAFER2 system in routine mutagenicity assay", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=7528343{\&}dopt=Abstract", volume = "334", year = "1995", } @article{Willems2010, author = "Petra Willems and Liezel August and Jacobus Slabbert and Horst Romm and Ursula Oestreicher and Hubert Thierens and Anne Vral", abstract = "PURPOSE: In case of a large-scale radiation accident when hundreds of people may be exposed, it is important to distinguish the severely exposed individuals (> or =1 gray), who require early medical treatment, from those less exposed. The aim of our study was to develop a quick population triage method based on automated micronucleus (MN) scoring. MATERIALS AND METHODS: Using the MN software module developed by MetaSystems specifically for the Metafer4 platform, about 60 blood samples can be scored in one day. Standard dose response curves were determined for manual and automated MN scoring. RESULTS: The automated MN assay results were closely correlated with MN yields obtained with the manual procedure. A dose of 1 Gy can be estimated with an uncertainty of 0.2 Gy. Corrections for false positives and false negatives by visual inspection of the image gallery did not result in an improved accuracy or reproducibility. To test the automated MN assay in a multicenter setting, an inter-laboratory comparison was performed whereby irradiated blood samples were processed in Ghent University (Belgium) and BfS (Bundesamt fuer Strahlenschutz; Germany). Both laboratories obtained comparable results. CONCLUSIONS: These results confirm the efficacy of the automated MN assay for fast population triage in a multicenter setting, in the case of large radiation accidents.", doi = "10.3109/09553000903264481", journal = "Int J Radiat Biol", keywords = "Metafer MNScore", month = "Jan", number = "1", pages = "2--11", title = "Automated micronucleus (MN) scoring for population triage in case of large scale radiation events.", url = "http://dx.doi.org/10.3109/09553000903264481", volume = "86", year = "2010", } @article{Rossnerova2011, author = "Andrea Rossnerova and Milada Spatova and Christian Schunck and Radim J Sram", abstract = "Automated image analysis scoring of micronuclei (MN) in cells can facilitate the objective and rapid measurement of genetic damage in mammalian and human cells. This approach was repeatedly developed and tested over the past two decades but none of the systems were sufficiently robust for routine analysis of MN until recently. New methodological, hardware and software developments have now allowed more advanced systems to become available. This mini-review presents the current stage of development and validation of the Metasystems Metafer MNScore system for automated image analysis scoring of MN in cytokinesis-blocked binucleated lymphocytes, which is the best-established method for studying MN formation in humans. The results and experience of users of this system from 2004 until today are reviewed in this paper. Significant achievements in the application of this method in research related to mutagen sensitivity phenotype in cancer risk, radiation biodosimetry and biomonitoring studies of air pollution (enriched by new data) are described. Advantages as well as limitations of automated image analysis in comparison with traditional visual analysis are discussed. The current increased use of the Metasystems Metafer MNScore system in various studies and the growing number of publications based on automated image analysis scoring of MN is promising for the ongoing and future application of this approach.", journal = "Mutagenesis", keywords = "Metafer MNScore Micronuclei", month = "Jan", number = "1", pages = "169--175", title = "Automated scoring of lymphocyte micronuclei by the MetaSystems Metafer image cytometry system and its application in studies of human mutagen sensitivity and biodosimetry of genotoxin exposure.", url = "http://dx.doi.org/10.1093/mutage/geq057", volume = "26", year = "2011", } @article{DeMoors2012, author = "De Moors, A. and Fr{\'e}geau, C.J.", abstract = "The MetaSystems Metafer image analysis software system was purchased three years ago in the hope of developing a routine approach in the RCMP Forensic Laboratories to automate the scoring of human spermatozoa in sexual assault exhibits. This would enhance case throughput, increase assay sensitivity and standardize the search for spermatozoa. The development of appropriate classifiers was challenging but essential to teach the software system to specifically recognize human spermatozoa fluorescently stained using the Sperm Hy-Liter™ kit (Independent Forensics). Optimized classifiers were tested/validated using a diverse set of slides prepared from mock sexual assault samples containing a limited or a large number of spermatozoa (fecal swabs, vaginal swabs, all mixed with different semen dilutions in addition to urine, blood and yeasts for a subset of those swabs). The performance of Metafer was recorded with respect to false positive counts, false negative counts and time required for the detection of spermatozoa in each sample. Automated spermatozoa counts were further compared to manual spermatozoa scoring in addition to comparing the time spent executing the identification. An excellent concordance was noted between automated and manual counts. The results of this study indicate that automated scoring of fluorescently stained spermatozoa in mock sexual assault exhibits can be carried out reliably and reproducibly using well-developed classifiers for the MetaSystems Metafer image analysis software system. The automated scoring of spermatozoa combining Sperm Hy-Liter™/MetaSystems Metafer will be tested on a large number of sexual assault cases as part of a pilot project within an operational setting.", journal = "Forensic Science International: Genetics Supplement Series", keywords = "Metafer MetaCyte Sperms Forensics", number = "1", pages = "e35-e36", title = "Automated scoring of Sperm Hy-Liter™-stained spermatozoa by the MetaSystems Metafer image analysis software system in sexual assault specimens.", url = "http://www.scopus.com/record/display.url?eid=2-s2.0-82455171985{\&}origin=inward{\&}txGid=zjsEShsaHFOBRguUwvsgsWQ%3a2", volume = "3", year = "2012", } @article{pa11, author = "Pajor, Gabor and Alpar, Donat and Kajtar, Bela and Melegh, Bela and Somogyi, Laszlo and Kneif, Maria and Bollmann, Daniel and Pajor, Laszlo and Sule, Norbert", abstract = "OBJECTIVE: Signal pattern enumeration of Urovysion Fluorescence in Situ Hybridization test is tedious and requires great experience. Our aim was to eliminate human interaction by automating the process, using an adoptable, automated image acquisition, and analysis system. METHODS: For extensive analytical analysis control, cell populations were used, while preliminary clinical study was performed on 21 patients with clinical suspicion for bladder cancer. All investigations were carried out using an automated user‐trainable workstation (Metafer4‐Metacyte). RESULTS: The system identified nuclei with a specificity and sensitivity of 92.7 and 96.6%, respectively, while signal detection accuracy was 81.1% on average. Both analytical and diagnostic accuracy of automated analysis was comparable to manual approach (94.8 and 71% vs. 97.9 and 76%, respectively), but classification accuracy increased with degree of polysomy, thus diagnostic sensitivity in low grade, low stage cases was poor. CONCLUSION: It is possible to automate signal enumeration of Urovysion using a user‐trainable system, and achieve efficiency comparable to manual analysis. Previously introduced automated immunophenotypic targeting should further increase diagnostic sensitivity, while resulting in a comprehensively automated method. However, the problem of reduced detection accuracy in cases featured with low polysomy is likely to remain a great challenge of automated signal enumeration.", journal = "Microscopy Research and Technique", keywords = "Metafer MetaCyte UroVysion", title = "Automated signal pattern evaluation of a bladder cancer specific multiprobe‐fish assay applying a user‐trainable workstation", url = "http://www.chemie.de/fachpublikationen/325472/automated-signal-pattern-evaluation-of-a-bladder-cancer-specific-multiprobe-fish-assay-applying-a-user-trainable-workstation.html", year = "2011", } @article{00162, author = "G. M{\'e}hes and A. Luegmayr and C.M. Hattinger and T. L{\"o}rch and I.M. Ambros and H. Gadner and P.F. Ambros", journal = "Medical and Pediatric Oncology", keywords = "RCDetect", pages = "205- 209", title = "Automatic detection and genetic profiling of disseminated neuroblastoma cells", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11464886{\&}dopt=Abstract", volume = "36", year = "2001", } @article{00155, author = "G. M{\'e}hes and A. Luegmayr and C.M. Hattinger and T. L{\"o}rch and I.M. Ambros and H. Gadner and P.F. Ambros", journal = "Medical and Pediatric Oncology", keywords = "Metafer RCDetect", pages = "205- 209", title = "Automatic detection and genetic profiling of disseminated neuroblastoma cells.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=11464886{\&}query_hl=10{\&}itool=pubmed_docsum", volume = "36", year = "2001", } @article{00227, author = "A. Plesch and Th. L{\"o}rch", journal = "J Cancer Res Clin Oncol", keywords = "Metafer RCDetect MetaCyte", pages = "8- 8", title = "Automatic high throughput scanning for the detection of isolated tumor cells and FISH scoring in cytospins and tissue sections", url = "http://www.springerlink.com/content/v3536253120235w6/", volume = "127", year = "2003", } @article{00253, author = "C. Conrad and H. Erfle and P. Warnat and N. Daigle and T. L{\"o}rch and J. Ellenberg and R. Pepperkok and R. Eils", journal = "Genome Research", keywords = "Metafer MetaCyte", pages = "1130- 1136", title = "Automatic identification of subcellular phenotypes on human cell arrays", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15173118", volume = "14", year = "2004", } @article{00251, author = "R. Narath and T. L{\"o}rch and M. Rudas and P.F. Ambros", journal = "Cytometry Part B (Clinical Cytometry)", keywords = "Metafer MetaCyte", pages = "15- 22", title = "Automatic quantification of gene amplification in clinical samples by IQ-FISH", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=14696059{\&}dopt=Abstract", volume = "57", year = "2004", } @article{00278, author = "R. Narath and T. L{\"o}rch and K.M. Greulich-Bode and P. Boukamp and P.F. Ambros", journal = "Cytometry", keywords = "Metafer MetaCyte", pages = "113- 120", title = "Automatic telomere length measurements in interphase nuclei by IQ-FISH.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=16228977{\&}query_hl=1", volume = "68", year = "2005", } @article{00298, author = "R.R. Tubbs and J.D. Pettay and E. Swain and P.C. Roche and W. Powell and D.G. Hicks and T. Grogan", journal = "Appl Immunohistochem Mol Morphol", keywords = "Metafer MetaCyte TMA", pages = "436- 440", title = "Automation of manual components and image quantification of direct dual label fluorescence in situ hybridization (FISH) for HER2 gene amplification: A feasibility study.", url = "http://www.ncbi.nlm.nih.gov/pubmed/17122642?ordinalpos=5{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDoc", volume = "14", year = "2006", } @article{Silva2008, author = "Maria Luiza Macedo Silva and Susana C Raimondi and Eliana Abdelhay and Madeleine Gross and Hasmik Mkrtchyan and de Figueiredo, Amanda Faria and Raul C Ribeiro and de Jesus Marques-Salles, Terezinha and Elaine S Sobral and Marcelo Poirot Gerardin Land and Thomas Liehr", abstract = "The acute myeloid leukemia (AML) subtype M4Eo occurs in 5\% of all AML cases and is usually associated with either an inv(16)(p13.1q22) or a t(16;16)(p13.1;q22) chromosomal abnormality. At the molecular level, these abnormalities generate a CBFB-MYH11 fusion gene. Patients with this genetic alteration are usually assigned to a low-risk group and thus receive standard chemotherapy. AML-M4Eo is rarely found in infants. We describe clinical, conventional banding, and molecular cytogenetic data for a 12-month-old baby with AML-M4Eo and a chimeric CBFB-MYH11 fusion gene masked by a novel rearrangement between chromosomes 1 and 16. This rearrangement characterizes a new type of inv(16)(p13.1q22) masked by a chromosome translocation.", doi = "10.1016/j.cancergencyto.2007.12.014", journal = "Cancer Genet Cytogenet", keywords = "Chromosome Banding; Chromosomes, Human, Pair 1; Chromosomes, Human, Pair 16; Humans; In Situ Hybridization, Fluorescence; Infant; Karyotyping; Leukemia, Myelomonocytic, Acute, genetics; Male; Oncogene Proteins, Fusion; Translocation, Genetic", month = "Apr", number = "1", pages = "56--60", title = "Banding and molecular cytogenetic studies detected a CBFB-MYH11 fusion gene that appeared as abnormal chromosomes 1 and 16 in a baby with acute myeloid leukemia FAB M4-Eo.", url = "http://dx.doi.org/10.1016/j.cancergencyto.2007.12.014", volume = "182", year = "2008", } @article{Al-Achkar2011, author = "Walid Al-Achkar and Abdulsamad Wafa and Elisabeth Klein and Abdulmunim Aljapawe", abstract = "ABSTRACT:Myelodysplastic syndrome (MDS) represents a group of clonal hematological disorders characterized by progressive cytopenia, and reflects to defects in erythroid, myeloid and megakaryocytic maturation. MDS is more frequently observed in older aged patients with cytogenetic abnormalities like monosomy of chromosome(s) 5 and/or 7. In 50\% of de novo MDS cases, chromosomal aberrations are found and rearrangements involving the retinoblastoma (RB1) gene in 13q14 are found.Here, we are presenting a case report of a rare biclonal MDS with a karyotype of 45, XY,-4, der(6)t(4;6)(p15.1;p21.3), der(8)t(4;8)(q31.2;q22), t(13;16)(q21.3;p11.2)11/45, XY, der(7)t(7;13)(p22.2~22.3;q21.3),-13 9. The patient was diagnosed according to WHO classification as refractory anemia with excess of blasts (RAEB-II).Immunophenotyping was positive for CD11b, CD11c, CD10, CD13, CD15, CD16 and CD33.We report, a novel and cytogenetically rare case of a biclonal MDS with complex chromosomal aberrations and deletion of RB1-gene in both clones. These findings are associated with a poor prognosis as the patient died 3 months after diagnosis.", journal = "Mol Cytogenet", keywords = "Ikaros Isis mFISH mBAND XCyte XCP", pages = "16", title = "Biclonal myelodysplastic syndrome involving six chromosomes and monoallelic loss of RB1 - A rare case.", url = "http://dx.doi.org/10.1186/1755-8166-4-16", volume = "4", year = "2011", } @article{00013, author = "C. Lindholm and S. Salomaa and M. Tekkel and W. Paile and A. Koivistoinen and T. Ilus and T. Veidebaum", journal = "International Journal of Radiation Biology", keywords = "Isis", pages = "647- 656", title = "Biodosimetry after accidental radiation exposure by conventional chromosome analysis and FISH", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8980661{\&}dopt=Abstract", volume = "70", year = "1996", } @article{00147, author = "D.J. Brenner and N. Okladnikova and P. Hande and L. Burak and C.R. Geard and T. Azizova", journal = "Radiation Protection Dosimetry", keywords = "Isis mBAND", pages = "69- 73", title = "Biomarkers specific to densely-ionising (high LET) radiations.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=11763360{\&}query_hl=12{\&}itool=pubmed_docsum", volume = "97", year = "2001", } @article{00119, author = "E. Trelles-Sticken and J. Loidl and H. Scherthan", journal = "Journal of Cell Science", pages = "651- 658", title = "Bouquet formation in budding yeast: initiation of recombination is not required for meitoic telomere clustering", url = "http://jcs.biologists.org/cgi/reprint/112/5/651.pdf", volume = "112", year = "1999", } @article{00242, author = "A. Heller and I.F. Loncarevic and M. Glaser and E. Gebhart and U. Trautmann and U. Claussen and T. Liehr", journal = "International Journal of Oncology", keywords = "Isis mBAND", pages = "127- 136", title = "Breakpoint differentiation in chromosomal aberrations of hematological malignancies: identification of 33 previously unrecorded breakpoints", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=14654949{\&}dopt=Abstract", volume = "24", year = "2004", } @article{00322, author = "L. Li and A.A. McCormack and J.M. Nicholson and A. Fabarius and R. Hehlmann and R.K. Sachs and P.H. Duesberg", journal = "Cancer Genet Cytogenet", keywords = "Isis mFISH", pages = "1- 25", title = "Cancer-causing karyotypes: chromosomal equilibria between destabilizing aneuploidy and stabilizing selection for oncogenic function.", url = "http://www.ncbi.nlm.nih.gov/pubmed/19061776?ordinalpos=18{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDo", volume = "188", year = "2009", } @article{00184, author = "D. Leroux and F. Mugneret and M. Callanan and I. Radford-Weiss and N. Dastugue and J. Feuillard and F. Le M{\'e}e and G. Plessis and P. Talmant and N. Gachard and F. Uettwiller and M.-P. Pages and M.-J. Mozzionacci and V. Eclache and C. Sibille and H. Avet-Loiseau and M.- Lafage-P.", journal = "Blood", keywords = "Probes", pages = "4154- 4159", title = "CD4(+), CD56(+) DC2 acute leukemia is characterized by recurrent clonal chromosomal changes affecting 6 major targets: a study of 21 cases by the Groupe Francais de Cytogenetique Hematologique.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=12010820{\&}query_hl=2{\&}itool=pubmed_DocSum", volume = "99", year = "2002", } @article{00086, author = "T. Haferlach and H. L{\"o}ffler and C. Nickenig and L. Ramm-Petersen and M. Meeder and R. Schoch and B. Schlegelberger and S. Schnittger and C. Schoch and W. Hiddemann W", journal = "Br J Haematol", pages = "93- 99", title = "Cell lineage specific involment in acute promyelocytic leukaemia (APL) using a combination of May-Gr{\"u}nwald-Giemsa staining and flourescence in situ hybridization techniques for the detection of the translocation t(15/17)(q22:q12).", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9792295{\&}dopt=Abstract", volume = "103", year = "1998", } @article{Asaithamby2009, author = "Aroumougame Asaithamby and David J Chen", abstract = "DNA double-strand breaks (DSBs) are a serious threat to genome stability and cell viability. Although biological effects of low levels of radiation are not clear, the risks of low-dose radiation are of societal importance. Here, we directly monitored induction and repair of single DSBs and quantitatively analyzed the dynamics of interaction of DNA repair proteins at individual DSB sites in living cells using 53BP1 fused to yellow fluorescent protein (YFP-53BP1) as a surrogate marker. The number of DSBs formed was linear with dose from 5 mGy to 1 Gy. The DSBs induced by very low radiation doses (5 mGy) were repaired with efficiency similar to repair of DSBs induced at higher doses. The YFP-53BP1 foci are dynamic structures: 53BP1 rapidly and reversibly interacted at these DSB sites. The time frame of recruitment and affinity of 53BP1 for DSB sites were indistinguishable between low and high doses, providing mechanistic evidence for the similar DSB repair after low- and high-dose radiation. These findings have important implications for estimating the risk associated with low-dose radiation exposure on human health.", journal = "Nucleic Acids Res", keywords = "foci, Metafer MetaCyte", month = "Jul", number = "12", pages = "3912--3923", title = "Cellular responses to DNA double-strand breaks after low-dose gamma-irradiation.", url = "http://dx.doi.org/10.1093/nar/gkp237", volume = "37", year = "2009", } @article{00078, author = "A. Taubald and T. Liehr and J. Ries and S. Girod and E. Ha{\ss}futter and E. Gebhart", journal = "Int. J. Mol. Med", keywords = "Isis CGH", pages = "555- 560", title = "CGH-detected DNA sequence copy number amplifications can be confirmed by interphase-FISH: New possibilities for prognostic approaches in oral squamous cell carcinomas", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9858651{\&}dopt=Abstract", volume = "2", year = "1998", } @article{00105, author = "M. Van Gele and F. Speleman and J. Vandesompele and N. Van Roy and J.H. Leonard", journal = "Cancer Research", keywords = "Isis CGH", pages = "1503- 1508", title = "Characteristic Pattern of Chromosomal Gains and Losses in Merkel Cell Carcinoma Detected by Comparative Genomic Hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9537255{\&}dopt=Abstract", volume = "58", year = "1999", } @article{Marquez2011, author = "B{\'e}atrice Marquez and Genevi{\`e}ve Ameye and Coralie M Vallet and Paul M Tulkens and H{\'e}l{\`e}ne A Poirel and Fran{\c{c}}oise Van Bambeke", abstract = "Exposure of J774 mouse macrophages to stepwise increasing concentrations of ciprofloxacin, an antibiotic inhibiting bacterial topoisomerases, selects for resistant cells that overexpress the efflux transporter Abcc4 (Marquez et al. [2009] Antimicrob. Agents Chemother. 53: 2410-2416), encoded by the Abcc4 gene located on Chromosome 14qE4. In this study, we report the genomic alterations occurring along the selection process. Abcc4 expression progressively increased upon selection rounds, with exponential changes observed between cells exposed to 150 and 200 µM of ciprofloxacin, accompanied by a commensurate decrease in ciprofloxacin accumulation. Molecular cytogenetics experiments showed that this overexpression is linked to Abcc4 gene overrepresentation, grading from a partial trisomy of Chr 14 at the first step of selection (cells exposed to 100 µM ciprofloxacin), to low-level amplifications (around three copies) of Abcc4 locus on 1 or 2 Chr 14 (cells exposed to 150 µM ciprofloxacin), followed by high-level amplification of Abcc4 as homogeneous staining region (hsr), inserted on 3 different derivative Chromosomes (cells exposed to 200 µM ciprofloxacin). In revertant cells obtained after more than 60 passages of culture without drug, the Abcc4 hsr amplification was lost in approx. 70\% of the population. These data suggest that exposing cells to sufficient concentrations of an antibiotic with low affinity for eukaryotic topoisomerases can cause major genomic alterations that may lead to the overexpression of the transporter responsible for its efflux. Gene amplification appears therefore as a mechanism of resistance that can be triggered by non-anticancer agents but contribute to cross-resistance, and is partially and slowly reversible.", journal = "PLoS One", keywords = "Ikaros Isis", number = "12", pages = "e28368", title = "Characterization of Abcc4 gene amplification in stepwise-selected mouse J774 macrophages resistant to the topoisomerase II inhibitor ciprofloxacin.", url = "http://dx.doi.org/10.1371/journal.pone.0028368", volume = "6", year = "2011", } @article{00127, author = "D. Grimwade and A. Biondi and M.-J. Mozzionacci and A. Hagemeijer and R. Berger and M. Neat and K. Howe and N. Dastugue and J. Jansen and I. Radford-Weiss and F. Lo Coco and M. Lessard and J.-M. Hernandez and E. Delabesse and D. Head and V. Liso and D. Sainty and G. Flandrin and E. Solomon and M. Lafage-Pochitalof", journal = "Blood", keywords = "Isis mFISH mBAND", pages = "1297- 1308", title = "Characterization of acute promyelocytic leukemia cases lacking the classic t(15;17): results of the European Working Party.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=10942371{\&}query_hl=4", volume = "96", year = "2000", } @article{00128, author = "D. Grimwade and A. Biondi and M.-J. Mozziconacci and A. Hagemeijer and R. Berger and M. Neat and K. Howe and N. Dastugue and J. Jansen and I. Radford-Weiss and F. Lo Coco and M. Lessard and J.-M. Hernandez and E. Delabesse and D. Head and V. Liso and D. Sainty and G. Flandrin and E. Solomon and et al.", journal = "Blood", keywords = "Isis mFISH mBAND", pages = "1297- 1308", title = "Characterization of acute promyelocytic leukemia cases lacking the classic t(15;17): results of the European Working Party. Groupe Francais de Cytogenetique Hematologique, Groupe de Francais d'Hematologie Cellulaire, UK Cancer Cytogenetics Group and BIOME", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=10942371{\&}query_hl=2{\&}itool=pubmed_DocSum", volume = "15", year = "2000", } @article{00209, author = "T. Liehr and A. Nietzel and H. Starke and A. Heller and A. Weise and A. Kuechler and G. Senger and S. Ebner and T. Martin and M. Stumm and R. Wegner and H. T{\"o}nnies and C. Hoppe and U. Claussen and von Eggeling, F.", journal = "J. Assoc. Genet. Technol.", keywords = "Isis mBAND mFISH", pages = "5- 10", title = "Characterization of small marker chromosomes (SMC) by recently developed molecular cytogenetic approaches", volume = "29", year = "2003", } @article{00134, author = "S. Stein and T. Liehr and K. Eschrich", journal = "Gene", pages = "215- 224", title = "Characterization of the mouse liver fructose-1,6-biphosphatase gene", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11250076{\&}dopt=Abstract", volume = "264", year = "2000", } @article{00085, author = "C. Fuchs and T. Liehr and S. {\"O}zbey and A. Ekici and H. Grehl and B. Rautenstrauss", journal = "Neurogenetics", pages = "43- 46", title = "Charcot-Marie-Tooth diesase type 1A and herediatry neuropathy with liability to pressure palsies: a SacI polymorphism in proximal CMT1A-REP elements may lead to genetic misdiagnosis", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9933299{\&}dopt=Abstract", volume = "2", year = "1998", } @article{00302, author = "P.M. De Angelis and T. Stokke and M. Beigi and G. Flatberg and M. Enger and K. Haug and H.C.D. Aass and A. Schj{\o}lberg and P.A. Andresen and S. Ariansen and A.S. B{\o} and O. Mj{\aa}land and O.P. Clausen", journal = "Int J Cancer", keywords = "Isis CGH", pages = "2734- 2738", title = "Chromosomal 20q gain in the DNA diploid component of aneuploid colorectal carcinomas.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=17354231{\&}query_hl=9{\&}itool=pubmed_docsum", volume = "120", year = "2007", } @article{00234, author = "G. M{\'e}hes and N. Speich and M. Bollmann and R. Bollmann", journal = "Pathol Oncol Res", keywords = "Isis", pages = "142- 148", title = "Chromosomal aberrations accumulate in polyploid cells of high-grade squamous intraepithelial lesions (HSIL).", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=15448749{\&}query_hl=1{\&}itool=pubmed_docsum", volume = "10", year = "2004", } @article{Hartel2009, author = "Carola Hartel and Anna Nikoghosyan and Marco Durante and Sylwester Sommer and Elena Nasonova and Claudia Fournier and Ryonfa Lee and J{\"u}rgen Debus and Daniela Schulz-Ertner and Sylvia Ritter", abstract = "BACKGROUND AND PURPOSE: To investigate the cytogenetic damage in blood lymphocytes of patients treated for prostate cancer with different radiation qualities and target volumes. MATERIALS AND METHODS: Twenty patients receiving carbon-ion boost irradiation followed by IMRT or IMRT alone for the treatment of prostate cancer entered the study. Cytogenetic damage induced in peripheral blood lymphocytes of these patients was investigated at different times during the radiotherapy course using Giemsa staining and mFISH. A blood sample from each patient was taken before initiation of radiation therapy and irradiated in vitro to test for individual radiosensitivity. In addition, in vitro dose-effect curves for the induction of chromosomal exchanges by X-rays and carbon ions of different energies were measured. RESULTS: The yield of chromosome aberrations increased during the therapy course, and the frequency was lower in patients irradiated with carbon ions as compared to patients treated with IMRT with similar target volumes. A higher frequency of aberrations was measured by increasing the target volume. In vitro, high-LET carbon ions were more effective than X-rays in inducing aberrations and yielded a higher fraction of complex exchanges. The yield of complex aberrations observed in vivo was very low. CONCLUSION: The investigation showed no higher aberration yield induced by treatment with a carbon-ion boost. In contrast, the reduced integral dose to the normal tissue is reflected in a lower chromosomal aberration yield when a carbon-ion boost is used instead of IMRT alone. No cytogenetic "signature" of exposure to densely ionizing carbon ions could be detected in vivo.", journal = "Radiother Oncol", keywords = "Isis mFISH", pages = "73-78", title = "Chromosomal aberrations in peripheral blood lymphocytes of prostate cancer patients treated with IMRT and carbon ions.", url = "http://dx.doi.org/10.1016/j.radonc.2009.08.031", volume = "95", year = "2010", } @article{00283, author = "R. Li and R. Hehlman and R. Sachs and P. Duesberg", journal = "Cancer Genet Cytogenet", keywords = "mFISH", pages = "44- 56", title = "Chromosomal alterations cause the high rates and wide ranges of drug resistance in cancer cells.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=16271955{\&}query_hl=5{\&}itool=pubmed_docsum", volume = "163", year = "2005", } @article{00046, author = "W. EI-Rifai and E. Elonen and M. Larramendy and T. Ruutu and S. Knuutila", journal = "Leukemia", pages = "958- 963", title = "Chromosomal breakpoints and changes in DNA copy number in refractory acute myeloid leukemia", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9204975{\&}dopt=Abstract", volume = "11", year = "1997", } @article{00241, author = "J. Nishio and H. Iwasaki and Y. Ohjimi and M. Ishiguro and K. Kobayashi and K. Nabeshima and M. Naito and M. Kikuchi", journal = "Int J Mol Med", keywords = "Isis CGH", pages = "13- 16", title = "Chromosomal imbalances in angioleiomyomas by comparative genomic hybridization.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=14654964{\&}query_hl=14{\&}itool=pubmed_docsum", volume = "13", year = "2004", } @article{00270, author = "M. Horstmann and M. Durante and C. Johannes and G. Obe", journal = "Advances in Space Research", keywords = "Isis mBAND", pages = "276- 279", title = "Chromosomal intrachanges induced by swift iron ions", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15161369{\&}query_hl=23", volume = "35", year = "2005", } @article{Hieber2011, author = "Ludwig Hieber and Reinhard Huber and Verena Bauer and Quirin Sch{\"a}ffner and Herbert Braselmann and Geraldine Thomas and Tatjana Bogdanova and Horst Zitzelsberger", abstract = "Structural genomic rearrangements are frequent findings in human cancers. Therefore, papillary thyroid carcinomas (PTCs) were investigated for chromosomal aberrations and rearrangements of the RET proto-oncogene. For this purpose, primary cultures from 23 PTC have been established and metaphase preparations were analysed by spectral karyotyping (SKY). In addition, interphase cell preparations of the same cases were investigated by fluorescence in situ hybridisation (FISH) for the presence of RET/PTC rearrangements using RET-specific DNA probes. SKY analysis of PTC revealed structural aberrations of chromosome 11 and several numerical aberrations with frequent loss of chromosomes 20, 21, and 22. FISH analysis for RET/PTC rearrangements showed prevalence of this rearrangement in 72\% (16 out of 22) of cases. However, only subpopulations of tumour cells exhibited this rearrangement indicating genetic heterogeneity. The comparison of visual and automated scoring of FISH signals revealed concordant results in 19 out of 22 cases (87\%) indicating reliable scoring results using the optimised scoring parameter for RET/PTC with the automated Metafer4 system. It can be concluded from this study that genomic rearrangements are frequent in PTC and therefore important events in thyroid carcinogenesis.", journal = "J Biomed Biotechnol", keywords = "Adolescent; Adult; Chernobyl Nuclear Accident; Radiation; MetaCyte", pages = "693691", title = "Chromosomal rearrangements in post-Chernobyl papillary thyroid carcinomas: evaluation by spectral karyotyping and automated interphase FISH.", url = "http://dx.doi.org/10.1155/2011/693691", volume = "2011", year = "2011", } @article{00126, author = "C. Stock and L. Kager and F.-M. Fink and H. Gadner and P.F. Ambros", journal = "Genes, Chromososmes {\&} Cancer", keywords = "Isis CGH", pages = "329- 336", title = "Chromosomal regions involved in the pathogenesis of osteosarcomas.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=10862039{\&}query_hl=14{\&}itool=pubmed_docsum", volume = "28", year = "2000", } @article{00188, author = "A. Weise and H. Starke and A. Heller and H. T{\"o}nnies and M. Volleth and M. Stumm and S. Gabriele and A. Nietzel and U. Claussen and T. Liehr", journal = "J. Med. Genet.", keywords = "Isis mBAND", pages = "434- 439", title = "Chromosome 2 aberrations in clinical cases characterised by high resolution multicolour banding and region specific FISH probes", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12070255{\&}dopt=Abstract", volume = "39", year = "2002", } @article{00054, author = "M. Lessard and A. Herry and C. Berthou and M.-C. L{\'e}glise and J.-F. Abgrall and I. Luquet and N. Dastugue and E. Duchayne and F. Rigal-Huguet and M. Lafage and D. Sainty and J. Reiffers and P. Bernard", journal = "Leukemia and Lymphoma", pages = "127- 135", title = "Chromosome 8 Tetrasomies and Pentasomies - A Clonal Abnormality Closely Associated with Acute Monocytic Leukaemia", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9373204{\&}dopt=Abstract", volume = "27", year = "1997", } @article{00266, author = "A. Ketupanya and N. Aranyakasemsuk and C. Tocharoentanaphol and C. Vuthiwong", journal = "J. Med. Assoc. Thai", keywords = "Isis CGH", pages = "1- 6", title = "Chromosome analysis of uncultured amniocytes by comparative genomic hybridization in early amniocentesis.", volume = "88", year = "2005", } @article{00150, author = "R. Karhu and M. Ahlstedt-Soini and M. Bittner and P. Meltzer and J.M. Trent and J.J. Isola", journal = "Genes Chromosomes Cancer", keywords = "Isis mFISH", pages = "105- 109", title = "Chromosome arm-specific multicolor FISH", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11107184{\&}dopt=Abstract", volume = "30", year = "2001", } @article{00316, author = "D. Pignalosa and A. Bertucci and G. Gialanella and G. Grossi and L. Manti and M. Pugliese and P. Scampoli and M. Durante", journal = "Radiation Research", keywords = "Isis mFISH XaCyte", pages = "458- 466", title = "Chromosome inter- and intrachanges detected by arm-specific DNA probes in the progeny of human lymphocytes exposed to energetic heavy ions.", url = "http://www.ncbi.nlm.nih.gov/pubmed/19024653?ordinalpos=7{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDoc", volume = "170", year = "2008", } @article{00248, author = "C. Johannes and M. Horstmann and M. Durante and I. Chudoba and G. Obe", journal = "Radiation Research", keywords = "Isis mFISH mBAND", pages = "540- 548", title = "Chromosome intrachanges and interchanges detected by multicolor banding in lymphocytes: searching for clastogen signatures in the human genome", volume = "161", year = "2004", } @article{Zhang2011, author = "Luoping Zhang and Qing Lan and Weihong Guo and Alan E. Hubbard and Guilan Li and Stephen M. Rappaport and Cliona M. McHale and Min Shen and Zhiying Ji and Roel Vermeulen and Songnian Yin and Nathaniel Rothman and Martyn T. Smith", abstract = "Evidence suggests that de novo, therapy-related and benzene-induced acute myeloid leukemias (AML) occur via similar cytogenetic and genetic pathways, several of which involve aneuploidy, the loss or gain of chromosomes. Aneuploidy of specific chromosomes has been detected in benzene-related leukemia patients as well as in healthy benzene-exposed workers, suggesting that aneuploidy precedes and may be a potential mechanism underlying benzene-induced leukemia. Here, we analyzed the peripheral blood lymphocytes of 47 exposed workers and 27 unexposed controls using a novel OctoChrome fluorescence in situ hybridization (FISH) technique that simultaneously detects aneuploidy in all 24 chromosomes. Through this chromosome-wide aneuploidy study (CWAS) approach, we found heterogeneity in the monosomy and trisomy rates of the 22 autosomes when plotted against continuous benzene exposure. In addition, statistically significant, chromosome-specific increases in the rates of monosomy [5, 6, 7, 10, 16 and 19] and trisomy [5, 6, 7, 8, 10, 14, 16, 21 and 22] were found to be dose dependently associated with benzene exposure. Furthermore, significantly higher rates of monosomy and trisomy were observed in a priori defined 'susceptible' chromosome sets compared with all other chromosomes. Together, these findings confirm that benzene exposure is associated with specific chromosomal aneuploidies in hematopoietic cells, which suggests that such aneuploidies may play roles in benzene-induced leukemogenesis.", journal = "Carcinogenesis", keywords = "Metafer MSearch", month = "Apr", number = "4", pages = "605--612", title = "Chromosome-wide aneuploidy study (CWAS) in workers exposed to an established leukemogen, benzene.", url = "http://dx.doi.org/10.1093/carcin/bgq286", volume = "32", year = "2011", } @article{00066, author = "R. Weide and H. Rieder and Y. Mehraein and M. Wolf and U. Kaiser and U. Seifart and C. G{\"o}rg and K. Havemann", journal = "Br J Haematology", pages = "117- 123", title = "Chronic eosinophilic leukaemia (CEL): a distinct myeloproliferative disease", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9012697{\&}dopt=Abstract", volume = "96", year = "1997", } @article{Kumareswaran2012, author = "Ramya Kumareswaran and Olga Ludkovski and Alice Meng and Jenna Sykes and Melania Pintilie and Robert G. Bristow", abstract = "Hypoxic cells have been linked to genetic instability and tumor progression. However, little is known about the exact relationship between DNA repair and genetic instability in hypoxic cells. We therefore tested whether the sensing and repair of DNA double-strand breaks (DNA-dsbs) is altered in irradiated cells kept under continual oxic, hypoxic or anoxic conditions. Synchronized G0-G1 human fibroblasts were irradiated (0-10 Gy) after initial gassing with 0\% O(2) (anoxia), 0.2\% O(2) (hypoxia) or 21\% O(2) (oxia) for 16 hours. The response of phosphorylated histone H2AX ({\~a}-H2AX), phosphorylated ataxia telangiectasia mutated [ATM(Ser1981)], and the p53 binding protein 1 (53BP1) was quantified by intranuclear DNA repair foci and western blotting. At 24 hours following DNA damage, residual {\~a}-H2AX, ATM(Ser1981) and 53BP1 foci were observed in hypoxic cells. This increase in residual DNA-dsbs under hypoxic conditions was confirmed using neutral comet assays. Clonogenic survival was also reduced in chronically hypoxic cells, which is consistent with the observation of elevated G1-associated residual DNA-dsbs. We also observed an increase in the frequency of chromosomal aberrations in chronically hypoxic cells. We conclude that DNA repair under continued hypoxia leads to decreased repair of G1-associated DNA-dsbs, resulting in increased chromosomal instability. Our findings suggest that aberrant DNA-dsb repair under hypoxia is a potential factor in hypoxia-mediated genetic instability.", journal = "J Cell Sci", keywords = "mFISH, Isis", month = "Jan", number = "Pt 1", pages = "189--199", title = "Chronic hypoxia compromises repair of DNA double-strand breaks to drive genetic instability.", url = "http://dx.doi.org/10.1242/jcs.092262", volume = "125", year = "2012", } @article{00156, author = "G. M{\'e}hes and A. Witt and E. Kubista and P.F. Ambros", journal = "Am J Pathol", keywords = "Metafer RCDetect", pages = "17- 20", title = "Circulating breast cancer cells are frequently apoptotic.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=11438448{\&}query_hl=1{\&}itool=pubmed_docsum", volume = "159", year = "2001", } @article{Talamo2010, author = "Anna Talamo and Yves Chalandon and Alfio Marazzi and Martine Jotterand", abstract = "Although aneuploidy has many possible causes, it often results from underlying chromosomal instability (CIN) leading to an unstable karyotype with cell-to-cell variation and multiple subclones. To test for the presence of CIN in high hyperdiploid acute lymphoblastic leukemia (HeH ALL) at diagnosis, we investigated 20 patients (10 HeH ALL and 10 non-HeH ALL), using automated four-color interphase fluorescence in situ hybridization (I-FISH) with centromeric probes for chromosomes 4, 6, 10, and 17. In HeH ALL, the proportion of abnormal cells ranged from 36.3\% to 92.4\%, and a variety of aneuploid populations were identified. Compared with conventional cytogenetics, I-FISH revealed numerous additional clones, some of them very small. To investigate the nature and origin of this clonal heterogeneity, we determined average numerical CIN values for all four chromosomes together and for each chromosome and patient group. The CIN values in HeH ALL were relatively high (range, 22.2-44.7\%), compared with those in non-HeH ALL (3.2-6.4\%), thus accounting for the presence of numerical CIN in HeH ALL at diagnosis. We conclude that numerical CIN may be at the origin of the high level of clonal heterogeneity revealed by I-FISH in HeH ALL at presentation, which would corroborate the potential role of CIN in tumor pathogenesis.", journal = "Cancer Genet Cytogenet", keywords = "Metafer MetaCyte", month = "Dec", number = "2", pages = "209--214", title = "Clonal heterogeneity and chromosomal instability at disease presentation in high hyperdiploid acute lymphoblastic leukemia.", url = "http://dx.doi.org/10.1016/j.cancergencyto.2010.09.005", volume = "203", year = "2010", } @article{00153, author = "G. M{\'e}hes and A. Luegmayr and I.M. Ambros and R. Ladenstein and P.F. Ambros", journal = "Clinical Cancer Res", keywords = "Metafer RCDetect", pages = "1969- 1975", title = "Combined automatic immunological and molecular cytogenetic analysis allows exact identification and quantification of tumor cells in the bone marrow.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=11448912{\&}query_hl=3{\&}itool=pubmed_docsum", volume = "7", year = "2001", } @article{00181, author = "M. Van Gele and J.H. Leonard and N. Van Roy and H. Van Limbergen and S. Van Belle and V. Cocquyt and H. Salwen and A. De Paepe and F. Speleman", journal = "Int. J. Cancer", keywords = "Isis mFISH CGH Ikaros", pages = "137- 145", title = "Combined karyotyping, CGH and m-FISH analysis allows detailed characterization of unidentified chromosomal rearrangements in Merkel cell carcinoma", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12209990{\&}dopt=Abstract", volume = "101", year = "2002", } @article{00152, author = "N. Van Roy and H. Van Limbergen and J. Vandesompele and M. Van Gele and B. Poppe and H. Salwen and G. Laureys and N. Manoel and A. De Paepe and F. Speleman", journal = "Genes, Chromosomes {\&} Cancer", keywords = "Isis mFISH CGH", pages = "274- 282", title = "Combined M-FISH and CGH analysis allows comprehensive description of genetic alterations in neuroblastoma cells", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11550280{\&}dopt=Abstract", volume = "30", year = "2001", } @article{00244, author = "G. Lim and J. Karaskova and B. Vukovic and J. Bayani and B. Beheshti and M. Bernardini and J.A. Squire and M. Zielenska", journal = "Cancer Genetics and Cytogenetics", keywords = "Isis mBAND", pages = "158- 164", title = "Combined spectral karyotyping, multicolor banding, and microarray comparative genomic hybridization analysis provides a detailed characterization of complex structural chromosomal rearrangements associated with gene amplification in the osteosarcoma cell ", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15350306", volume = "153", year = "2004", } @article{Yusuf2011, author = "Mohammed Yusuf and David L V Bauer and Daniel M Lipinski and Robert E MacLaren and Richard Wade-Martins and Kalim U Mir and Emanuela V Volpi", abstract = "Physical mapping of transgenic insertions by Fluorescence in situ Hybridization (FISH) is a reliable and cost-effective technique. Chromosomal assignment is commonly achieved either by concurrent G-banding or by a multi-color FISH approach consisting of iteratively co-hybridizing the transgenic sequence of interest with one or more chromosome-specific probes at a time, until the location of the transgenic insertion is identified.Here we report a technical development for fast chromosomal assignment of transgenic insertions at the single cell level in mouse and rat models. This comprises a simplified 'single denaturation mixed hybridization' procedure that combines multi-color karyotyping by Multiplex FISH (M-FISH), for simultaneous and unambiguous identification of all chromosomes at once, and the use of a Quantum Dot (QD) conjugate for the transgene detection.Although the exploitation of the unique optical properties of QD nanocrystals, such as photo-stability and brightness, to improve FISH performance generally has been previously investigated, to our knowledge this is the first report of a purpose-designed molecular cytogenetic protocol in which the combined use of QDs and standard organic fluorophores is specifically tailored to assist gene transfer technology.", journal = "BMC Biotechnol", keywords = "22XRat Probes", pages = "121", title = "Combining M-FISH and Quantum Dot technology for fast chromosomal assignment of transgenic insertions.", url = "http://dx.doi.org/10.1186/1472-6750-11-121", volume = "11", year = "2011", } @article{00224, author = "L. Roy and M. Delbos and N. Paillole and V. Durand and P. Voisin", journal = "Radioprotection", keywords = "Metafer MSearch DCScore", pages = "323- 340", title = "Comparaison de syst{\`e}mes d'analyse d'images cytologiques en dosim{\'e}trie biologique (FRENCH)", volume = "38", year = "2003", } @article{00042, author = "V.-M. Wasenius and A. Jekunen and O. Monni and H. Joensuu and S. Aebi and S.B. Howell and S. Knuutila", journal = "Genes, Chromosomes {\&} Cancer", keywords = "Isis CGH", pages = "286- 291", title = "Comparative genomic hybridization analysis of chromosomal changes occurring during development of acquired resistance to cisplatin in human ovarian carcinoma cells", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9349519{\&}dopt=Abstract", volume = "18", year = "1997", } @article{00041, author = "N. Van Roy and A. Jauch and M. Van Gele and G. Laureys and R. Versteeg and A. De Paepe and T. Cremer and F. Speleman", journal = "Cancer Genet Cytogenet", keywords = "Isis CGH", pages = "135- 142", title = "Comparative Genomic Hybridization Analysis of Human Neuroblastomas: Detection of Distal 1p Deletions and Further Molecular Genetic Characterization of Neuroblastoma Cell Lines", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9283597{\&}dopt=Abstract", volume = "97", year = "1997", } @article{00145, author = "H. T{\"o}nnies and M. Stumm and R.-D. Wegner and I. Chudoba and V. Kalscheuer and H. Neitzel", journal = "Cytogenet. Cell Genet.", keywords = "Isis CGH", pages = "188- 194", title = "Comparative genomic hybridization based strategy for the analysis of different chromosome imbalances detected in conventional cytogenetic diagnostics", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11528111{\&}dopt=Abstract", volume = "93", year = "2001", } @article{00180, author = "A. Weise and T. Liehr and T. Efferth and A. Kuechler and E. Gebhart", journal = "Cytogenet Genome Res", keywords = "Isis mFISH CGH", pages = "118- 125", title = "Comparative m-FISH and CGH analyses in sensitive and drug-resistent human T-cell acute leukemia cell lines", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12697993{\&}dopt=Abstract", volume = "98", year = "2002", } @article{Schaefer2012, author = "S. Sch{\"a}fer and B. Hamer and B. Treursic and C. M{\"o}hlenkamp and D. Spira and M. Korlevic and G. Reifferscheid and E. Claus", journal = "Arch Environ Contam Toxicol", keywords = "Metafer CometScan", month = "May", number = "4", pages = "614--627", title = "Comparison of Bioaccumulation and Biomarker Responses in Dreissenapolymorpha and D. bugensis After Exposure to Resuspended Sediments.", url = "http://dx.doi.org/10.1007/s00244-011-9735-2", volume = "62", year = "2012", } @article{00167, author = "C. Schoch and S. Schnittger and S. Bursch and D. Gerstner and A. Hochhaus and U. Berger and R. Hehlmann and W. Hiddemann and T. Haferlach", journal = "Leukemia", keywords = "Ikaros Isis", pages = "53- 59", title = "Comparison of chromosome banding analysis, interphase- and hypermetaphase-FISH, qualitative and quantitative PCR for diagnosis and for follow-up in chronic myolid leukemia: a study on 350 cases", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11840263{\&}dopt=Abstract", volume = "16", year = "2002", } @article{00068, author = "C. Lindholm and S. Luomahaara and A. Koivistoinen and T. Ilus and A.A. Edwards and S. Salomaa", journal = "Int J Radiat Biol", keywords = "Ikaros Isis", pages = "27- 34", title = "Comparison of dose-response curves for chromosomal aberrations established by chromosome painting and conventional analysis.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=9687972{\&}query_hl=33{\&}itool=pubmed_docsum", volume = "74", year = "1998", } @article{00159, author = "V. Bureau and S. Marionneau and A. Cailleau-Thomas and B. Le Mouilac-Vaidye and T. Liehr and J. Le Pendu", journal = "Eur. J. Biochem", pages = "1006- 1019", title = "Comparison of the three rat GDP-L-fucose: {\ss}-D-galactoside 2-alpha-L-fucosyltransferases FTA, FTB and FTC", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11179967{\&}dopt=Abstract", volume = "268", year = "2001", } @article{00163, author = "A. Rump and G. Kasper and C. Hayes and G. Wen and H. Starke and T. Liehr and R. Lehmann and D. Lagemann and A. Rosenthal", journal = "Genomics", keywords = "Isis", pages = "50- 55", title = "Complex arrangement of genes within a 220-kb region of double-duplicated DNA on human 2q37.1", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11352565{\&}dopt=Abstract", volume = "73", year = "2001", } @article{00272, author = "M Prakash Hande and TV Azizova and LF Burak and VF Khokhryakov and CR Geard and DJ Brenner", journal = "Genes Chromosomes Cancer", keywords = "Isis mFISH", pages = "1- 9", title = "Complex chromosome aberrations persist in individuals many years after occupational exposure to densely ionizing radiation: an mFISH study", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15912529{\&}query_hl=3", volume = "44", year = "2005", } @article{Lee2010, author = "Ryonfa Lee and Sylwester Sommer and Carola Hartel and Elena Nasonova and Marco Durante and Sylvia Ritter", abstract = "The purpose of the present study was to investigate as to what extent differences in the linear energy transfer (LET) are reflected at the chromosomal level. For this study human lymphocytes were exposed to 9.5 MeV/u C-ions (1 or 2 Gy, LET=175 keV/microm) or X-rays (1-6 Gy), harvested at 48, 72 or 96 h post-irradiation and aberrations were scored in first cycle metaphases using 24 color fluorescence in situ hybridization (mFISH). Additionally, in selected samples aberrations were measured in prematurely condensed G2-phase cells. Analysis of the time-course of aberrations in first cycle metaphases showed a stable yield of simple and complex exchanges after X-ray irradiation. In contrast, after C-ion exposure the yields profoundly increased with harvesting time complicating the estimation of the frequency of aberrations produced by high LET particles within the entire cell population. This is especially true for the yield of complex exchanges. Complex aberrations dominate the aberration spectrum produced by C-ions. Their fraction was about 50\% for the two measured doses. In contrast, isodoses of X-rays induced smaller proportions of complex aberrations (i.e. 5\% and 15\%, respectively). For both radiation qualities the fraction of complexes did not change with harvesting time. As expected from the different dose deposition of high and low LET radiation, complex exchanges produced by high LET C-ions involved more breaks and more chromosomes than those induced by isodoses of X-rays. Noteworthy, C-ions but not X-rays induced a small number of complex chromatid-isochromatid exchanges that are not expected for cells exposed in the G0-phase. The results obtained so far for cells arrested in G2-phase confirm these patterns. Altogether our data show that the increased effectiveness of C-ions for the induction of aberrations in first cycle cells is determined by complex exchanges, whereas for simple exchanges the relative biological effectiveness is about one.", journal = "Mutat Res", keywords = "Carbon; Chromosome Aberrations; G2 Phase; Heavy Ions; Humans; Linear Energy Transfer; Lymphocytes, radiation effects; Mitosis; Relative Biological Effectiveness; X-Rays; Isis; mFISH; mBAND", month = "Aug", number = "1", pages = "52--59", title = "Complex exchanges are responsible for the increased effectiveness of C-ions compared to X-rays at the first post-irradiation mitosis.", url = "http://dx.doi.org/10.1016/j.mrgentox.2010.03.004", volume = "701", year = "2010", } @article{Mehra2007, author = "R Mehra and SA Tomlins and R Shen and O Nadeem and L Wang and JT Wei and KJ Pienta and D Ghosh and MA Rubin and AM Chinnaiyan and RB Shah", abstract = "Novel recurrent gene fusions between the androgen-regulated gene TMPRSS2 and the ETS family members ERG, ETV1, or ETV4 have been recently identified as a common molecular event in prostate cancer development. We comprehensively analyzed the frequency and risk of disease progression for the TMPRSS2 and ETS family genes rearrangements in a cohort of 96 American men surgically treated for clinically localized prostate cancer. Using three break apart (TMPRSS2, ERG, ETV4) and one fusion (TMPRSS:ETV1) fluorescence in situ hybridization (FISH) assays, we identified rearrangements in TMPRSS2, ERG, ETV1, and ETV4 in 65, 55, 2, and 2% of cases, respectively. Overall, 54 and 2% of cases demonstrated TMPRSS2:ERG and TMPRSS2:ETV1 fusions, respectively. As intronic loss of genomic DNA between TMPRSS2 and ERG has been identified as a mechanism of TMPRSS2:ERG fusion, our assays allowed us to detect deletion of the 3' end of TMPRSS2 and the 5' end of ERG in 41 and 39% of cases rearranged for respective genes. Prostate cancers demonstrating TMPRSS2 gene rearrangement were associated with high pathologic stage (P=0.04). Our results confirm that recurrent chromosomal aberrations in TMPRSS2 and/or ETS family members are found in about 70% of prostate cancers. Importantly, we define a novel approach to study these gene fusions and identified cases where TMPRSS2 was rearranged without rearrangement of ERG, ETV1 or ETV4 and cases with ETS family gene rearrangement without TMPRSS2 rearrangement, suggesting that novel 5' and 3' partners may be involved in gene fusions in prostate cancer.", journal = "Mod Pathol", keywords = "Isis", number = "5", pages = "538-44", title = "Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancer", url = "http://dx.doi.org/10.1038/modpathol.3800769", volume = "20", year = "2007", } @article{00308, author = "R. Mehra and S.A. Tomlins and R. Shen and O. Nadeem and L. Wang and J.T. Wei and K.J. Pienta and D. Ghosh and M.A. Rubin and A.M. Chinnaiyan and R.B. Shah", journal = "Modern Pathology", keywords = "Metafer MetaCyte", pages = "538- 544", title = "Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancer.", url = "http://www.ncbi.nlm.nih.gov/pubmed/17334343?ordinalpos=22{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", volume = "20", year = "2007", } @article{00142, author = "Y. Aalto and L. Eriksson and S. Seregard and O. Larsson and S. Knuutila", journal = "Investigative Ophthalmology {\&} Visual Science", keywords = "Isis CGH", pages = "313- 317", title = "Concomitant loss of chromosome 3 and whole arm losses and gains of chromosome 1, 6, or 8 in metastasizing primary uveal melanoma", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=11157859", volume = "42", year = "2001", } @article{00267, author = "E. Kilic and N.C. Naus and van Gils, W. and C.C. Klaver and van Til, M.E. and M.M. Verbiest and T. Stijnen and C.M. Mooy and D. Paridaens and H.B. Beverloo and G.P. Luyten and de Klein, A.", journal = "Invest Ophthalmol Vis Sci", keywords = "Isis CGH", pages = "2253- 2257", title = "Concurrent loss of chromosome arm 1p and chromosome 3 predicts a decreased disease-free survival in uveal melanoma patients.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=15980208{\&}query_hl=4{\&}itool=pubmed_DocSum", volume = "46", year = "2005", } @article{00191, author = "T. Liehr and M. Ziegler and H. Starke and A. Heller and A. Kuechler and G. Kittner and V. Beensen and J. Seidel and H. H{\"a}{\ss}ler and J. M{\"u}sebeck and U. Claussen", journal = "Clin Genet", keywords = "Ikaros Isis", pages = "166- 167", title = "Conspicuous GTG-banding results of the centromere-near region can be caused by alphoid DNA heteromorphism", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12859415{\&}dopt=Abstract", volume = "64", year = "2003", } @article{00121, author = "K. Foitzik and G. Lindner and S. Mueller-Roever and M. Maurer and N. Botchkareva and V. Botchkarev and B. Handjiski and M. Metz and T. Hibino and T. Soma and G.P. Dotto and R. Paus", journal = "FASEB Journal", keywords = "Isis", pages = "752- 760", title = "Control of murine hair follicle regression (catagen) by TGF-beta1 in vivo.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=10744631{\&}query_hl=12{\&}itool=pubmed_docsum", volume = "14", year = "2000", } @article{Pickett2009, author = "HA Pickett and AJ Cesare and RL Johnston and AA Neumann and RR Reddel", abstract = "Telomere lengths are maintained in many cancer cells by the ribonucleoprotein enzyme telomerase but can be further elongated by increasing telomerase activity through the overexpression of telomerase components. We report here that increased telomerase activity results in increased telomere length that eventually reaches a plateau, accompanied by the generation of telomere length heterogeneity and the accumulation of extrachromosomal telomeric repeat DNA, principally in the form of telomeric circles (t-circles). Telomeric DNA was observed in promyelocytic leukemia bodies, but no intertelomeric copying or telomere exchange events were identified, and there was no increase in telomere dysfunction-induced foci. These data indicate that human cells possess a mechanism to negatively regulate telomere length by trimming telomeric DNA from the chromosome ends, most likely by t-loop resolution to form t-circles. Additionally, these results indicate that some phenotypic characteristics attributed to alternative lengthening of telomeres (ALT) result from increased mean telomere length, rather than from the ALT mechanism itself.", journal = "EMBO J", number = "7", pages = "799-809", title = "Control of telomere length by a trimming mechanism that involves generation of t-circles", url = "http://dx.doi.org/10.1038/emboj.2009.42", volume = "28", year = "2009", } @article{00183, author = "M. Sayed Aly and A. Wojcik and C. Schunck and G. Obe", journal = "International Journal of Radiation Biology", keywords = "Metafer2 ReloSys", pages = "1037- 1044", title = "Correlation of chromosomal aberrations and sister chromatid exchanges in individual CHO cells pre-labelled with BrdU and treated with DNaseI or X-rays", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=12456291", volume = "78", year = "2002", } @article{00084, author = "D.J. Clarke and J.F. Gim{\'e}nez-Abi{\'a}n and H. T{\"o}nnies and H. Neitzel and K. Sperling and C.S. Downes and R.T. Johnson", journal = "Proc. Natl. Acad. Sci. USA", pages = "167- 171", title = "Creation of monosomic derivatives of human cultured cell lines", url = "http://www.pnas.org/cgi/content/full/95/1/167", volume = "95", year = "1998", } @article{00176, author = "V.S. Lestou and J.X. O'Connell and M. Robichaud and C. Salski and J. Mathers and J. Maguire and I. Chudoba and P.H.B. Sorensen and W. Lam and D.E. Horsman", journal = "Cancer Genet. Cytogenet.", keywords = "Isis mFISH", pages = "153- 156", title = "Cryptic t(X;18), ins(6;18), and SYT-SSX2 gene fusion in a case of intraneural monophasic synovial sarcoma", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12505262{\&}dopt=Abstract", volume = "138", year = "2002", } @article{00190, author = "L. Harder and S. Gesk and J.I. Martin-Subero and H. Merz and A. Hochhaus and E. Maa{\ss} and A. Feller and W. Grote and R. Siebert and S. Fetscher", journal = "Cancer Genet. Cytogenet.", keywords = "Ikaros", pages = "80- 82", title = "Cytogenetic and molecular characterization of simultaneous chronic and acute myelotic leukemia.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=12660040{\&}query_hl=6", volume = "142", year = "2003", } @article{Wong2013, author = "K. F. Wong and Lisa L P. Siu and E. Ainsbury and J. Moquet", abstract = "Dicentric assay is the international gold standard for cytogenetic biodosimetry after radiation exposure, despite being very labour-intensive, time-consuming, and highly expertise-dependent. It involves the identification of centromeres and structure of solid-stained chromosomes and the enumeration of dicentric chromosomes in a large number of first-division metaphases of cultured T lymphocytes. The dicentric yield is used to estimate the radiation exposure dosage according to a statistically derived and predetermined dose-response curve. It can be used for population triage after large-scale accidental over-exposure to ionising radiation or with a view to making clinical decisions for individual patients receiving substantial radiation. In this report, we describe our experience in the establishment of a cytogenetic biodosimetry laboratory in Queen Elizabeth Hospital, Hong Kong. This was part of the contingency plan for emergency measures against radiation accidents at nuclear power stations.", journal = "Hong Kong Med J", keywords = "Metafer MSearch ReloSys", month = "Apr", number = "2", pages = "168--173", title = "Cytogenetic biodosimetry: what it is and how we do it.", url = "http://www.ncbi.nlm.nih.gov/pubmed/23535678", volume = "19", year = "2013", } @article{00137, author = "H. Schmidt and H. Taubert and P. W{\"u}rl and M. Bache and F. Bartel and H.-J. Holzhausen and R. Hinze", journal = "Cancer Genet. Cytogenet.", keywords = "Ikaros Isis CGH", pages = "14- 23", title = "Cytogenetic characterization of six malignant peripheral nerve sheath tumors: comparison of karyotyping and comparative genomic hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11454424{\&}dopt=Abstract", volume = "128", year = "2001", } @article{00058, author = "H. Schmidt and S. K{\"o}rber and R. Hinze and H. Taubert and A. Meye and P. W{\"u}rl and H.-J. Holzhausen and H. Dralle and F.-W. Rath", journal = "Cancer Genet Cytogenet", pages = "134- 142", title = "Cytogenetic Characterization of Ten Malignant Fibrous Histiocytomas", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9428357{\&}dopt=Abstract", volume = "100", year = "1997", } @article{00201, author = "D. Pantou and H. Tsarouha and A. Papandopoulou and L. Mahaira and I. Kyriazoglou and N. Apostolikas and S. Markidou and T. Trangas and N. Pandis and G. Bardi", journal = "Neoplasia", keywords = "Isis CGH", pages = "23- 31", title = "Cytogenetic profile of unknown primary tumors: clues for their pathogenesis and clinical management", volume = "5", year = "2003", } @article{00026, author = "J. Szymanska and M. Tarkkanen and T. Wiklund and M. Virolainen and C. Blomqvist and S. AskoSeljavaara and E. Tukiainen and I. Elomaa and S. Knuutila", journal = "Cancer Genet Cytogenet", pages = "170- 173", title = "Cytogenetic study of extraskeletal mesenchymal chondrosarcoma - a case report", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8603349{\&}dopt=Abstract", volume = "86", year = "1996", } @article{00299, author = "L. Migliore and A. Naccarati and F. Copped{\`e} and E. Bergamaschi and G. De Palma and A. Voho and P. Manini and H. J{\"a}rventaus and A. Mutti and H. Norppa and A. Hirvonen", journal = "Pharmacogen Genom", keywords = "Metafer MSearch", pages = "87- 99", title = "Cytogenmetic biomarkers, urinary metabolites and metabolic gene polymorphisms in workers exposed to styrene.", volume = "16", year = "2006", } @article{Cariou2010, author = "Olivier Cariou and Nathalie Laroche-Prigent and Sandrine Ledieu and Isabelle Guizon and Fran{\c{c}}oise Paillard and V{\'e}ronique Thybaud", abstract = "Cytosine arabinoside (a nucleoside analogue that inhibits the gap-filling step of excision repair), vinblastine (an aneugen that inhibits tubulin polymerisation), 5-fluorouracil (a nucleoside analogue with a steep response profile), and 2-aminoanthracene (a metabolism-dependent reference genotoxin) were tested in the in vitro micronucleus assay with L5178Y mouse lymphoma cells, without cytokinesis block. The four chemicals were independently evaluated in two Sanofi Aventis laboratories, one of which used an image analyser to score micronuclei, while the other scored micronucleated cells manually. Very similar results were obtained in the two laboratories, highlighting the robustness of the assay. The four test chemicals induced significant increases in the incidence of micronucleated cells at concentrations that produced no more than a 55+/-5\% reduction in survival growth, as measured with the three parameters recommended in the draft OECD Test Guideline on In Vitro Mammalian Cell Micronucleus Test (MNvit) for chemical testing, namely the relative increase in cell counts, relative population doubling, and the relative cell count. These results support the premise that the relative increase in cell counts and relative population doubling, that take into account both cell death and cytostasis, are appropriate measures of survival growth reduction in the in vitro micronucleus test conducted in the absence of cytokinesis block, as recommended in MNvit.", journal = "Mutat Res", keywords = "Metafer MNScore", month = "Apr", title = "Cytosine arabinoside, vinblastine, 5-fluorouracil and 2-aminoanthracene testing in the in vitro micronucleus assay with L5178Y mouse lymphoma cells at Sanofi Aventis, with different cytotoxicity measurements, in support of the draft OECD Test Guidel", url = "http://dx.doi.org/10.1016/j.mrgentox.2010.04.005", year = "2010", } @article{Stindl2008, author = "Reinhard Stindl", abstract = "Recently, an influential sequencing study found that more than 1700 genes had non-silent mutations in either a breast or colorectal cancer, out of just 11 breast and 11 colorectal tumor samples. This is not surprising given the fact that genomic instability is the hallmark of cancer cells. The plethora of genomic alterations found in every carcinoma does not obey the 'law of genotype-phenotype correlation', since the same histological subtype of cancer harbors different gene mutations and chromosomal aberrations in every patient. In an attempt to make sense out of the observed genetic and chromosomal chaos in cancer, I propose a cascade model. According to this model, tissue regeneration depends on the proliferation and serial activation of stem cells. Replicative telomere erosion limits the proliferative life span of adult stem cells and results in the Hayflick limit (M1). However, local tissue exhaustion or old age might promote the activation of M1-deficient tissue stem cells. Extended proliferation of these cells leads to telomere-driven chromosomal instability and aneuploidy (abnormal balance of chromosomes and/or chromosome material). Several of the aforementioned steps have been already described in the literature. However, in contrast to common theories, it is proposed here that the genomic damage blocks the epigenetic differentiation switch. As a result of aneuploidy, differentiation-specific genes cannot be activated by modification of methylation patterns. Consequently, the phenotype of cancer tissue is largely determined by the epigenetic maturation arrest of tissue stem cells, which in addition enables a fraction of cancer cells to proliferate, invade and metastasize, as normal adult stem cells do. The new model combines genetic and epigenetic alterations of cancer cells in one causative cascade and offers an explanation for why identical histologic cancer types harbor a confusing variety of chromosomal and gene aberrations. The Viennese Cascade, as presented here, may end the debate on if and how 'tumor-unspecific' aneuploidy leads to cancer.", journal = "Med Hypotheses", keywords = "Isis mFISH", number = "1", pages = "126--140", title = "Defining the steps that lead to cancer: replicative telomere erosion, aneuploidy and an epigenetic maturation arrest of tissue stem cells.", url = "http://dx.doi.org/10.1016/j.mehy.2008.01.010", volume = "71", year = "2008", } @article{00314, author = "R. Stindl", journal = "Medical Hypotheses", keywords = "Isis mFISH", pages = "0- 0", title = "Defining the steps that lead to cancer: Replicative telomere erosion, aneuploidy and an epigenetic maturation arrest of tissue stem cells.", url = "http://www.ncbi.nlm.nih.gov/pubmed/18294777?ordinalpos=1{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", year = "2008", } @article{00124, author = "E. Gebhart and I. Verdorfer and W. Saul and U. Trautmann and L. Brecevic", journal = "Int. J. Oncol.", keywords = "Isis CGH", pages = "1099- 1105", title = "Delimiting the use of comparative genomic hybridization in human myeloid neoplastic disorders", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=10811980{\&}query_hl=6", volume = "16", year = "2000", } @article{00189, author = "D.B. Zimonjic and M.W. Brooks and N. Popescu and R.A. Weinberg and W.C. Hahn", journal = "Cancer Research", pages = "8838- 8844", title = "Derivation of human tumor cells in vitro without widespread genomic instability.", volume = "61", year = "2002", } @article{00303, author = "S. Gazzo and I. Chudoba and A. Traverse-Glehen and L. Baseggio and P. Felman and F. Berger and G. Salles and S. Hayette and J.-P. Magaud and E. Callet-Bauchu", journal = "Cancer Genet Cytogenet.", keywords = "Isis mBAND", pages = "159- 165", title = "Detailed characterization of 7q deletions by multicolor banding (mBAND) in marginal zone cell lymphoma.", url = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed{\&}Cmd=ShowDetailView{\&}TermToSearch=17556073{\&}ordinalpos=1{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Res", volume = "175", year = "2007", } @article{00219, author = "K. Mrasek and A. Heller and N. Rubtsov and V. Trifonov and H. Starke and U. Claussen and T. Liehr", journal = "Int J Mol Med", keywords = "Isis mFISH mBAND", pages = "139- 146", title = "Detailed Hylobates lar karyotype defined by 25-color FISH and multicolor banding", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12851708{\&}dopt=Abstract", volume = "12", year = "2003", } @article{00065, author = "J.A. Veltman and A.H.N. Hopman and F.J. Bot and F.C.S. Ramaekers and J.J. Manni", journal = "Cancer", pages = "309- 314", title = "Detection of Chromosomal Aberrations in Cytologic Brush Specimens from Head and Neck Squamous Cell Carcinoma", volume = "81", year = "1997", } @article{00225, author = "G. M{\'e}hes and A. Luegmayr and R. Kornm{\"u}ller and I.M. Ambros and R. Ladenstein and H. Gadner and P.F. Ambros", journal = "Am J Pathol", keywords = "Metafer RCDetect", pages = "393- 399", title = "Detection of disseminated tumor cells in neuroblastoma: 3 log improvement in sensitivity by automatic immunofluorescence plus FISH (AIPF) analysis compared with classical bone marrow cytology.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=12875961{\&}query_hl=8{\&}itool=pubmed_docsum", volume = "2003", year = "2003", } @article{Laszlo2010, author = "Ren{\'a}ta L{\'a}szl{\'o} and Don{\'a}t Alp{\'a}r and B{\'e}la Kajt{\'a}r and Agnes Lacza and G{\'a}bor Ott{\'o}ffy and Csongor Kiss and Katalin Bartyik and K{\'a}lm{\'a}n Nagy and L{\'a}szl{\'o} Pajor", abstract = "DNA-, RNA-, and cell-based methods provide different biologic information for determining the presence of minimal residual disease (MRD). We monitored the responses of patients with pediatric acute lymphoblastic leukemia (pALL) using DNA markers, TEL/AML1 expression, and scanning fluorescence microscopy (SFM). Using SFM, 36\% of patients exhibited 1.5-3.1 log and 2.9-4.2 log higher MRD levels compared with those based on DNA and RNA markers, respectively. CD10+ ancestor cells with germline antigen receptors, but silent TEL/AML1 expression, may reside in the lymphoid stem cell compartment of treated t(12;21)-positive patients and might act as a potential source of cells for late relapses.", journal = "Pediatr Blood Cancer", keywords = "Metafer, RCDetect, MetaCyte", month = "Jan", number = "1", pages = "158--160", title = "Detection of early precursors of t(12;21) positive pediatric acute lymphoblastic leukemia during follow-up.", url = "http://dx.doi.org/10.1002/pbc.22300", volume = "54", year = "2010", } @article{Hartmann2011, author = "Luise Hartmann and Julie Sanford Biggerstaff and Douglas B. Chapman and Janice M. Scott and Krystal R. Johnson and Keely M. Ghirardelli and Wayne K. Fritschle and Dolores L. Martinez and Richard K. Bennington and Monica E. {de Baca} and Denise A. Wells and Michael R. Loken and Barbara K. Zehentner", abstract = "Multiple myeloma (MM) is a hematopoietic neoplasm characterized by malignant plasma cells (PCs) that accumulate in the bone marrow. A number of different genomic abnormalities are associated with MM; however, detection of these by fluorescence in situ hybridization (FISH) can be limited by the percentage of PCs in the specimen. In this study, we tested 20 bone marrow specimens with known MM and a low concentration of monoclonal PCs for the presence of genomic abnormalities using FISH in combination with various PC enrichment techniques: magnetic cell sorting, targeted manual scoring, and automated image analysis. In addition, flow cytometric cell sorting of PCs in combination with FISH analysis was also tested for minimal residual disease applications. Different parameters were evaluated when assessing the detection efficiency of each approach. FISH results are highly dependent on the chosen enrichment method. We describe the evaluation of different techniques applicable for various laboratory settings and specimen parameters.", journal = "Am J Clin Pathol", keywords = "Metafer, MetaCyte", month = "Nov", number = "5", pages = "712--720", title = "Detection of genomic abnormalities in multiple myeloma: the application of FISH analysis in combination with various plasma cell enrichment techniques.", url = "http://dx.doi.org/10.1309/AJCPF7NFLW8UAJEP", volume = "136", year = "2011", } @article{00033, author = "R.J. Van Oostenbrugg and A.H.N. Hopman and M.H. Lenders and P. Van Heerde and J.-W. Arends and F.C.S. Ramaekers and A. Twijnstra", journal = "J Neuropathol Exp Neurol", keywords = "Isis", pages = "743- 748", title = "Detection of Malignant Cells in Cerebrospinal Fluid Using Fluorescence In Situ Hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9184665{\&}dopt=Abstract", volume = "56", year = "1997", } @article{Vaurijoux2012, author = "Aurelie Vaurijoux and Eric Gregoire and Sandrine Roch-Lefevre and Pascale Voisin and Cecile Martin and Philippe Voisin and Laurence Roy and Gaetan Gruel", abstract = "In accidental exposure to ionizing radiation, it is essential to estimate the dose received by the victims. Currently dicentric scoring is the best biological indicator of exposure. The standard biological dosimetry procedure (500 metaphases scored manually) is suitable for a few dose estimations, but the time needed for analysis can be problematic in the case of a large-scale accident. Recently, a new methodology using automatic detection of dicentrics has greatly decreased the time needed for dose estimation and preserves the accuracy of the estimation. However, the capability to detect nonhomogeneous partial-body exposures is an important advantage of dicentric scoring-based biodosimetry, and this remains to be tested with automatic scoring. Thus we analyzed the results obtained with in vitro blood dilutions and in real cases of accidental exposure (partial- or whole-body exposure) using manual scoring and automatic detection of dicentrics. We confirmed that automatic detection allows threefold quicker dicentric scoring than the manual procedure with similar dose estimations and uncertainty intervals. The results concerning partial-body exposures were particularly promising, and homogeneously exposed samples were correctly distinguished from heterogeneously exposed samples containing 5\% to 75\% of blood irradiated with 2 Gy. In addition, the results obtained for real accident cases were similar whatever the methodology used. This study demonstrates that automatic detection of dicentrics is a credible alternative for recent and acute cases of whole- and partial-body accidental exposures to ionizing radiation.", journal = "Radiat Res", keywords = "DCScore Metafer Biodosimetry", month = "Oct", number = "4", pages = "357--364", title = "Detection of partial-body exposure to ionizing radiation by the automatic detection of dicentrics.", url = "http://www.ncbi.nlm.nih.gov/pubmed/22171959", volume = "178", year = "2012", } @article{00025, author = "M. Poetsch and K. Weber-Matthiesen and H.-J. Plendl and W. Grote and B. Schlegelberger", journal = "Journal of Clinical Oncology", pages = "963- 969", title = "Detection of the t(14/18) Chromosomal Translocation by Interphase Cytogenetics With Yeast-Artificial-Chromosome Probes in Follicular Lymphoma and Nonneoplastic Lymphoproliferation", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8622046{\&}dopt=Abstract", volume = "14", year = "1996", } @article{00284, author = "R. Genghini and I. Tiranti and E. Bress{\'a}n and E. Zamorano-Ponce and J. Fernand{\'e}z and F. Dulout", journal = "Mutagenesis", keywords = "CometImager", pages = "213- 217", title = "Determination of genotoxicity of classical swine fever vaccine in vitro by cytogenetic and comet tests.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=16571637{\&}query_hl=1{\&}itool=pubmed_docsum", volume = "21", year = "2006", } @article{00320, author = "H. Nitta and B. Hauss-Wegrzyniak and M. Lehrkamp and A.E. Murillo and F. Gaire and M. Farrell and E. Walk and F. Penault-Llorca and M. Kurosumi and M. Dietel and L. Wang and M. Loftus and J. Pettay and R.R. Tubbs and T.M. Grogan", journal = "Diagn Pathol", keywords = "Metafer MetaCyte", pages = "0- 0", title = "Development of automated brightfield double In Situ hybridization (BDISH) application for HER2 gene and chromosome 17 centromere (CEN 17) for breast carcinomas and an assay performance comparison to manual dual color HER2 fluorescence In Situ hybridizatio", url = "http://www.ncbi.nlm.nih.gov/pubmed/18945356?ordinalpos=14{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDo", volume = "3", year = "2008", } @article{00226, author = "P.F. Ambros and G. Mehes and I.M. Ambros and R. Ladenstein", journal = "Cancer letters", keywords = "Metafer RCDetect Isis", pages = "29- 34", title = "Disseminated tumour cells in the bone marrow - chances and consequences of microscopical detection methods", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12880956{\&}dopt=Abstract", volume = "197", year = "2003", } @article{00203, author = "H. Richter and P. Slezak and A. Walch and M. Werner and H. Braselmann and E. Jaramillo and {\AA}. {\"O}st and I. Hirata and K. Takahama and H. Zitzelsberger", journal = "Am J Pathol", keywords = "Isis CGH", pages = "287- 294", title = "Distinct chromosomal imbalances in nonpolypoid and polypoid colorectal adenomas indicate different genetic pathways in the development of colorectal neoplasms.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=12819033{\&}query_hl=10{\&}itool=pubmed_docsum", volume = "163", year = "2003", } @article{00301, author = "S.A. Tomlins and B. Laxman and S.M. Dhanasekaran and B.E. Helgeson and X. Cao and D.S. Morris and A. Menon and X. Jing and Q. Ciao and B. Han and J. Yu and L. Wang and J.E. Montie and M.A. Rubin and K.J. Pienta and D. Roulston and R.B. Shah and S. Varambally and R. Mehra and A.M. Chinnaiyan", journal = "Nature", keywords = "Isis", pages = "595- 599", title = "Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer.", url = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed{\&}Cmd=ShowDetailView{\&}TermToSearch=17671502{\&}ordinalpos=3{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Res", volume = "448", year = "2007", } @article{Botchkareva2000, author = "N. V. Botchkareva and V. A. Botchkarev and K. M. Albers and M. Metz and R. Paus", abstract = "Increasing evidence suggests that neurotrophins play an important part in the control of the development of ectodermal derivatives, such as the hair follicle. Here, we show that, during hair follicle morphogenesis in C57BL/6 mice, nerve growth factor, brain-derived neurotrophic factor and their corresponding high-affinity tyrosine kinase receptors, TrkA and TrkB, show stringently controlled spatiotemporal expression patterns in the follicular epithelium and mesenchyme. Constitutive overexpression of nerve growth factor in mice is associated with a discrete, but significant acceleration of hair follicle morphogenesis, whereas this is not seen in brain-derived neurotrophic factor transgenic mice. In neonatal skin organ culture, nerve growth factor and brain-derived neurotrophic factor differentially influence hair follicle development: nerve growth factor accelerates late stages of hair follicle morphogenesis, whereas brain-derived neurotrophic factor does not show significant effects. This suggests that the morphogenetic properties of locally generated neurotrophins in the skin, similar to their classical neurotrophic functions, are quite distinct and depend on the response patterns of the corresponding neurotrophin target receptor-expressing cells in the developing hair follicle. These data further strengthen the concept that neurotrophin signaling is an important element in controlling the rate of hair follicle morphogenesis, yet also highlight the complexity of this signaling system.", journal = "J Invest Dermatol", keywords = "Isis", month = "Feb", number = "2", pages = "314--320", title = "Distinct roles for nerve growth factor and brain-derived neurotrophic factor in controlling the rate of hair follicle morphogenesis.", url = "http://dx.doi.org/10.1046/j.1523-1747.2000.00864.x", volume = "114", year = "2000", } @article{00077, author = "S. Knuutila and A.-M. Bj{\"o}rkqvist and K. Autio and M. Tarkkanen and et al, M. Wolf", journal = "American Journal of Pathology", keywords = "Isis CGH", pages = "1107- 1123", title = "DNA Copy Number Amplifications In Human Neoplasms", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9588877{\&}dopt=Abstract", volume = "152", year = "1998", } @article{00074, author = "M.L. Larramendy and T. Huhta and K. Heinonen and K. Vettenranta and E. Mahlam{\"a}ki and P. Riikonen and U. Saarinen-Pihkala and S. Knuutila", journal = "Haematologia", keywords = "Isis CGH", pages = "890- 895", title = "DNA copy number changes in childhood acute lymphoblastic leukemia", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=9830797", volume = "83", year = "1998", } @article{00024, author = "O. Monni and H. Joensuu and K. Franssila and S. Knuutila", journal = "Blood", pages = "5269- 5278", title = "DNA copy number changes in diffuse large B-cell lymphoma - Comparative genomic hybridization study", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8652842{\&}dopt=Abstract", volume = "87", year = "1996", } @article{00021, author = "W. El-Rifai and M. Sarlomo-Rikala and M. Miettinen and S. Knuutila and L. Andersson", journal = "Cancer Research", pages = "3230- 3233", title = "DNA Copy Number Losses in Chromosome 14: An Early Change in Gastrointestinal Stromal Tumors", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8764113{\&}dopt=Abstract", volume = "56", year = "1996", } @article{Schmidt2011, author = "Wolfgang M Schmidt and Mohammed H Uddin and Sandra Dysek and Karin Moser-Thier and Christine Pirker and Harald H{\"o}ger and Inge M Ambros and Peter F Ambros and Walter Berger and Reginald E Bittner", abstract = "Albeit genetically highly heterogeneous, muscular dystrophies (MDs) share a convergent pathology leading to muscle wasting accompanied by proliferation of fibrous and fatty tissue, suggesting a common MD-pathomechanism. Here we show that mutations in muscular dystrophy genes (Dmd, Dysf, Capn3, Large) lead to the spontaneous formation of skeletal muscle-derived malignant tumors in mice, presenting as mixed rhabdomyo-, fibro-, and liposarcomas. Primary MD-gene defects and strain background strongly influence sarcoma incidence, latency, localization, and gender prevalence. Combined loss of dystrophin and dysferlin, as well as dystrophin and calpain-3, leads to accelerated tumor formation. Irrespective of the primary gene defects, all MD sarcomas share non-random genomic alterations including frequent losses of tumor suppressors (Cdkn2a, Nf1), amplification of oncogenes (Met, Jun), recurrent duplications of whole chromosomes 8 and 15, and DNA damage. Remarkably, these sarcoma-specific genetic lesions are already regularly present in skeletal muscles in aged MD mice even prior to sarcoma development. Accordingly, we show also that skeletal muscle from human muscular dystrophy patients is affected by gross genomic instability, represented by DNA double-strand breaks and age-related accumulation of aneusomies. These novel aspects of molecular pathologies common to muscular dystrophies and tumor biology will potentially influence the strategies to combat these diseases.", journal = "PLoS Genet", keywords = "Isis, Metafer, MetaCyte", month = "Apr", number = "4", pages = "e1002042", title = "DNA damage, somatic aneuploidy, and malignant sarcoma susceptibility in muscular dystrophies.", url = "http://dx.doi.org/10.1371/journal.pgen.1002042", volume = "7", year = "2011", } @article{00255, author = "A. Hruska and R. Bollmann and R.B. Kov{\'a}cs and M. Bollmann and M. Bod{\'o} and Z. S{\'a}pi", journal = "Cellular Oncology", keywords = "Metafer MetaCyte", pages = "335- 345", title = "DNA ploidy and chromosome (FISH) pattern analysis of peripheral nerve sheath tumors", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15623944", volume = "26", year = "2004", } @article{Tobin1998, author = "D. J. Tobin and E. Hagen and V. A. Botchkarev and R. Paus", abstract = "The fate of the hair follicle pigmentary unit during the cyclical involution of anagen hair follicles is unknown. Using the C57BL/6 mouse model for hair research, hair follicle melanocytes were examined during the anagen-catagen transformation, comparing spontaneous and pharmacologically induced catagen development. This study shows that both spontaneous catagen and dexamethasone-induced catagen display similar changes in the pigmentary unit. Catagen hair follicles exhibited pigment incontinence in the dermal papilla and in selected outer root sheath keratinocytes. Melanocytes deleted by apoptosis were detected in spontaneous catagen and, more commonly, in dexamethasone-induced catagen, and were identified using transmission electron microscopy by the presence of free premelanosomes in affected cells lacking epithelial specializations, and by the colocalization of TUNEL positivity and tyrosinase-related protein-1 immunoreactivity. By contrast, cyclophosphamide-induced catagen was characterized by the initial retention of melanogenic and dendritic melanocytes in the presence of widespread keratinocyte apoptosis. Melanocyte incontinence and the ectopic distribution of melanin were more severe than in the other forms of catagen. Whereas much of this melanin was extruded, via the hair canal, to the skin surface, hair follicle-derived pigment was also detected within the epidermis, probably derived from pigment-carrying migrating outer root sheath keratinocytes from the proximal hair follicle. Thus, apoptosis may account, at least in part, for the loss of melanogenic melanocytes during spontaneous catagen. Although dexamethasone-induced catagen may provide a useful model for general hair pigmentation research, catagen induced by cyclophosphamide offers an interesting model for studying the response, and relative resistance, of melanocytes to chemical injury.", journal = "J Invest Dermatol", keywords = "Isis", month = "Dec", number = "6", pages = "941--947", title = "Do hair bulb melanocytes undergo apoptosis during hair follicle regression (catagen)?", url = "http://dx.doi.org/10.1046/j.1523-1747.1998.00417.x", volume = "111", year = "1998", } @article{00257, author = "Y. Zou and A. Sfeir and S.M. Gryaznov and J.W. Shay and W.E. Wright", journal = "Molecular Biology of the Cell", keywords = "Metafer MSearch", pages = "3709- 3718", title = "Does a sentinel or a subset of short telomeres determine replicative senescence?", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15181152{\&}query_hl=11", volume = "15", year = "2004", } @article{00245, author = "Z. Sieglov{\'a} and S. Zilovcov{\'a} and J. Cerm{\'a}k and H. R{\'i}hov{\'a} and D. Brezinov{\'a} and R. Dvor{\'a}kov{\'a} and M. Markov{\'a} and J. Maaloufov{\'a} and J. Sajdov{\'a} and J. Brezinov{\'a} and Z. Zemanov{\'a} and K. Michalov{\'a}", journal = "Leukemia Research", keywords = "Isis mFISH", pages = "1013- 1021", title = "Dynamics of telomere erosion and its association with genome instability in myelodysplastic syndromes (MDS) and acute myelogenous leukemia arising from MDS: a marker of disease prognosis?", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15289012", volume = "28", year = "2004", } @article{Vandersickel2010, author = "Veerle Vandersickel and Julie Depuydt and Bram {Van Bockstaele} and Gianpaolo Perletti and Jan Philippe and Hubert Thierens and Anne Vral", abstract = "A better understanding of the underlying mechanisms of DNA repair after exposure to ionizing radiation represents a research priority aimed at improving the outcome of clinical radiotherapy. Because of the close association with DNA double strand break (DSB) repair, phosphorylation of the histone H2AX protein ({\~a}H2AX), quantified by immunodetection, has recently been used as a method to study DSB induction and repair at low and clinically relevant radiation doses. However, the lack of consistency in literature points to the need to further validate the role of H2AX phosphorylation in DSB repair and the use of this technique to determine intrinsic radiosensitivity. In the present study we used human mammary epithelial MCF10A cells, characterized by a radiosensitive phenotype due to reduced levels of the Ku70 and Ku80 repair proteins, and investigated whether this repair-deficient cell line displays differences in the phosphorylation pattern of H2AX protein compared to repair-proficient MCF10A cells. This was established by measuring formation and disappearance of {\~a}H2AX foci after irradiating synchronized cell populations with (60)Co {\~a}-rays. Our results show statistically significant differences in the number of {\~a}H2AX foci between the repair-deficient and -proficient cell line, with a higher amount of {\~a}H2AX foci present at early times post-irradiation in the Ku-deficient cell line. However, the disappearance of those differences at later post-irradiation times questions the use of this assay to determine intrinsic radiosensitivity, especially in a clinical setting.", journal = "J Radiat Res", keywords = "Foci, Metafer, MetaCyte, H2AX", number = "6", pages = "633--641", title = "Early increase of radiation-induced {\~a}H2AX foci in a human Ku70/80 knockdown cell line characterized by an enhanced radiosensitivity.", volume = "51", year = "2010", } @article{00315, author = "M.A. Wahab and E.M. Nickless and R. Najar-M'Kacher and C. Parmentier and J.V. Podd and R.E. Rowland", journal = "Cytogenet. Genome Res.", keywords = "Isis mFISH mBAND", pages = "79- 87", title = "Elevated chromosome translocation frequencies in New Zealand nuclear test veterans.", url = "http://www.ncbi.nlm.nih.gov/pubmed/18544930?ordinalpos=4{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", volume = "121", year = "2008", } @article{00223, author = "L. Hughes-Davies and D. Huntsman and M. Ruas and F. Fuks and J. Bye and S.-F. Chin and J. Milner and L.A. Brown and F. Hsu and B. Gilks and T. Nielsen and M. Schulzer and S. Chia and J. Ragaz and A. Cahn and L. Linger and H. Ozdag and E. Cattaneo and E.S. Jordanova and et al.", journal = "Cell", keywords = "Metafer MetaCyte", pages = "523- 535", title = "EMSY links the BRCA2 pathway to sporadic breast and ovarian cancer.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=14651845{\&}query_hl=20{\&}itool=pubmed_docsum", volume = "115", year = "2003", } @article{00195, author = "V. Trifonov and J. Seidel and H. Starke and M. Prechtel and V. Beensen and M. Ziegler and I. Hartmann and A. Heller and A. Nietzel and U. Claussen and T. Liehr", journal = "Prenatal Diagnosis", keywords = "Ikaros Isis mFISH mBAND", pages = "427- 434", title = "Enlarged chromosome 13 p-arm hiding a cryptic partial trisomy 6p22.2-pter (Letter to the Editor)", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12749042{\&}dopt=Abstract", volume = "23", year = "2003", } @article{Majumder2008, author = "Shubhra Majumder and Anuradha Lohia", abstract = "The formin family of proteins mediates dynamic changes in actin assembly in eukaryotes, and therefore it is important to understand the function of these proteins in Entamoeba histolytica, where actin forms the major cytoskeletal network. In this study we have identified the formin homologs encoded in the E. histolytica genome based on sequence analysis. Using multiple tools, we have analyzed the primary sequences of the eight E. histolytica formins and discovered three subsets: (i) E. histolytica formin-1 to -3 (Ehformin-1 to -3), (ii) Ehformin-4, and (iii) Ehformin-5 to -8. Two of these subsets (Ehformin-1 to -3 and Ehformin-4) showed significant sequence differences from their closest homologs, while Ehformin-5 to -8 were unique among all known formins. Since Ehformin-1 to -3 showed important sequence differences from Diaphanous-related formins (DRFs), we have studied the functions of Ehformin-1 and -2 in E. histolytica transformants. Like other DRFs, Ehformin-1 and -2 associated with F-actin in response to serum factors, in pseudopodia, in pinocytic and phagocytic vesicles, and at cell division sites. Ehformin-1 and -2 also localized with the microtubular assembly in the nucleus, indicating their involvement in genome segregation. While increased expression of Ehformin-1 and -2 did not affect phagocytosis or motility, it clearly showed an increase in the number of binucleated cells, the number of nuclei in multinucleated cells, and the average DNA content of each nucleus, suggesting that these proteins regulate both mitosis and cytokinesis in E. histolytica.", journal = "Infect Immun", keywords = "Animals; Cell Division; Protozoan DNA; Entamoeba histolytica; Gene Expression Regulation; Microfilament Proteins; Multigene Family; Phylogeny; MetaCyte", month = "Jun", number = "6", pages = "2368--2378", title = "Entamoeba histolytica encodes unique formins, a subset of which regulates DNA content and cell division.", url = "http://dx.doi.org/10.1128/IAI.01449-07", volume = "76", year = "2008", } @article{00317, author = "S. Majumder and A. Lohia", journal = "Infection and Immunity", keywords = "Metafer MetaCyte", pages = "2368- 2378", title = "Entamoeba histolytica encodes unique formins, a subset of which regulates DNA content and cell division.", url = "http://www.ncbi.nlm.nih.gov/pubmed/18347041?ordinalpos=6{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", volume = "76", year = "2008", } @article{00089, author = "H. Iwasaki and Y. Ohjimi and M. Ishiguro and T. Isayama and Y. Kaneko and S. Yoh and G. Emoto and M. Kikuchi", journal = "Cancer Genet Cytogenet", pages = "46- 52", title = "Epithelioid Sarcoma with an 18q Aberration", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8908166{\&}dopt=Abstract", volume = "91", year = "1998", } @article{Brown2008, author = "Lindsay A. Brown and Jeremy Hoog and Suet-Feung Chin and Yu Tao and Abd Alnaser Zayed and Koei Chin and Andrew E. Teschendorff and John F. Quackenbush and John C. Marioni and Samuel Leung and Charles M. Perou and Torsten O. Neilsen and Matthew Ellis and Joe W. Gray and Philip S. Bernard and David G. Huntsman and Carlos Caldas", journal = "Nat Genet", keywords = "Metafer, MetaCyte, TMA", month = "Jul", number = "7", pages = "806--7; author reply", title = "ESR1 gene amplification in breast cancer: a common phenomenon?", url = "http://dx.doi.org/10.1038/ng0708-806", volume = "40", year = "2008", } @article{00096, author = "S. Neubauer and T. Liehr and S. Biekenhake and E. Gebhart and R. Fietkau and R. Sauer", journal = "Genet Analysis: Biomolec Engineer", pages = "121- 124", title = "Estimation of DNA single-strand breaksby single cell gel electrophoresis in tumor cells", volume = "14", year = "1998", } @article{Greve2012, author = "Burkhard Greve and Tobias B{\"o}lling and Susanne Amler and Ute R{\"o}ssler and Maria Gomolka and Claudia Mayer and Odilia Popanda and Kristin Dreffke and Astrid Rickinger and Eberhard Fritz and Friederike Eckardt-Schupp and Christina Sauerland and Herbert Braselmann and Wiebke Sauter and Thomas Illig and Dorothea Riesenbeck and Stefan K{\"o}nemann and Normann Willich and Simone M{\"o}rtl and Hans Theodor Eich and Peter Schmezer", abstract = "Radiotherapy is a powerful cure for several types of solid tumours, but its application is often limited because of severe side effects in individual patients. With the aim to find biomarkers capable of predicting normal tissue side reactions we analysed the radiation responses of cells from individual head and neck tumour and breast cancer patients of different clinical radiosensitivity in a multicentric study. Multiple parameters of cellular radiosensitivity were analysed in coded samples of peripheral blood lymphocytes (PBLs) and derived lymphoblastoid cell lines (LCLs) from 15 clinical radio-hypersensitive tumour patients and compared to age- and sex-matched non-radiosensitive patient controls and 15 lymphoblastoid cell lines from age- and sex- matched healthy controls of the KORA study. Experimental parameters included ionizing radiation (IR)-induced cell death (AnnexinV), induction and repair of DNA strand breaks (Comet assay), induction of yH2AX foci (as a result of DNA double strand breaks), and whole genome expression analyses. Considerable inter-individual differences in IR-induced DNA strand breaks and their repair and/or cell death could be detected in primary and immortalised cells with the applied assays. The group of clinically radiosensitive patients was not unequivocally distinguishable from normal responding patients nor were individual overreacting patients in the test system unambiguously identified by two different laboratories. Thus, the in vitro test systems investigated here seem not to be appropriate for a general prediction of clinical reactions during or after radiotherapy due to the experimental variability compared to the small effect of radiation sensitivity. Genome-wide expression analysis however revealed a set of 67 marker genes which were differentially induced 6 h after in vitro-irradiation in lymphocytes from radio-hypersensitive and non-radiosensitive patients. These results warrant future validation in larger cohorts in order to determine parameters potentially predictive for clinical radiosensitivity.", journal = "PLoS One", keywords = "Metafer CometScan", number = "10", pages = "e47185", title = "Evaluation of different biomarkers to predict individual radiosensitivity in an inter-laboratory comparison--lessons for future studies.", url = "http://dx.doi.org/10.1371/journal.pone.0047185", volume = "7", year = "2012", } @article{Weer2008a, author = "An De Weer and Bruce Poppe and Barbara Cauwelier and Andre Carlier and Jan Dierick and Bruno Verhasselt and Jan Philipp{\'e} and Nadine Van Roy and Frank Speleman", journal = "BMC Cancer", keywords = "Ikaros Isis", pages = "193", title = "EVI1 activation in blast crisis CML due to juxtaposition to the rare 17q22 partner region as part of a 4-way variant translocation t(9;22).", url = "http://dx.doi.org/10.1186/1471-2407-8-193", volume = "8", year = "2008", } @article{00207, author = "T. Liehr and H. Starke and A. Heller and A. Weise and V. Beensen and G. Senger and G. Kittner and M. Prechtel and U. Claussen and J. Seidel", journal = "Int J Mol Med", keywords = "Isis mBAND", pages = "575- 577", title = "Evidence for a new microdeletion syndrome in 15q21", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12684692{\&}dopt=Abstract", volume = "11", year = "2003", } @article{00063, author = "J. Tapper and R. B{\"u}tzow and T. Wahlstr{\"o}m and M. Sepp{\"a}l{\"a} and S. Knuutila", journal = "Br J Cancer", pages = "1782- 1787", title = "Evidence for divergence of DNA copy number changes in serous, mucinous and endometrioid ovarian carcinomas", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9192982{\&}dopt=Abstract", volume = "75", year = "1997", } @article{00197, author = "K. Rothkamm and M. L{\"o}brich", journal = "Proc Natl Acad Sci (USA)", keywords = "Isis", pages = "5057- 5062", title = "Evidence for lack of DNA double-strand break repair in human cells exposed to very low X-ray doses", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12679524{\&}dopt=Abstract", volume = "100", year = "2003", } @article{Klammer2010, author = "Holger Klammer and Munira Kadhim and George Iliakis", abstract = "Adaptive response (AR) is a term describing resistance to ionizing radiation-induced killing or formation of aberrant chromosomes that is mediated by pre-exposure to low ionizing radiation doses. The mechanism of AR remains elusive. Because cell killing and chromosome aberration formation derive from erroneous processing of DNA double-strand breaks (DSB), AR may reflect a modulation of DSB processing by nonhomologous end joining (NHEJ) or homologous recombination repair. Here, we use plasmid end-joining assays to quantify modulations induced by low ionizing radiation doses to NHEJ, the dominant pathway of DSB repair in higher eukaryotes, and investigate propagation of this response through medium transfer to nonirradiated bystander cells. Mouse embryo fibroblasts were conditioned with 10 to 1000 mGy and NHEJ quantified at different times thereafter by challenging with reporter plasmids containing a DSB. We show robust increases in NHEJ efficiency in mouse embryo fibroblasts exposed to ionizing radiation >100 mGy, irrespective of reporter plasmid used. Human tumor cells also show AR of similar magnitude that is compromised by caffeine, an inhibitor of DNA damage signaling acting by inhibiting ATM, ATR, and DNA-PKcs. Growth medium from pre-irradiated cells induces a caffeine-sensitive AR in nonirradiated cells, similar in magnitude to that seen in irradiated cells. In bystander cells, {\~a}H2AX foci are specifically detected in late S-G(2) phase and are associated with Rad51 foci that signify the function of homologous recombination repair, possibly on DNA replication-mediated DSBs. The results point to enhanced NHEJ as a mechanism of AR and suggest that AR may be transmitted to bystander cells through factors generating replication-mediated DSBs. Cancer Res; 70(21); 8498-506. ©2010 AACR.", journal = "Cancer Res", keywords = "Metafer MetaCyte H2AX foci", month = "Oct", title = "Evidence of an Adaptive Response Targeting DNA Nonhomologous End Joining and Its Transmission to Bystander Cells.", url = "http://dx.doi.org/10.1158/0008-5472.CAN-10-1181", year = "2010", } @article{Morse2009, author = "Alison M Morse and Daniel G Peterson and M. Nurul Islam-Faridi and Katherine E Smith and Zenaida Magbanua and Saul A Garcia and Thomas L Kubisiak and Henry V Amerson and John E Carlson and C. Dana Nelson and John M Davis", abstract = "Genome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, however the elements involved are poorly understood.Gymny is a previously undescribed retrotransposon family in Pinus that is related to Athila elements in Arabidopsis. Gymny elements are dispersed throughout the modern Pinus genome and occupy a physical space at least the size of the Arabidopsis thaliana genome. In contrast to previously described retroelements in Pinus, the Gymny family was amplified or introduced after the divergence of pine and spruce (Picea). If retrotransposon expansions are responsible for genome size differences within the Pinaceae, as they are in angiosperms, then they have yet to be identified. In contrast, molecular divergence of Gymny retrotransposons together with other families of retrotransposons can account for the large genome complexity of pines along with protein-coding genic DNA, as revealed by massively parallel DNA sequence analysis of Cot fractionated genomic DNA.Most of the enormous genome complexity of pines can be explained by divergence of retrotransposons, however the elements responsible for genome size variation are yet to be identified. Genomic resources for Pinus including those reported here should assist in further defining whether and how the roles of retrotransposons differ in the evolution of angiosperm and gymnosperm genomes.", journal = "PLoS One", keywords = "Pine, Pinus, Plant, Genetics, Metafer MSearch", number = "2", pages = "e4332", title = "Evolution of genome size and complexity in Pinus.", url = "http://dx.doi.org/10.1371/journal.pone.0004332", volume = "4", year = "2009", } @article{00069, author = "A.-K. Fridolfsson and H. Cheng and N.G. Copeland and N.A. Jenkins and H.-C. Liu and T. Raudsepp and T. Woodage and B. Chowdhary and J. Halverson and H. Ellegren", journal = "PNAS", keywords = "Isis", pages = "8147- 8152", title = "Evolution of the avia sex chromosomes from an anchestral pair of autosomes", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=9653155{\&}query_hl=7{\&}itool=pubmed_docsum", volume = "95", year = "1998", } @article{Nagy2011, author = "Zs{\'o}fia Nagy and B{\'e}la Kajt{\'a}r and P{\'a}l J{\'a}ks{\'o} and Mariann D{\'a}vid and Szabolcs Kosztol{\'a}nyi and Judit Hermesz and L{\'a}szl{\'o} Kereskai and L{\'a}szl{\'o} Pajor and Don{\'a}t Alp{\'a}r", abstract = "Bone marrow specimens from 185 patients with plasma cell disorders (PCD) were investigated by fluorescence in situ hybridization (FISH) in order to determine the temporal sequence of cytogenetic aberrations. In 25 cases combined FISH analysis has also been performed at single cell level. Clonal evolution was observed in 16\% of cases. The ?13 was preceded by t(4;14)(p16;q32) and t(14;16)(q32;q23) translocations. Deletion of p53 gene was a secondary aberration compared to ?13 and t(11;14)(q13;q32) translocation. In 22\% of all cases with recurrent IGH translocation, this aberration was presented only in a subset of purified plasma cells questioning its initiating role.", journal = "Leuk Res", keywords = "Metafer MetaCyte Isis", month = "Aug", number = "8", pages = "1114--1116", title = "Evolutionary sequence of cytogenetic aberrations during the oncogenesis of plasma cell disorders. Direct evidence at single cell level.", url = "http://dx.doi.org/10.1016/j.leukres.2011.02.010", volume = "35", year = "2011", } @article{00166, author = "Y.X. Yu and A. Heller and T. Liehr and C.C. Smith and L. Aurelian", journal = "International Journal of Oncology", keywords = "Isis mFISH", pages = "905- 911", title = "Expression analysis and chromosome location of a novel gene (H11) associated with the growth of human melanoma cells", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11295034{\&}dopt=Abstract", volume = "18", year = "2001", } @article{00114, author = "K. H{\"u}hne and O. Park and T. Liehr and B. Rautenstrauss", journal = "J. Neuroscience Res.", pages = "624- 631", title = "Expression Analysis of the PMP22 Gene in Glioma and Osteogenic Sarcoma Cell Lines", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10561690{\&}dopt=Abstract", volume = "58", year = "1999", } @article{00099, author = "B. Rautenstrauss and U. Zechner and H. Hameister and H. Grehl and T. Liehr", journal = "Journal of the Peripheral Nervous System", pages = "117- 124", title = "Expression Pattern of the Peripherial Myelin Protein 22kDa (PMP22) in Neural and Non-neural Tissue Types of Adult Wildtype and Trembler Mice - a Comparative Study", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10959245{\&}dopt=Abstract", volume = "3", year = "1998", } @article{00202, author = "F. Al-Mulla and M. Al-Maghrebi and G. Varadharaj", journal = "J Clin Pathol: Mol Pathol", keywords = "Isis CGH", pages = "210- 217", title = "Expressive genomic hybridisation: gene expression profiling at the cytogenetic level.", volume = "56", year = "2003", } @article{Mattedi2007, author = "RL Mattedi and C Bernardi Fdel and CE Bacchi and SA Siqueira and T Mauad", abstract = "Primary pulmonary lymphoma is rare. The most common histological type is the bronchus-associated lymphoid tissue lymphoma. This type of lymphoma has an indolent course and excellent response to therapy. One-third of all cases are diagnosed incidentally. However, due to the rarity of this disease, little is known about its natural history in terms of dissemination and evolution. Herein, we report the unusual case of a 61-year-old man who refused treatment after being diagnosed with bronchus-associated lymphoid tissue lymphoma and died 2 years later from massive lung infiltration without dissemination to other organs.", journal = "J Bras Pneumol", keywords = "Isis", number = "4", pages = "487-91", title = "Fatal outcome in bronchus-associated lymphoid tissue lymphoma", url = "http://www.ncbi.nlm.nih.gov/pubmed/17982544?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum{\&}ordinalpos=2", volume = "33", year = "2007", } @article{00281, author = "B. Christensen and J. Philip and S. K{\o}lvraa and L. Lykke-Hansen and I. Hromadnikova and D. Gohel and T. L{\"o}rch and A. Plesch and J. Bang and S. Smidt-Jensen and J. Hertz and H. Djursing", journal = "Fetal Diagnosis and Therapy", keywords = "Metafer RCDetect", pages = "106- 112", title = "Fetal cells in maternal blood: a comparison of methods for cell isolation and identification.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=15692203{\&}query_hl=1{\&}itool=pubmed_docsum", volume = "20", year = "2005", } @article{00139, author = "C.M. Hattinger and S. Rumpler and H. Kovar and P.F. Ambros", journal = "Cytogenet Cell Genet", keywords = "Isis", pages = "29- 35", title = "Fine-mapping of cytogenetically undetectable EWS/ERG fusions on DNA fibers of Ewing tumors.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=11474174{\&}query_hl=12{\&}itool=pubmed_docsum", volume = "93", year = "2001", } @article{00185, author = "T. Liehr and M. Schmidt and H. Starke and M. Ziegler and G. Kittner and A. Heller and N. Rubtsov and V. Trifonov and U. Claussen", journal = "Fetal Diagn Ther", keywords = "Isis mBAND", pages = "133- 136", title = "First case of trisomy 13 plus mosaic trisomy 1q", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11914563{\&}dopt=Abstract", volume = "17", year = "2002", } @article{00217, author = "H. Starke and B. Mitulla and A. Nietzel and A. Heller and V. Beensen and G. Grosswendt and U. Claussen and von Eggeling, F. and T. Liehr", journal = "American Journal of Medical Genetics", keywords = "Isis mFISH mBAND", pages = "26- 30", title = "First Patient with trisomy 21 accompanied by an aditional der(4)(:p11->q11:) plus partial uniparental disomy 4p15-16", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12476447{\&}dopt=Abstract", volume = "116", year = "2003", } @article{Moore2011, author = "Mathew W. Moore and Robert Gasparini", abstract = "The accuracy of melanoma diagnosis continues to challenge the pathology community, even today with sophisticated histopathologic techniques. Melanocytic lesions exhibit significant morphological heterogeneity. While the majority of biopsies can be classified as benign (nevus) or malignant (melanoma) using well-established histopathologic criteria, there exists a cohort for which the prediction of clinical behaviour and invasive or metastatic potential is difficult if not impossible to ascertain on the basis of morphological features alone. Multiple studies have shown that there is significant disagreement between pathologists and even expert dermatopathologists in the diagnosis of this subgroup of difficult melanocytic lesions.A four probe FISH assay was utilized to analyse a cohort of 500 samples including 157 nevus, 176 dysplastic nevus and 167 melanoma specimens.Review of the lesions determined the assay identified genetic abnormalities in a total of 83.8\% of melanomas, and 1.9\% of nevus without atypia, while genetic abnormalities were identified in 6.3\%, 6.7\%, and 10.3\% of nevus identified with mild, moderate and severe atypia, respectively.Based on this study, inheritable genetic damage/instability identified by FISH testing is a hallmark of a progressive malignant process, and a valuable diagnostic tool for the identification of high risk lesions.", journal = "Diagn Pathol", keywords = "Metafer MetaCyte", pages = "76", title = "FISH as an effective diagnostic tool for the management of challenging melanocytic lesions.", volume = "6", year = "2011", } @article{00071, author = "M. Lessard and A. Herry and C. Bertou and M C. L{\'e}glise and J.-F. Abgrall and P. Morice and G. Flandrin", journal = "Leukemia Res", keywords = "Isis", pages = "303- 312", title = "FISH investigation of 5q and 7p deletions in MSD/AML reveals hidden in translocations, insertions and fragmentions of the same chromosome", volume = "22", year = "1998", } @article{00109, author = "O. Bartsch and A. Wagner and G.K. Hinkel and P. Krebs and M. Stumm and B. Schmalenberger and S. Bohm and S. Balci and F. Majewski", journal = "European Journal of Human Genetics", pages = "748- 756", title = "FISH studies in 45 patients with Rubenstein-Taybi sysndrome: deletions associated with polysplenia, hypoplastic left heart and death in infancy", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10573006{\&}dopt=Abstract", volume = "7", year = "1999", } @article{00288, author = "D. Scheie and P. A. Andresen and M. Cvancarova and A. S. B{\o} and E. helseth and K. Skullerud and K. Beiske", journal = "Am J Surg Pathol", keywords = "Isis", pages = "828- 837", title = "Fluorescence in situ hybridization (FISH) on touch preparations: a reliable method for detecting loss of heterozygosity at 1p and 19q in oligodendroglial tumors.", url = "http://www.ncbi.nlm.nih.gov/pubmed/16819324?ordinalpos=14{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDo", volume = "30", year = "2006", } @article{00232, author = "E.B. Baart and D. Van Opstal and F.J. Los and B.C.J.M. Fauser and E.Martini", journal = "Hum Reprod", keywords = "Isis", pages = "685- 693", title = "Fluorescence in situ hybridization analysis of two blastomeres from day 3 frozen-thawed embryos followed by analysis of the remaining embryo on day 5.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=14998971{\&}query_hl=1{\&}itool=pubmed_docsum", volume = "19", year = "2004", } @article{00279, author = "J. Terry and T.S. Barry and D.E. Horsman and F.D. Hsu and A.M. Gown and D.G. Huntsman and T.O. Nielsen", journal = "Diagn Mol Pathol", keywords = "Metafer MetaCyte", pages = "77- 82", title = "Fluorescence in situ hybridization for the detection of t(X;18)(p11.2;q11.2) in a Synovial Sarcoma tissuemicroarray using a breakapart-style probe.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=15905690{\&}query_hl=37{\&}itool=pubmed_DocSum", volume = "14", year = "2005", } @article{00228, author = "P. Madon and A. Athalye and V. Bandkar and S. Dhumal and A. Sopariwala and F. Parikh", journal = "Int. J. Hum. Genet.", keywords = "Ikaros Isis", pages = "115- 119", title = "Fluorescence-in-situ-hybridization (FISH) - a rapid and useful technique for diagnosis and management in leukemia.", url = "https://docs.google.com/viewer?a=v{\&}q=cache:GvQLTfjKue8J:www.krepublishers.com/02-Journals/IJHG/IJHG-03-0-000-000-2003-Web/IJHG-03-2-069-134-2003-Abst-PDF/IJHG-03-2-115-119-2003-Madon/IJHG-03-2-115-119-2003-Madon.pdf+Fluorescence-in-situ-hybridization+(FIS", volume = "3", year = "2003", } @article{00076, author = "R. Karhu and J. Rummukainen and T. L{\"o}rch and J. Isola", journal = "Genes Chromsomes Cancer", keywords = "Isis CGH", pages = "112- 118", title = "Four-Color CGH: A New Method for Quality Control of Comparative Genomic Hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9885977{\&}dopt=Abstract", volume = "24", year = "1998", } @article{Rossnerova2010, author = "A. Rossnerova and I. Balascak and P. Rossner and R. J. Sram", abstract = "The capital city of Prague is one of the most polluted areas of the Czech Republic. The impact of air pollution on the level of chromosomal aberrations was systematically studied: analyses were performed using fluorescence in situ hybridization (FISH) with whole-chromosome painting for chromosomes #1 and #4. In the present study, we analyzed the levels of stable (one-way and two-way translocations) and unstable (acentric fragments) chromosomal aberrations in 42 mothers living in Prague and in their newborns. The average age of the mothers was 29 years (range, 20-40 years). Blood samples were collected from October 2007 to February 2008. The average levels of carcinogenic polycyclic aromatic hydrocarbons (c-PAHs) and benzo[a]pyrene (B[a]P) in respirable particles (PM2.5), as determined by stationary monitoring, were 21.0+/-12.3ng/m(3) and 2.9+/-1.8ng/m(3), respectively. We did not observe any effect of either c-PAH or B[a]P exposure on the genomic frequency of translocations (per 100 cells, F(G)/100) in either group due to their similar exposure during the winter months. The mean values of F(G)/100 representing stable aberrations were 0.09+/-0.13 vs 0.80+/-0.79 (p", journal = "Mutat Res", keywords = "Metafer MSearch", month = "Jun", number = "1-2", pages = "29--34", title = "Frequency of chromosomal aberrations in Prague mothers and their newborns.", url = "http://dx.doi.org/10.1016/j.mrgentox.2010.04.015", volume = "699", year = "2010", } @article{00034, author = "Y. Zhang and K. Weber-Matthiesen and R. Siebert and P. Matthiesen and B. Schlegelberger", journal = "Genes, Chromosomes {\&} Cancer", keywords = "Isis", pages = "310- 313", title = "Frequent Deletions of 6q23-24 in B-Cell Non-Hodgkin's Lymphomas Detected by Fluorescence In Situ Hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9087572{\&}dopt=Abstract", volume = "18", year = "1997", } @article{00236, author = "J. Tchinda and S. Volpert and M. Kropff and W.E. Berdel and J. Kienast and F. Meinhardt and J. Horst", journal = "Am J Clin Pathol", keywords = "Isis CGH", pages = "875- 882", title = "Frequent gains of the short arm of chromosome 9 in Multiple Myeloma with normal G-banded karyotype detected by comparative genomic hybridization.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15539380", volume = "122", year = "2004", } @article{00094, author = "T. Liehr and J. Ries and E. Wolff and W. Fiedler and R. Dahse and et al, G. Ernst", journal = "Int. J. Mol. Med.", pages = "173- 179", title = "Gain of DNA copy number on chromosome 3q26-qter and 5p14-pter is a frequent finding in head and neck squamous cell carcinomas", volume = "2", year = "1998", } @article{00020, author = "J. Szymanska and M. Tarkkanen and T. Wiklund and M. Virolainen and C. Blomqvist and S. Asko Seljavaara and E. Tukiainen and I. Elomaa and S. Knuutila", journal = "Genes Chromosom Cancer", keywords = "Isis CGH", pages = "89- 94", title = "Gains and losses of DNA sequences in liposarcomas evaluated by comparative genomic hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8834171{\&}dopt=Abstract", volume = "15", year = "1996", } @article{00022, author = "P. Kivipensas and A.-M. Bj{\"o}rkqvist and R. Karhu and K. Pelin and K. Linnainmaa and L. Tammilehto and K. Mattson and O.-P. Kallioniemi and S. Knuutila", journal = "Cancer Genet Cytogenet", pages = "7- 13", title = "Gains and losses of DNA sequences in malignant mesothelioma by comparative genomic hybridisation", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8689616{\&}dopt=Abstract", volume = "89", year = "1996", } @article{00005, author = "M. Tarkkanen and R. Karhu and A. Kallioniemi and I. Elomaa and A.H. Kivioja and J. Nevalainen and T. B{\"o}hling and E. Karaharju and E. Hyytinen and S. Knuutila and O.P. Kallioniemi", journal = "Cancer Research", keywords = "Isis CGH", pages = "1334- 1338", title = "Gains and losses of DNA sequences in osteosarcomas by comparative genomic hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=7882332{\&}dopt=Abstract", volume = "55", year = "1995", } @article{00039, author = "M.L. Larramendy and M. Tarkkanen and J. Valle and A.H. Kivioja and H. Ervasti and E. Karaharju and T. Salmivalli and I. Elomaa and S. Knuutila", journal = "Am J Pathol", keywords = "Isis CGH", pages = "685- 691", title = "Gains, losses and amplifications of DNA sequences evaluated by comparative genomic hybridization in chondrosarcomas", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9033281{\&}dopt=Abstract", volume = "150", year = "1997", } @article{00321, author = "K.C. Rayeroux and L.J. Campbell", journal = "Cancer Genet. Cytogenet.", keywords = "Isis mBAND", pages = "44- 53", title = "Gene amplification in myeloid leukemias elucidated by fluorescence in situ hybridization.", url = "http://www.ncbi.nlm.nih.gov/pubmed/19602463?ordinalpos=2{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDoc", volume = "193", year = "2009", } @article{00125, author = "P. Starostik and A. Greiner and A. Schultz and A. Zettl and K. Peters and A. Rosenwald and M. Kolve and H.K. M{\"u}ller-Hermelin", journal = "Blood", keywords = "Isis CGH", pages = "1180- 1187", title = "Genetic aberrations common in gastric high-grade large B-cell lymphoma.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=10666188{\&}query_hl=14", volume = "15", year = "2000", } @article{00104, author = "K. Ohshima and M. Ishiguro and A. Ohgami and M. Sugihara and S. Haraoka and J. Suzumiya and M. Kikuchi", journal = "Int J Cancer", keywords = "Isis CGH", pages = "250- 255", title = "Genetic Analysis of Sorted Hodgkin and Reed-Sternberg Cells using Comparative Genomic Hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10389760{\&}dopt=Abstract", volume = "82", year = "1999", } @article{00080, author = "J. Vandesompele and N. Van Roy and et al, M. Van Gele", journal = "Genes, Chromsomes {\&} Cancer", keywords = "Isis CGH", pages = "141- 152", title = "Genetic Heterogeneity of Neuroblastoma Studied by Comparative Genomic Hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9739017{\&}dopt=Abstract", volume = "23", year = "1998", } @article{00158, author = "G. Alves and A. Heller and W. Fiedler and M. Mendes Campos and U. Claussen and A.A. Ornellas and T. Liehr", journal = "Genes Chromosomes Cancer", pages = "48- 53", title = "Genetic imbalances in 26 cases of penile squamous cell carcinoma", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11284035{\&}dopt=Abstract", volume = "31", year = "2001", } @article{00289, author = "F. Al-Mulla and A.I. Behbehani and M.S. Bitar and G. Varadharaj and J.J. Going", journal = "Modern Pathology", keywords = "Isis CGH", pages = "648- 658", title = "Genetic profiling of stage I and II colorectal cancer may predict metastatic relapse.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=16528379{\&}query_hl=3{\&}itool=pubmed_docsum", volume = "19", year = "2006", } @article{00238, author = "B. Orsetti and M. Nugoli and N. Cervera and L. Lasorsa and P. Chuchana and L. Ursule and C. Nguyen and R. Redon and du Manoir, S. and C. Rodriguez and C. Theillet", journal = "Cancer research", keywords = "Isis CGH", pages = "6453- 6460", title = "Genomic and expression profiling of chromosome 17 in breast cancer reveals complex patterns of alterations and novel candidate genes", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15374954{\&}query_hl=9{\&}itool=pubmed_docsum", volume = "64", year = "2004", } @article{00237, author = "H. Kohlhammer and C. Schwaenen and S. Wessendorf and K. Holzmann and H.A. Kestler and D. Kienle and T.F.E. Barth and P. M{\"o}ller and G. Ott and J. Kalla and B. Radlwimmer and A. Pscherer and S. Stilgenbauer and H. D{\"o}hner and P. Lichter and M. Bentz", journal = "Blood", keywords = "Isis CGH", pages = "795- 801", title = "Genomic DNA-chip hybridization in t(11;14)-positive mantle cell lymphomas shows a high frequency of aberrations and allows a refined characterization of consensus regions.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15090459{\&}query_hl=16", volume = "104", year = "2004", } @article{00117, author = "H. Schmid and P. W{\"u}rl and H. Taubert and A. Meye and M. Bache and H.-J. Holzhausen and R. Hinze", journal = "Genes, Chromosomes {\&} Cancer", pages = "205- 211", title = "Genomic Imbalances of 7p and 17q in Malignant Peripheral Nerve Sheath Tumors Are Clinically Relevant", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10379866{\&}dopt=Abstract", volume = "25", year = "1999", } @article{00059, author = "A. Selvakumar and U. Steffens and N. Palanisamy and R.S.K. Chaganti and B. Dupont", journal = "Tissue Antigens", pages = "564- 573", title = "Genomic organization and allelic polymorphism of the human killer cell inhibitory receptor gene KIR103", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9234477{\&}dopt=Abstract", volume = "49", year = "1997", } @article{00265, author = "T.M. Karpinski and M. Kostrzewska-P. and I. Stachecki and A. Mikstacki and K. Szyfter", journal = "J Appl Genet", keywords = "Isis", pages = "319- 325", title = "Genotoxicity of the volatile anaesthetic desflurane in human lymphocytes in vitro, established by comet assay.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=16110191{\&}query_hl=16{\&}itool=pubmed_docsum", volume = "46", year = "2005", } @article{Surowy2011, author = "Harald Surowy and Antje Rinckleb and Manuel Luedeke and Madeleine Stuber and Anna Wecker and Dominic Varga and Christiane Maier and Josef Hoegel and Walther Vogel", abstract = "The scoring of micronuclei (MN) is widely used in biomonitoring and mutagenicity testing as a surrogate marker of chromosomal damage inflicted by clastogenic agents or by aneugens. Individual differences in the response to a mutagenic challenge are known from studies on cancer patients and carriers of mutations in DNA repair genes. However, it has not been studied to which extent genetic factors contribute to the observed variability of individual MN frequencies. Our aim was to quantify this heritable genetic component of both baseline and radiation-induced MN frequencies. We performed a twin study comprising 39 monozygotic (MZ) and 10 dizygotic (DZ) twin pairs. Due to the small number of DZ pairs, we had to recruit controls from which 38 age- and gender-matched random control pairs (CPs) were generated. For heritability estimates, we used biometrical modelling of additive genetic, common environmental, and unique environmental components (ACE model) of variance and direct comparison of variance between the sample groups. While heritability estimates from MZ to DZ comparisons produced inconclusive results, both estimation methods revealed a high degree of heritability (h(2)) for baseline MN frequency (h(2) = 0.68 and h(2) = 0.72) as well as for the induced frequency (h(2) = 0.68 and h(2) = 0.57) when MZ were compared to CP. The result was supported by the different intraclass correlation coefficients of MZ, DZ and CP for baseline (r = 0.63, r = 0.31 and r = 0.0, respectively) as well as for induced MN frequencies (r = 0.79, r = 0.74 and r = 0.0, respectively). This study clearly demonstrates that MN frequencies are determined by genetic factors to a major part. The strong reflection of the genetic background supports the idea that MN frequencies represent an intermediate phenotype between molecular DNA repair mechanisms and the cancer phenotype and affirms the approaches that are made to utilise them as predictors of, for example, cancer risk.", journal = "Mutagenesis", keywords = "Metafer MNScore Micronuclei", month = "Jan", number = "1", pages = "111--117", title = "Heritability of baseline and induced micronucleus frequencies.", url = "http://dx.doi.org/10.1093/mutage/geq059", volume = "26", year = "2011", } @article{00246, author = "I Wlodarska and M Stul and C De Wolf-Peeters and A Hagemeijer", journal = "Haematologica", keywords = "Isis mFISH", pages = "965- 972", title = "Heterogeneity of BCL6 rearrangements in nodular lymphocyte predominant Hodgkin's lymphoma", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15339680{\&}itool=iconfft{\&}query_hl=12", volume = "89", year = "2004", } @article{Gown2008, author = "AM Gown and LC Goldstein and TS Barry and SJ Kussick and PL Kandalaft and PM Kim and CC Tse", abstract = "The American Society of Clinical Oncologists and College of American Pathologists have recently released new guidelines for laboratory testing of HER2 status in breast cancer, which require high levels (95%) of concordance between immunohistochemistry positive (3+) and fluorescence in situ hybridization-amplified cases, and between immunohistochemistry negative (0/1+) and fluorescence in situ hybridization-nonamplified cases; these required levels of concordance are significantly higher than those found in most published studies. We tested the hypothesis that a modification of the HER2 immunohistochemistry scoring system could significantly improve immunohistochemistry and fluorescence in situ hybridization concordance. A total of 6604 breast cancer specimens were evaluated for HER2 status by both immunohistochemistry and fluorescence in situ hybridization using standard methodologies. Results were compared when the standard immunohistochemistry scoring system was replaced by a normalized scoring system in which the HER2 score was derived by subtracting the score on the non-neoplastic breast epithelium from that on the tumor cells. Among the 6604 tumors, using a non-normalized immunohistochemistry scoring system, 267/872 (30.6%) of the immunohistochemistry 3+ cases proved to be fluorescence in situ hybridization nonamplified, whereas using the normalized scoring system only 30/562 (5.3%) of immunohistochemistry 3+ cases proved to be 'false positive'. The concordance rate between immunohistochemistry 3+ and fluorescence in situ hybridization-amplified cases using the normalized scoring method was 94.7%, whereas the concordance using the non-normalized method was only 69.4%. Extremely high concordance between immunohistochemistry and fluorescence in situ hybridization assessment of HER2 status in breast cancer is achievable, but to attain this high level of concordance, modification of the FDA-approved immunohistochemistry scoring system is required.", journal = "Mod Pathol", keywords = "Metafer MetaCyte Metafer-PV", number = "10", pages = "1271-7", title = "High concordance between immunohistochemistry and fluorescence in situ hybridization testing for HER2 status in breast cancer requires a normalized IHC scoring system", url = "http://dx.doi.org/10.1038/modpathol.2008.83", volume = "21", year = "2008", } @article{Lugthart2008, author = "Sanne Lugthart and van Drunen, Ellen and van Norden, Yvette and van Hoven, Antoinette and Claudia A J Erpelinck and Peter J M Valk and H. Berna Beverloo and Bob L{\"o}wenberg and Ruud Delwel", abstract = "Inappropriate expression of EVI1 (ecotropic virus integration-1), in particular splice form EVI1-1D, through chromosome 3q26 lesions or other mechanisms has been implicated in the development of high-risk acute myeloid leukemia (AML). To validate the clinical relevance of EVI1-1D, as well as of the other EVI1 splice forms and the related MDS1/EVI1 (ME) gene, real-time quantitative polymerase chain reaction was performed in 534 untreated adults with de novo AML. EVI1-1D was highly expressed in 6\% of cases (n = 32), whereas 7.8\% were EVI1(+) (n = 41) when all splice variants were taken into account. High EVI1 predicted a distinctly worse event-free survival (HR = 1.9; P = .002) and disease-free survival (HR = 2.1, P = .006) following multivariate analysis. Importantly, we distinguished a subset of EVI1(+) cases that lacked expression of ME (EVI1(+)ME(-); n = 17) from cases that were ME(+) (EVI1(+)ME(+); n = 24). The atypical EVI1(+)ME(-) expression pattern exhibited cytogenetically detectable chromosomal 3q26 breakpoints in 8 cases. Fluorescence in situ hybridization revealed 7 more EVI1(+)ME(-) cases that carried cryptic 3q26 breakpoints, which were not found in the EVI1(+)ME(+) group. EVI1(+)ME(-) expression predicts an extremely poor prognosis distinguishable from the general EVI1(+) AML patients (overall survival [OS]: P ", journal = "Blood", keywords = "Isis", month = "Apr", number = "8", pages = "4329--4337", title = "High EVI1 levels predict adverse outcome in acute myeloid leukemia: prevalence of EVI1 overexpression and chromosome 3q26 abnormalities underestimated.", url = "http://dx.doi.org/10.1182/blood-2007-10-119230", volume = "111", year = "2008", } @article{Talamo2012, author = "Anna Talamo and Alfio Marazzi and Alicia Rovo and Urs Schanz and Andr{\'e} Tichelli and Yves Chalandon and Martine Jotterand", journal = "Ann Hematol", keywords = "Metafer MetaCyte", month = "May", number = "5", pages = "793--796", title = "High hyperdiploid acute lymphoblastic leukemia in adults shows clonal heterogeneity and chromosomal instability at diagnosis and during the course of the disease.", url = "http://dx.doi.org/10.1007/s00277-011-1317-x", volume = "91", year = "2012", } @article{00106, author = "I. Chudoba and A. Plesch and T. L{\"o}rch and J. Lemke and U. Claussen and G. Senger", journal = "Cytogenetics and Cell Genetics", keywords = "Isis mBAND", pages = "156- 160", title = "High resolution multicolor-banding:a new technique for refined FISH analysis of human chromosomes", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10393418{\&}dopt=Abstract", volume = "84", year = "1999", } @article{00067, author = "C.A. Werner and H. D{\"o}hner and S. Joos and L. H. Tr{\"u}mper and M. Bautz and T.F.E. Barth and G. Ott and P. M{\"o}ller and P. Lichter and M. Bentz", journal = "Am J Pathol", pages = "335- 342", title = "High-level amplifications are common genetic aberrations in B-cell neoplasm", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9250147{\&}dopt=Abstract", volume = "151", year = "1997", } @article{00171, author = "H. Starke and J. Seidel and W. Henn and S. Reichardt and M. Volleth and M. Stumm and C. Behrend and K.R. Sandig and C. Kelbova and G. Senger and B. Albrecht and I. Hansmann and A. Heller and U. Claussen and T. Liehr", journal = "European Journal of Human Genetics", keywords = "Isis mBAND", pages = "790- 800", title = "Homologous sequences at human chromosome 9 bands p12 and q13-21.1 are involved in different patterns of pericentric rearrangements", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12461685{\&}dopt=Abstract", volume = "10", year = "2002", } @article{00213, author = "A. Schaeferhenrich and G. Beyer-Sehlmeyer and G. Festag and A. Kuechler and N. Haag and A. Weise and T. Liehr and U. Claussen and B. Marian and W. Sendt and J. Scheele and B.L. Pool-Zobel", journal = "Mutation Reserach", keywords = "Isis mFISH", pages = "19- 32", title = "Human adenoma cells are highly suspectible to the genotoxic action of 4-hydroxy-2-nonenal", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12714179{\&}dopt=Abstract", volume = "526", year = "2003", } @article{00138, author = "H. Omran and K. H{\"a}ffner and S. Burth and C. Fernandez and B. Fargier and A. Villaquiran and H.-G. Nothwang and S. Schnittger and H. Lehrach and D. Woo and M. Brandis and R. Sudbrak and F. Hildebrandt", journal = "J. Am. Soc. nephrol.", keywords = "Isis", pages = "107- 113", title = "Human adolescent nephronophthisis: gene locus synteny with polycystic kidney disease in pcy mice.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=11134256{\&}query_hl=16{\&}itool=pubmed_docsum", volume = "12", year = "2001", } @article{00112, author = "von Deimling, F. and J.M. Scharf and T. Liehr and M. Rothe and A.-R. Kelter and P. Albers and W.F. Dietrich and L.M. Kunkel and N. Wehnert and B. Wirth", journal = "Human Genetics", pages = "17- 27", title = "Human and mouse RAD17 genes: Identification, localization, genomic structure and histological expression pattern in normal testis and seminoma", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10480350{\&}dopt=Abstract", volume = "105", year = "1999", } @article{Catalina2008, author = "Puri Catalina and Rosa Montes and Gertru Ligero and Laura Sanchez and de la Cueva, Teresa and Clara Bueno and Paola E Leone and Pablo Menendez", abstract = "BACKGROUND: The use of human embryonic stem cells (hESCs) in research is increasing and hESCs hold the promise for many biological, clinical and toxicological studies. Human ESCs are expected to be chromosomally stable since karyotypic changes represent a pitfall for potential future applications. Recently, several studies have analysed the genomic stability of several hESC lines maintained after prolonged in vitro culture but controversial data has been reported. Here, we prompted to compare the chromosomal stability of three hESC lines maintained in the same laboratory using identical culture conditions and passaging methods. RESULTS: Molecular cytogenetic analyses performed in three different hESC lines maintained in parallel in identical culture conditions revealed significant differences among them in regard to their chromosomal integrity. In feeders, the HS181, SHEF-1 and SHEF-3 hESC lines were chromosomally stable up to 185 passages using either mechanical or enzymatic dissection methods. Despite the three hESC lines were maintained under identical conditions, each hESC line behaved differently upon being transferred to a feeder-free culture system. The two younger hESC lines, HS181 (71 passages) and SHEF-3 (51 passages) became chromosomally unstable shortly after being cultured in feeder-free conditions. The HS181 line gained a chromosome 12 by passage 17 and a marker by passage 21, characterized as a gain of chromosome 20 by SKY. Importantly, the mosaicism for trisomy 12 gradually increased up to 89\% by passage 30, suggesting that this karyotypic abnormality provides a selective advantage. Similarly, the SHEF-3 line also acquired a trisomy of chromosome 14 as early as passage 10. However, this karyotypic aberration did not confer selective advantage to the genetically abnormal cells within the bulk culture and the level of mosaicism for the trisomy 14 remained overtime between 15\%-36\%. Strikingly, however, a much older hESC line, SHEF-1, which was maintained for 185 passages in feeders did not undergo any numerical or structural chromosomal change after 30 passages in feeder-free culture and over 215 passages in total. CONCLUSION: These results support the concept that feeder-free conditions may partially contribute to hESC chromosomal changes but also confirm the hypothesis that regardless of the culture conditions, culture duration or splitting methods, some hESC lines are inherently more prone than others to karyotypic instability.", journal = "Mol Cancer", keywords = "Ikaros Isis mFISH CGH ", pages = "76", title = "Human ESCs predisposition to karyotypic instability: Is a matter of culture adaptation or differential vulnerability among hESC lines due to inherent properties?", url = "http://dx.doi.org/10.1186/1476-4598-7-76", volume = "7", year = "2008", } @article{Jazedje2009, author = "Tatiana Jazedje and Paulo M Perin and Carlos E Czeresnia and Mariangela Maluf and Silvio Halpern and Mariane Secco and Daniela F Bueno and Natassia M Vieira and Eder Zucconi and Mayana Zatz", abstract = "BACKGROUND: The possibility of using stem cells for regenerative medicine has opened a new field of investigation. The search for sources to obtain multipotent stem cells from discarded tissues or through non-invasive procedures is of great interest. It has been shown that mesenchymal stem cells (MSCs) obtained from umbilical cords, dental pulp and adipose tissue, which are all biological discards, are able to differentiate into muscle, fat, bone and cartilage cell lineages. The aim of this study was to isolate, expand, characterize and assess the differentiation potential of MSCs from human fallopian tubes (hFTs). METHODS: Lineages of hFTs were expanded, had their karyotype analyzed, were characterized by flow cytometry and underwent in vitro adipogenic, chondrogenic, osteogenic, and myogenic differentiation. RESULTS: Here we show for the first time that hFTs, which are discarded after some gynecological procedures, are a rich additional source of MSCs, which we designated as human tube MSCs (htMSCs). CONCLUSION: Human tube MSCs can be easily isolated, expanded in vitro, present a mesenchymal profile and are able to differentiate into muscle, fat, cartilage and bone in vitro.", journal = "J Transl Med", keywords = "Ikaros", pages = "46", title = "Human fallopian tube: a new source of multipotent adult mesenchymal stem cells discarded in surgical procedures.", url = "http://dx.doi.org/10.1186/1479-5876-7-46", volume = "7", year = "2009", } @article{00256, author = "L.M. Pirzio and M.A. Freulet and Y. Bai and B. Fouladi and J.P. Murnane and L. Sabatier and C. Desmaze", journal = "Cytogenet. Genome Res.", keywords = "Metafer MetaCyte", pages = "87- 94", title = "Human fibroblasts expressing hTERT show remarkable karyotype stability even after exposure to ionizing radiation.", url = "http://www.ncbi.nlm.nih.gov/pubmed/15162019?ordinalpos=5{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", volume = "104", year = "2004", } @article{00295, author = "N. Shiomi and M. Mori and H. Tsuji and T. Imai and H. Inoue and S. Tateishi and M. Yamaizumi and T. Shiomi", journal = "Nucl Acids Res (ePub)", keywords = "Metafer CometScan", pages = "0- 0", title = "Human RAD18 is involved in S phase-specific single-strand break reapir without PCNA monoubiquitination.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=17158148{\&}query_hl=31{\&}itool=pubmed_docsum", volume = "35", year = "2006", } @article{00323, author = "J.L. Wise and R.J. Crout and D.W. McNeil and R.J. Weyant and M.L.Marazita and S.L. Wenger", journal = "PLoS One", keywords = "Isis Telomere", pages = "0- 0", title = "Human telomere length correlates to the size of the associated chromosome arm.", url = "http://www.ncbi.nlm.nih.gov/pubmed/19547752?ordinalpos=1{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDoc", volume = "4", year = "2009", } @article{00300, author = "C.B. Hunt and R.K. Pandita and A. Laszlo and R. Higashikubo and M. Agarwal and T. Kitamura and A. Gupta and N. Rief and N. Horikoshi and R. Baskaran and J.-H. Lee and M. L{\"o}brich and T.T. Paull and J.L. Roti Roti and T.K. Pandita", journal = "Cancer Res", keywords = "Isis", pages = "3010- 3017", title = "Hyperthermia activates a subset of Ataxia-telangiectasia mutated effectors independent of DNA strand breaks and heat shock protein 70 status.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=17409407{\&}query_hl=9{\&}itool=pubmed_docsum", volume = "67", year = "2007", } @article{00179, author = "H. Van Limbergen and B. Poppe and L. Michaux and C. Herens and J. Brown and L. Noens and Z. Berneman and R. De Bock and A. De Paepe and F. Speleman", journal = "Genes, Chromosomes {\&} Cancer", keywords = "Isis mFISH", pages = "60- 72", title = "Identification of cytogenetic subclasses and recurring chromosomal aberrations in AML and MDS with complex karyotypes using M-FISH", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11746988{\&}dopt=Abstract", volume = "33", year = "2002", } @article{Fabarius2011, author = "Alice Fabarius and Armin Leitner and Andreas Hochhaus and Martin C M{\"u}ller and Benjamin Hanfstein and Claudia Haferlach and Gudrun G{\"o}hring and Brigitte Schlegelberger and Martine Jotterand and Andreas Reiter and Susanne Jung-Munkwitz and Ulrike Proetel and Juliana Schwaab and Wolf-Karsten Hofmann and J{\"o}rg Schubert and Hermann Einsele and Anthony D Ho and Christiane Falge and Lothar Kanz and Andreas Neubauer and Michael Kneba and Frank Stegelmann and Michael Pfreundschuh and Cornelius F Waller and Karsten Spiekermann and Gabriela M Baerlocher and Michael Lauseker and Markus Pfirrmann and Joerg Hasford and Susanne Saussele and R{\"u}diger Hehlmann and f{\"u}r Klinische Krebsforschung (SAKK), Schweizerische Arbeitsg and the German CML Study Group,", abstract = "The prognostic relevance of additional cytogenetic findings at diagnosis of chronic myeloid leukemia (CML) is unclear. The impact of additional cytogenetic findings at diagnosis on time to complete cytogenetic (CCR) and major molecular remission (MMR) and progression-free (PFS) and overall survival (OS) was analyzed using data from 1151 Philadelphia chromosome-positive (Ph(+)) CML patients randomized to the German CML Study IV. At diagnosis, 1003 of 1151 patients (87\%) had standard t(9;22)(q34;q11) only, 69 patients (6.0\%) had variant t(v;22), and 79 (6.9\%) additional cytogenetic aberrations (ACAs). Of these, 38 patients (3.3\%) lacked the Y chromosome (-Y) and 41 patients (3.6\%) had ACAs except -Y; 16 of these (1.4\%) were major route (second Philadelphia [Ph] chromosome, trisomy 8, isochromosome 17q, or trisomy 19) and 25 minor route (all other) ACAs. After a median observation time of 5.3 years for patients with t(9;22), t(v;22), -Y, minor- and major-route ACAs, the 5-year PFS was 90\%, 81\%, 88\%, 96\%, and 50\%, and the 5-year OS was 92\%, 87\%, 91\%, 96\%, and 53\%, respectively. In patients with major-route ACAs, the times to CCR and MMR were longer and PFS and OS were shorter (P ", journal = "Blood", keywords = "XCyte mBAND Isis", month = "Dec", number = "26", pages = "6760--6768", title = "Impact of additional cytogenetic aberrations at diagnosis on prognosis of CML: long-term observation of 1151 patients from the randomized CML Study IV.", url = "http://bloodjournal.hematologylibrary.org/content/118/26/6760.full", volume = "118", year = "2011", } @article{00146, author = "J. Lemke and I. Chudoba and G. Senger and M. Stumm and I.F. Loncarevic and C. Henry and B. Zabel and U. Claussen", journal = "Hum Genet", keywords = "Isis mBAND", pages = "478- 483", title = "Improved definition of chromosomal breakpoints using high-resolution multicolour banding", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11499672{\&}dopt=Abstract", volume = "108", year = "2001", } @article{Lassmann2010, author = "Michael Lassmann and Heribert H{\"a}nscheid and Daniela Gassen and Johannes Biko and Viktor Meineke and Christoph Reiners and Harry Scherthan", abstract = "DNA double-strand breaks (DSBs) are critical cellular lesions that can result from ionizing radiation exposure. A marker for DSB formation is the phosphorylated form of the histone H2 variant H2AX (gamma-H2AX). DSBs also attract the damage sensor p53-binding protein 1 (53BP1) to the DSB-containing chromatin, because 53BP1 associates with the DSB-surrounding chromatin. We studied the induction, persistence, and disappearance of radiation-induced gamma-H2AX and 53BP1 foci after the first (131)I therapy of patients with differentiated thyroid carcinoma, a model for protracted, continuous, internal whole-body irradiation. METHODS: Twenty-six patients (7 men, 19 women; mean age +/- SD, 42 +/- 13 y) underwent posttherapeutic blood dosimetry according to the standard operating procedure of the European Association of Nuclear Medicine, including peripheral blood sampling and external dose rate measurements at 2-144 h after administration of (131)I for thyroid remnant ablation. The mean time curves of dose accumulation and dose rate to the blood were compared with the mean gamma-H2AX and 53BP1 foci counts over the same period in samples of mononuclear peripheral blood leukocytes. RESULTS: The mean absorbed dose to the blood in 24 patients evaluable for physical dosimetry was 0.31 +/- 0.10 Gy (minimum, 0.17 Gy; maximum, 0.57 Gy). After 24 h, the mean daily dose increment was less than 0.05 Gy. The excess focus counts per nucleus--that is, nuclear foci in excess of the low background count--peaked at 2 h after radioiodine administration (median excess foci for gamma-H2AX [n = 21 patients], 0.227, and for 53BP1 [n = 19 patients], 0.235) and progressively declined thereafter. Significantly elevated numbers of excess focus counts per nucleus (median excess foci for gamma-H2AX [n = 8 patients], 0.054, and for 53BP1 [n = 6 patients], 0.046) still were present at 120-144 h after therapy. Because the rate of occurrence of radiation-induced focus counts per nucleus per absorbed dose varied considerably among patients, a dose-response relationship could not be established for this series as a whole. The number of excess radiation-induced focus counts per nucleus per absorbed dose rate increased with time, potentially indicating a slower rate of DNA repair or, alternatively, a higher de novo rate of focus formation. The values over time of both radiation-induced DSB markers correlated closely (r(2) = 0.973). CONCLUSION: Radiation-induced gamma-H2AX and 53BP1 nuclear foci are useful markers for detecting radiation exposure after radionuclide incorporation, even for absorbed doses to the blood below 20 mGy.", journal = "J Nucl Med", keywords = "Isis", month = "Aug", number = "8", pages = "1318--1325", title = "In vivo formation of gamma-H2AX and 53BP1 DNA repair foci in blood cells after radioiodine therapy of differentiated thyroid cancer.", url = "http://dx.doi.org/10.2967/jnumed.109.071357", volume = "51", year = "2010", } @article{Toth2000, author = "T. T{\'o}th and R. T{\'o}th-Jakatics and S. Jimi and S. Takebayashi", abstract = "Renal interstitial fibrosis is the final common pathway leading to end-stage renal disease in various nephropathies including renal amyloidosis. However, the role of mast cells (MCs) in the fibrotic process of renal amyloidosis is not fully understood. We compared the distribution of MCs in renal biopsies from 30 patients with AA type renal amyloidosis and 20 control cases. Immunoreactivity of renal MCs to anti-tryptase and anti-chymase was studied. Interstitial myofibroblasts were stained with anti-alpha-smooth muscle actin (alpha-SMA) antibody, and inflammatory cells were identified by anti-CD45, -CD20, and -CD68 mAbs. Positively stained cells were counted, and the relative interstitial and fractional areas of anti-alpha-SMA stained cells were measured. Anti-CD29 mAb was used to detect beta1 integrin and anti-basic fibroblast growth factor (bFGF) mAb for the growth factor on MCs. MCs were rarely found in control samples. In contrast, samples showing amyloid deposition contained numerous tryptase-positive (MCT) (940.17 +/- 5.4 versus 6.74 +/- 1.1/mm2) but fewer chymase-positive (MCTC) cells (20.7 +/- 2.86 versus 1.7 +/- 0.76/mm2) in the renal interstitium. There was a significant relationship between interstitial MCT and creatinine clearance (r = -0.72), and between interstitial MCT and glomerular amyloid-index (GAI) (r = 0.723) and interstitial amyloid area (r = 0.824). Accumulation of MCs correlated significantly with the number of T lymphocytes (MCT: r = 0.694). There was also a significant relationship between mast cell (MC) number and the fractional area of alpha-SMA positive interstitium (r = 0.733) and interstitial fibrotic area (r = 0.6). Double immunostaining demonstrated intracytoplasmic presence of beta1 integrin on 87\% of MCT and correlated significantly with the interstitial amyloid area (r = 0.818, P = .001) and T-cell number (r = 0.639, P = .002). bFGF was also detected on 85.5\% of MCTC correlating well with the interstitial alpha-SMA-area (r = 0.789). Our results indicate that MCs constitute an integral part of the overall inflammatory process and play a crucial role in interstitial fibrosis in renal amyloidosis.", journal = "Mod Pathol", keywords = "Isis", month = "Sep", number = "9", pages = "1020--1028", title = "Increased density of interstitial mast cells in amyloid A renal amyloidosis.", url = "http://dx.doi.org/10.1038/modpathol.3880184", volume = "13", year = "2000", } @article{Pajor2008, author = "Gabor Pajor and Norbert Sule and Donat Alpar and Bela Kajtar and Maria Kneif and Daniel Bollmann and Laszlo Somogyi and Laszlo Pajor", abstract = "There is a steady search for procedure which could replace or at least reduce the frequency of the invasive cystoscopy in the surveillance of heterogeneous superficial transitional cell carcinoma (TCC) of the bladder. Recently, UroVysion FISH assay has been shown to provide with better sensitivity than the urine cytology except for the lowest stage pTa and grade I-II TCCs. Data indicate that this failure of the sensitive FISH might be due to mistargeting. Therefore, our aim was to elaborate a procedure enabling FISH analysis in phenotypically preselected urothelial cells, only. Cytokeratin 7 (CK-7) chromogenic immunolabeling was applied to various mixtures of negative and positive control cells as well as voided urine specimens. Cellular targets and CK-7 positive cells were identified by morphometric and pixel intensity indices using an automated microscope workstation. UroVysion FISH pattern was analyzed only in the subsequently relocalized CK-7 positive events. Automated phenotypical preselection of urothelial cells proved to have 97.3\% sensitivity, 96.1\% specificity, and 99.0\% accuracy, whereas combined pheno- and genotyping revealed 93.3\% sensitivity and 99.8\% specificity, respectively. In clinical samples, the overall 20.4\% FISH positivity gained by traditional target identification contrasted with the 55.6\% positivity obtained by the combined method, by which the efficiency of identifying chromosomally aberrant cells proved to be two to threefold higher even in grade I lesions. FISH analysis of phenotypically preselected urothelial cells might represent a reliable asset in surveillance of low stage-low grade TCCs.", journal = "Cytometry A", keywords = "Metafer, MetaCyte, UroVysion", month = "Mar", number = "3", pages = "259--265", title = "Increased efficiency of detecting genetically aberrant cells by UroVysion test on voided urine specimens using automated immunophenotypical preselection of uroepithelial cells.", url = "http://dx.doi.org/10.1002/cyto.a.20528", volume = "73", year = "2008", } @article{Mazor2008, author = "Ronit Mazor and Avital Korenstein-Ilan and Alexander Barbul and Yael Eshet and Avi Shahadi and Eli Jerby and Rafi Korenstein", abstract = "Mazor, R., Korenstein-Ilan, A., Barbul, A., Eshet, Y., Shahadi, A., Jerby, E. and Korenstein, R. Increased Levels of Numerical Chromosome Aberrations after In Vitro Exposure of Human Peripheral Blood Lymphocytes to Radiofrequency Electromagnetic Fields for 72 Hours. Radiat. Res. 169, 28-37 (2008). We investigated the effects of 72 h in vitro exposure of 10 human lymphocyte samples to radiofrequency electromagnetic fields (800 MHz, continuous wave) on genomic instability. The lymphyocytes were exposed in a specially designed waveguide resonator at specific absorption rates (SARs) of 2.9 and 4.1 W/kg in a temperature range of 36-37 degrees C. The induced aneuploidy of chromosomes 1, 10, 11 and 17 was determined by interphase FISH using semi-automated image analysis. We observed increased levels of aneuploidy depending on the chromosome studied as well as on the level of exposure. In chromosomes 1 and 10, there was increased aneuploidy at the higher SAR, while for chromosomes 11 and 17, the increases were observed only for the lower SAR. Multisomy (chromosomal gains) appeared to be the primary contributor to the increased aneuploidy. The effect of temperature on the level of aneuploidy was examined over the range of 33.5-40 degrees C for 72 h with no statistically significant difference in the level of aneuploidy compared to 37 degrees C. These findings suggest the possible existence of an athermal effect of RF radiation that causes increased levels of aneuploidy. These results contribute to the assessment of potential health risks after continuous chronic exposure to RF radiation at SARs close to the current levels set by ICNIRP guidelines.", journal = "Radiat Res", keywords = "Metafer MetaCyte", month = "Jan", number = "1", pages = "28--37", title = "Increased levels of numerical chromosome aberrations after in vitro exposure of human peripheral blood lymphocytes to radiofrequency electromagnetic fields for 72 hours.", url = "http://dx.doi.org/10.1667/RR0872.1", volume = "169", year = "2008", } @article{Mani2009, author = "Ram-Shankar Mani and Scott A Tomlins and Kaitlin Callahan and Aparna Ghosh and Mukesh K Nyati and Sooryanarayana Varambally and Nallasivam Palanisamy and Arul M Chinnaiyan", abstract = "Gene fusions play a critical role in cancer progression. The mechanisms underlying their genesis and cell type specificity are not well understood. About 50\% of human prostate cancers display a gene fusion involving the 5' untranslated region of TMPRSS2, an androgen-regulated gene, and the protein-coding sequences of ERG, which encodes an erythroblast transformation-specific (ETS) transcription factor. By studying human prostate cancer cells with fluorescence in situ hybridization, we show that androgen signaling induces proximity of the TMPRSS2 and ERG genomic loci, both located on chromosome 21q22.2. Subsequent exposure of the cells to gamma irradiation, which causes DNA double-strand breaks, facilitates the formation of the TMPRSS2-ERG gene fusion. These results may help explain why TMPRSS2-ERG fusions are restricted to the prostate, which is dependent on androgen signaling.", journal = "Science", keywords = "Metafer MetaCyte Isis", month = "Nov", number = "5957", pages = "1230", title = "Induced chromosomal proximity and gene fusions in prostate cancer.", url = "http://dx.doi.org/10.1126/science.1178124", volume = "326", year = "2009", } @article{m09, author = "Mani, R.S. and Tomlins, S.A. and Callahan, K. and Ghosh, A. and Nyati, M.K. and Varambally, S. and Palanisamy, N. and Chinnaiyan, A.M.", abstract = "Gene fusions play a critical role in cancer progression. The mechanisms underlying their genesis and cell type specificity are not well understood. About 50% of human prostate cancers display a gene fusion involving the 5’untranslated region of TMPRSS2, an androgen-regulated gene, and the protein-coding sequences of ERG, which encodes an ETS transcription factor. Studying human prostate cancer cells by fluorescence in situ hybridization, we show that androgen signaling induces proximity of the TMPRSS2 and ERG genomic loci, both located on chromosome 21q22.2. Subsequent exposure of the cells to gamma-irradiation, which causes DNA double strand breaks, facilitates the formation of the TMPRSS2-ERG gene fusion. These results may help explain why TMPRSS2-ERG fusions are restricted to the prostate, which is dependent on androgen signaling.", journal = "Science Express", keywords = "Metafer Metacyte Isis", month = "10/2009", title = "Induced chromosomal proximity and gene fusions in prostate cancer.", url = "http://www.sciencemag.org/cgi/content/abstract/1178124v1", volume = "29. Oct. 2009", year = "2009", } @article{Grudzenski2010, author = "Saskia Grudzenski and Antonia Raths and Sandro Conrad and Claudia E. R?be and Markus L?brich", abstract = "Ionizing radiation (IR) induces a variety of DNA lesions among which DNA double-strand breaks (DSBs) are the biologically most significant. It is currently unclear if DSB repair is equally efficient after low and high doses. Here, we use gamma-H2AX, phospho-ATM (pATM), and 53BP1 foci analysis to monitor DSB repair. We show, consistent with a previous study, that the kinetics of gamma-H2AX and pATM foci loss in confluent primary human fibroblasts are substantially compromised after doses of 10 mGy and lower. Following 2.5 mGy, cells fail to show any foci loss. Strikingly, cells pretreated with 10 microM H(2)O(2) efficiently remove all gamma-H2AX foci induced by 10 mGy. At the concentration used, H(2)O(2) produces single-strand breaks and base damages via the generation of oxygen radicals but no DSBs. Moreover, 10 microM H(2)O(2) up-regulates a set of genes that is also up-regulated after high (200 mGy) but not after low (10 mGy) radiation doses. This suggests that low radical levels induce a response that is required for the repair of radiation-induced DSBs when the radiation damage is too low to cause the induction itself. To address the in vivo significance of this finding, we established gamma-H2AX and 53BP1 foci analysis in various mouse tissues. Although mice irradiated with 100 mGy or 1 Gy show efficient gamma-H2AX and 53BP1 foci removal during 24 h post-IR, barely any foci loss was observed after 10 mGy. Our data suggest that the cellular response to DSBs is substantially different for low vs. high radiation doses.", journal = "Proc Natl Acad Sci U S A", keywords = "Metafer, MetaCyte, Foci, H2AX", month = "Aug", number = "32", pages = "14205--14210", title = "Inducible response required for repair of low-dose radiation damage in human fibroblasts.", url = "http://dx.doi.org/10.1073/pnas.1002213107", volume = "107", year = "2010", } @article{00233, author = "L. Wilkens and P. Flemming and M. Gebel and J. Bleck and C. Terkamp and L. Wingen and H. Kreipe and B. Schlegelberger", journal = "PNAS", keywords = "Isis", pages = "1309- 1314", title = "Induction of aneuploidy by increasing chromosomal instability during dedifferentiation of hepatocellular carcinoma.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=14745031{\&}query_hl=16{\&}itool=pubmed_docsum", volume = "101", year = "2004", } @article{Urcan2010, author = "Ebru Urcan and Harry Scherthan and Marianthi Styllou and Uschi Haertel and Reinhard Hickel and Franz-Xaver Reichl", abstract = "Dental resin composites and their reactive monomers/co-monomers have been shown to elicit cytotoxic responses in human gingival fibroblasts (HGF), and their metabolic radical intermediates have the potential to attack the DNA backbone, which may induce DNA double-strand breaks (DSBs). In this study we have tested the cytotoxicity and induction of DSBs by the most common composite resin monomers/co-monomers: BisGMA, HEMA, TEGDMA, and UDMA in gingival fibroblasts using the sensitive gamma-H2AX DNA repair focus assay. Our results show increasing monomer cytotoxicities in the order of BisGMA>UDMA>TEGDMA>HEMA, an order that was also observed for their capacity to induce DSBs. BisGMA at the EC50 concentration of 0.09 mm evoked the highest rate of gamma-H2AX foci-formation that was 11-fold higher DNA DSBs as compared to the negative controls that ranged between 0.25 and 0.5gamma-H2AX foci/HGF cell. Our results for the first time show that exposure to dental resin monomers can induce DSBs in primary human oral cavity cells, which underscores their genotoxic capacity.", journal = "Biomaterials", keywords = "Isis H2AX Foci", month = "Mar", number = "8", pages = "2010--2014", title = "Induction of DNA double-strand breaks in primary gingival fibroblasts by exposure to dental resin composites.", url = "http://dx.doi.org/10.1016/j.biomaterials.2009.11.065", volume = "31", year = "2010", } @article{Durante2010, author = "M. Durante and D. Pignalosa and J. A. Jansen and X. F. Walboomers and S. Ritter", abstract = "Interphase chromosomes are divided into discrete domains, with limited overlapping and movement. We explored the role of nuclear topology in the formation of chromosome aberrations by irradiating normal human fibroblasts with high-energy heavy ions from different directions. Cells with elliptical nuclei were grown in an aligned manner onto micrometer grooved culturing substrates to have a predetermined orientation with respect to the accelerated iron ions. Particles were directed either perpendicular to the cell layer or along the major or minor axis of the nucleus. Analysis of chromosome aberrations by mFISH showed that, at the same radiation dose, the yield of chromosomal damage and its complexity are largely modified by the irradiation geometry. The results demonstrate that the architecture of the cell nucleus determines the formation of chromosomal rearrangements.", journal = "Radiat Res", keywords = "Isis; mFISH", month = "Jul", number = "1", pages = "20--26", title = "Influence of nuclear geometry on the formation of genetic rearrangements in human cells.", url = "http://dx.doi.org/10.1667/RR2063.1", volume = "174", year = "2010", } @article{Garcia2012, author = "O. Garc{\'i}a and M. {Di Giorgio} and M. B. Vallerga and A. Radl and M. R. Taja and A. Seoane and J. {De Luca} and M. {Stuck Oliveira} and P. Valdivia and A. I. Lamadrid and J. E. Gonz{\'a}lez and I. Romero and T. Mandina and G. Pantelias and G. Terzoudi and C. Guerrero-Carbajal and C. {Arceo Maldonado} and M. Espinoza and N. Oliveros and W. Mart{\'i}nez-L{\'o}pez and M. V. {Di Tomaso} and L. M{\'e}ndez-Acu{\~n}a and R. Puig and L. Roy and J. F. Barquinero", abstract = "The bottleneck in data acquisition during biological dosimetry based on a dicentric assay is the need to score dicentrics in a large number of lymphocytes. One way to increase the capacity of a given laboratory is to use the ability of skilled operators from other laboratories. This can be done using image analysis systems and distributing images all around the world. Two exercises were conducted to test the efficiency of such an approach involving 10 laboratories. During the first exercise (E1), the participant laboratories analysed the same images derived from cells exposed to 0.5 and 3 Gy; 100 images were sent to all participants for both doses. Whatever the dose, only about half of the cells were complete with well-spread metaphases suitable for analysis. A coefficient of variation (CV) on the standard deviation of ?15 \% was obtained for both doses. The trueness was better for 3 Gy (0.6 \%) than for 0.5 Gy (37.8 \%). The number of estimated doses classified as satisfactory according to the z-score was 3 at 0.5 Gy and 8 at 3 Gy for 10 dose estimations. In the second exercise, an emergency situation was tested, each laboratory was required to score a different set of 50 images in 2 d extracted from 500 downloaded images derived from cells exposed to 0.5 Gy. Then the remaining 450 images had to be scored within a week. Using 50 different images, the CV on the estimated doses (79.2 \%) was not as good as in E1, probably associated to a lower number of cells analysed (50 vs. 100) or from the fact that laboratories analysed a different set of images. The trueness for the dose was better after scoring 500 cells (22.5 \%) than after 50 cells (26.8 \%). For the 10 dose estimations, the number of doses classified as satisfactory according to the z-score was 9, for both 50 and 500 cells. Overall, the results obtained support the feasibility of networking using electronically transmitted images. However, before its implementation some issues should be elucidated, such as the number and resolution of the images to be sent, and the harmonisation of the scoring criteria. Additionally, a global website able to be used for the different regional networks, like Share Points, will be desirable to facilitate worldwide communication.", journal = "Radiat Prot Dosimetry", keywords = "Metafer MSearch AutoCapt", month = "Aug", pages = "epub", title = "INTERLABORATORY COMPARISON OF DICENTRIC CHROMOSOME ASSAY USING ELECTRONICALLY TRANSMITTED IMAGES.", url = "http://dx.doi.org/10.1093/rpd/ncs139", volume = "epub", year = "2012", } @article{Ainsbury2009, author = "E. A. Ainsbury and G. K. Livingston and M. G. Abbott and J. E. Moquet and P. A. Hone and M. S. Jenkins and D. M. Christensen and D. C. Lloyd and K. Rothkamm", abstract = "The international radiation biodosimetry community has recently been engaged in activities focused on establishing cooperative networks for biodosimetric triage for radiation emergency scenarios involving mass casualties. To this end, there have been several recent publications in the literature regarding the potential for shared scoring in such an accident or incident. We present details from a medical irradiation case where two independently validated laboratories found very different yields of dicentric chromosome aberrations. The potential reasons for this disparity are discussed, and the actual reason is identified as being the partial-body nature of the radiation exposure combined with differing criteria for metaphase selection. In the context of the recent networking activity, this report is intended to highlight the fact that shared scoring may produce inconsistencies and that further validation of the scoring protocols and experimental techniques may be required before the networks are prepared to deal satisfactorily with a radiological or nuclear emergency. Also, the findings presented here clearly demonstrate the limitations of the dicentric assay for estimating radiation doses after partial-body exposures and bring into question the usefulness of rapid "triage mode" scoring in such exposure scenarios.", journal = "Radiat Res", keywords = "Metafer MSearch", month = "Dec", number = "6", pages = "746--752", title = "Interlaboratory variation in scoring dicentric chromosomes in a case of partial-body x-ray exposure: implications for biodosimetry networking and cytogenetic "triage mode" scoring.", url = "http://www.ncbi.nlm.nih.gov/pubmed/19929421", volume = "172", year = "2009", } @article{Tchirkov2007, author = "A. Tchirkov and T. Khalil and E. Chautard and K. Mokhtari and L. V{\'e}ron{\`e}se and B. Irthum and P. Vago and J-L. K{\'e}m{\'e}ny and P. Verrelle", abstract = "Interleukin-6 (IL-6) is known to promote tumour growth and survival. We evaluated IL-6 gene amplification in tumours from 53 glioma patients using fluorescence in situ hybridisation. Amplification events were detected only in glioblastomas (15 out of 36 cases), the most malignant tumours, and were significantly associated with decreased patient survival.", journal = "Br J Cancer", keywords = "Gene Amplification; MetaCyte; Glioblastoma; genetics; mortality; Humans; In Situ Hybridization; Fluorescence; Interleukin-6", month = "Feb", number = "3", pages = "474--476", title = "Interleukin-6 gene amplification and shortened survival in glioblastoma patients.", url = "http://dx.doi.org/10.1038/sj.bjc.6603586", volume = "96", year = "2007", } @article{Cossu-Rocca2008, author = "Paolo Cossu-Rocca and John N Eble and Shaobo Zhang and Stephen M Bonsib and Guido Martignoni and Matteo Brunelli and Liang Cheng", abstract = "Renal oncocytosis is characterized by the presence of multiple tumors with oncocytic features, often associated with small clusters of tubule-like structures with oncocytic change. The morphologic features of the oncocytic nodules encompass a spectrum of appearances, with patterns typical of renal oncocytoma or classic chromophobe renal cell carcinoma, as well as 'hybrid' tumors with features resembling both oncocytoma and chromophobe renal cell carcinoma. We utilized interphase cytogenetic methods to study 11 tumors from the kidneys of a 45-year-old woman. The tumors included morphologically classical oncocytomas and 'hybrid' tumors with features reminiscent of chromophobe carcinoma. The kidneys also showed foci of oncocytic change in renal tubules. Fluorescence in situ hybridization was performed with centromeric probes for chromosomes 1, 2, 6, 10, and 17 in each of the 11 tumors to determine whether or not there were losses of the chromosomes that are most frequently lost in chromophobe renal cell carcinomas. Neoplastic nuclei from each tumor were evaluated for the number of hybridization signals and scored according to the percentage of nuclei with one, two, and three or more signals. The normal renal parenchyma surrounding the tumors was used as control tissue. All 11 tumors from this patient with renal oncocytosis showed no loss of any of the chromosomes 1, 2, 6, 10, or 17, a pattern identical to that found in normal control tissues. These observations weigh against the concept that hybrid tumors of oncocytosis are closely related to chromophobe renal cell carcinoma.", journal = "Mod Pathol", keywords = "Isis", month = "Apr", number = "4", pages = "498--504", title = "Interphase cytogenetic analysis with centromeric probes for chromosomes 1, 2, 6, 10, and 17 in 11 tumors from a patient with bilateral renal oncocytosis.", url = "http://dx.doi.org/10.1038/modpathol.2008.16", volume = "21", year = "2008", } @article{00079, author = "R. Toder and Y. Xia and E. Bausch", journal = "Chromosome Res", keywords = "Isis CGH", pages = "478- 494", title = "Interspecies comparative genome hybridization and interspecies representational difference analysis reveal gross DNA differences between humans and great apes", volume = "6", year = "1998", } @article{00240, author = "H. Lyng and M. Beigi and D.H. Svendsrud and O.T. Brustugun and T. Stokke and G.B. Kristensen and K. Sundf{\o}r and A. Skj{\o}nsberg and P.M. De Angelis", journal = "Int J Cancer", keywords = "Isis CGH", pages = "358- 366", title = "Intratumor chromosomal heterogeneity in advanced carcinomas of the uterine cervix.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=15221962{\&}query_hl=11{\&}itool=pubmed_docsum", volume = "111", year = "2004", } @article{Pignalosa2010, author = "D. Pignalosa and S. Ritter and M. Durante", abstract = "Papillary thyroid carcinoma (PTC) is a known radiation-induced tumor. Rearrangements in human chromosome 10 and in particular intrachromosomal exchanges are often associated with PTC formation. In this study we measured intrachromosomal exchanges in human thyroid follicular cells exposed to sparsely or densely ionizing radiation. Assuming that inversions in chromosome 10 are a biomarker of PTC risk, we estimated the relative biological effectiveness (RBE) of heavy ions using a molecular marker in vitro. The analysis of chromosomal aberrations was performed with the mBAND technique, which allows detection of both inter- and intrachromosomal exchanges. Our results do not show any significant increase in the yield of intrachanges in samples exposed to heavy ions compared to X rays. Within the constraints imposed by the experimental model we used, we conclude that heavy ions would not necessarily be more effective than X rays in the induction of thyroid cancer.", journal = "Radiat Res", keywords = "Chromosome Inversion; Isis; mFISH", month = "Jul", number = "1", pages = "14--19", title = "Inversions in chromosome 10 of human thyroid cells induced by accelerated heavy ions.", url = "http://dx.doi.org/10.1667/RR1963.1", volume = "174", year = "2010", } @article{00120, author = "G. Lindner and A. Menrad and E. Gherardi and G. Merlino and P. Welker and B. Handjiski and B. Roloff and R. Paus", journal = "FASEB Journal", keywords = "Isis", pages = "319- 332", title = "Involvement of hepatocyte growth factor / scatter factor and Met receptor signaling in hair follicle morphogenesis and cycling", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=10657988{\&}query_hl=12{\&}itool=pubmed_docsum", volume = "14", year = "2000", } @article{Pernot2012, author = "Eileen Pernot and Janet Hall and Sarah Baatout and Mohammed Abderrafi Benotmane and Eric Blanchardon and Simon Bouffler and Houssein {El Saghire} and Maria Gomolka and Anne Guertler and Mats Harms-Ringdahl and Penny Jeggo and Michaela Kreuzer and Dominique Laurier and Carita Lindholm and Radhia Mkacher and Roel Quintens and Kai Rothkamm and Laure Sabatier and Soile Tapio and Florent {de Vathaire} and Elisabeth Cardis", abstract = "Ionizing radiation is a known human carcinogen that can induce a variety of biological effects depending on the physical nature, duration, doses and dose-rates of exposure. However, the magnitude of health risks at low doses and dose-rates (below 100mSv and/or 0.1mSvmin(-1)) remains controversial due to a lack of direct human evidence. It is anticipated that significant insights will emerge from the integration of epidemiological and biological research, made possible by molecular epidemiology studies incorporating biomarkers and bioassays. A number of these have been used to investigate exposure, effects and susceptibility to ionizing radiation, albeit often at higher doses and dose rates, with each reflecting time-limited cellular or physiological alterations. This review summarises the multidisciplinary work undertaken in the framework of the European project DoReMi (Low Dose Research towards Multidisciplinary Integration) to identify the most appropriate biomarkers for use in population studies. In addition to logistical and ethical considerations for conducting large-scale epidemiological studies, we discuss the relevance of their use for assessing the effects of low dose ionizing radiation exposure at the cellular and physiological level. We also propose a temporal classification of biomarkers that may be relevant for molecular epidemiology studies which need to take into account the time elapsed since exposure. Finally, the integration of biology with epidemiology requires careful planning and enhanced discussions between the epidemiology, biology and dosimetry communities in order to determine the most important questions to be addressed in light of pragmatic considerations including the appropriate population to be investigated (occupationally, environmentally or medically exposed), and study design. The consideration of the logistics of biological sample collection, processing and storing and the choice of biomarker or bioassay, as well as awareness of potential confounding factors, are also essential.", journal = "Mutat Res", keywords = "Metafer, CometScan, Biological Markers; Cells, Cultured; Chromosome Aberrations; DNA Damage; Epidemiologic Studies; Epigenesis, Genetic; Humans; Metabolomics; Molecular Epidemiology; Radiation, Ionizing; Reactive Oxygen Species", number = "2", pages = "258--286", title = "Ionizing radiation biomarkers for potential use in epidemiological studies.", url = "http://dx.doi.org/10.1016/j.mrrev.2012.05.003", volume = "751", year = "2012", } @article{00177, author = "A. Kuechler and S. Neubauer and G.G. Grabenhauer and U. Claussen and T. Liehr and R. Sauer and T.G. Wendt", journal = "Strahlentherapie und Onkologie", keywords = "Isis mFISH", pages = "209- 215", title = "Is 24-color FISH detection of in-vitro radiation-induced chromosomal aberrations suited to determine individual intrinsic radiosensitivity?", volume = "4", year = "2002", } @article{00095, author = "K.G. Michels-Rautens and C.Y. Mardin and W.M. Budde and T. Liehr and J. Polansky and T. Nguyen and V. Timmerman and C. Van Broeckhoven and G.O.H. Naumann and R.A. Pfeiffer and B.W. Rautenstrauss", journal = "Human Genetics", pages = "103- 106", title = "Juvenile open angle glaucoma: fine mapping of the TIGR gene to 1q24.3-q25.2 and mutation analysis", volume = "102", year = "1998", } @article{00214, author = "M. Oliver-Bonet and T. Liehr and A. Nietzel and A. Heller and H. Starke and U. Claussen and M. Codina-Pascual and A. Pujol and C. Abad and J. Egozcue and J. Navarro and J. Benet", journal = "European J Hum Genet", keywords = "Isis mFISH", pages = "879- 883", title = "Karyotyping of human synaptonemal complexes by cenM-FISH", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=14571274{\&}dopt=Abstract", volume = "11", year = "2003", } @article{00215, author = "M. Oliver-Bonet and T. Liehr and A. Nietzel and A. Heller and H. Starke and U. Claussen and M. Codina-Pascual and A. Pujol and C. Abad and J. Egozcue and J. Navarro and J. Benet", journal = "European J Hum Genet", keywords = "Isis mFISH", pages = "879- 883", title = "Karyotyping of human synaptonemal complexes by cenM-FISH", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=14571274{\&}dopt=Abstract", volume = "11", year = "2003", } @article{00170, author = "O.P.F. Clausen and M. Beigi and L. Bolund and S. K{\o}lvraa and P.J. Gjersvik and G. M{\o}rk and P.M. De Angelis", journal = "J Invest Dermatol", keywords = "Isis CGH", pages = "1367- 1372", title = "Keratoacanthomas frequently show chromosomal aberrations as assessed by comparative genomic hybridization.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=12485441{\&}query_hl=3{\&}itool=pubmed_DocSum", volume = "119", year = "2002", } @article{Cheang2009, author = "Maggie C U. Cheang and Stephen K. Chia and David Voduc and Dongxia Gao and Samuel Leung and Jacqueline Snider and Mark Watson and Sherri Davies and Philip S. Bernard and Joel S. Parker and Charles M. Perou and Matthew J. Ellis and Torsten O. Nielsen", abstract = "Gene expression profiling of breast cancer has identified two biologically distinct estrogen receptor (ER)-positive subtypes of breast cancer: luminal A and luminal B. Luminal B tumors have higher proliferation and poorer prognosis than luminal A tumors. In this study, we developed a clinically practical immunohistochemistry assay to distinguish luminal B from luminal A tumors and investigated its ability to separate tumors according to breast cancer recurrence-free and disease-specific survival.Tumors from a cohort of 357 patients with invasive breast carcinomas were subtyped by gene expression profile. Hormone receptor status, HER2 status, and the Ki67 index (percentage of Ki67-positive cancer nuclei) were determined immunohistochemically. Receiver operating characteristic curves were used to determine the Ki67 cut point to distinguish luminal B from luminal A tumors. The prognostic value of the immunohistochemical assignment for breast cancer recurrence-free and disease-specific survival was investigated with an independent tissue microarray series of 4046 breast cancers by use of Kaplan-Meier curves and multivariable Cox regression.Gene expression profiling classified 101 (28\%) of the 357 tumors as luminal A and 69 (19\%) as luminal B. The best Ki67 index cut point to distinguish luminal B from luminal A tumors was 13.25\%. In an independent cohort of 4046 patients with breast cancer, 2847 had hormone receptor-positive tumors. When HER2 immunohistochemistry and the Ki67 index were used to subtype these 2847 tumors, we classified 1530 (59\%, 95\% confidence interval [CI] = 57\% to 61\%) as luminal A, 846 (33\%, 95\% CI = 31\% to 34\%) as luminal B, and 222 (9\%, 95\% CI = 7\% to 10\%) as luminal-HER2 positive. Luminal B and luminal-HER2-positive breast cancers were statistically significantly associated with poor breast cancer recurrence-free and disease-specific survival in all adjuvant systemic treatment categories. Of particular relevance are women who received tamoxifen as their sole adjuvant systemic therapy, among whom the 10-year breast cancer-specific survival was 79\% (95\% CI = 76\% to 83\%) for luminal A, 64\% (95\% CI = 59\% to 70\%) for luminal B, and 57\% (95\% CI = 47\% to 69\%) for luminal-HER2 subtypes.Expression of ER, progesterone receptor, and HER2 proteins and the Ki67 index appear to distinguish luminal A from luminal B breast cancer subtypes.", journal = "J Natl Cancer Inst", keywords = "Metafer-P Metafer MetaCyte Her2", month = "May", number = "10", pages = "736--750", title = "Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer.", url = "http://dx.doi.org/10.1093/jnci/djp082", volume = "101", year = "2009", } @article{00083, author = "H. Baurmann and S. Nagel and T. Binder and A. Neubauer and W. Siegert and D. Huhn", journal = "Blood", pages = "3582- 3590", title = "Kinetics of the Graft-Versus-Leukemia Response After Donor Leukocyte Infusions for Relapsed Chronic Myeloid Leukemia After Bone Marrow Transplantations", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9808551{\&}dopt=Abstract", volume = "92", year = "1998", } @article{Vandewoestyne2010, author = "Mado Vandewoestyne and Dieter Deforce", abstract = "In forensic sciences, short tandem repeat (STR) analysis has become the prime tool for DNA-based identification of the donor(s) of biological stains and/or traces. Many traces, however, contain cells and, hence, DNA, from more than a single individual, giving rise to mixed genotypes and the subsequent difficulties in interpreting the results. An even more challenging situation occurs when cells of a victim are much more abundant than the cells of the perpetrator. Therefore, the forensic community seeks to improve cell-separation methods in order to generate single-donor cell populations from a mixed trace in order to facilitate DNA typing and identification. Laser capture microdissection (LCM) offers a valuable tool for precise separation of specific cells. This review summarises all possible forensic applications of LCM, gives an overview of the staining and detection options, including automated detection and retrieval of cells of interest, and reviews the DNA extraction protocols compatible with LCM of cells from forensic samples.", journal = "Int J Legal Med", keywords = "Metafer; forensics; Metafer P", month = "Nov", number = "6", pages = "513--521", title = "Laser capture microdissection in forensic research: a review.", url = "http://dx.doi.org/10.1007/s00414-010-0499-4", volume = "124", year = "2010", } @article{00193, author = "H. Starke and B. Mitulla and V. Beensen and V. Trifonov and N. Rubtsov and A. Heller and M. Ziegler and A. Neumann and U. Claussen and T. Liehr", journal = "Prenat Diagn", keywords = "Ikaros Isis mBAND", pages = "765- 767", title = "Letter to the editor: First postnatal case of mosaic del(22)/r(22)", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12975792{\&}dopt=Abstract", volume = "23", year = "2003", } @article{00208, author = "A. Heller and L. Brecevic and M. Glaser and I.F. Loncarevic and E. Gebhart and U. Claussen and T. Liehr", journal = "Cancer Genet Cytogenet", keywords = "Isis mBAND", pages = "81- 83", title = "Letter to the editor: Trisomy 8 as the sole chromosomal aberration in myelocytic malignancies: a comprehensive molecular cytogenetic analysis reveals no cryptic aberrations", volume = "146", year = "2003", } @article{00038, author = "A. Hemminki and I. Tomlinson and D. Markie and H. J{\"a}rvinen and P. Sistonen and A.-M. Bj{\"o}rkqvist and S. Knuutila and R. Salovaara and W. Bodmer and D. Shibata and de la Chapelle, A. and L.A. Aaltonen", journal = "Nature Genetics", keywords = "Isis CGH", pages = "87- 909", title = "Localization of a susceptibility locus for Peutz-Jeghers syndrome to 19p using comparative genomic hybridization and targeted linkage analysis", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8988175{\&}dopt=Abstract", volume = "15", year = "1997", } @article{00116, author = "L.T. Reiter and T. Liehr and B. Rautenstrauss and H.M. Robertson and J.R. Lupiski", journal = "Genome Res", pages = "839- 843", title = "Localization of mariner DNA Transposons in the Human Genome by PRINS", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10508842{\&}dopt=Abstract", volume = "9", year = "1999", } @article{00178, author = "C. Schoch and T. Haferlach and S. Bursch and D. Gerstner and S. Schnittger and M. Dugas and W. Kern and H. L{\"o}ffler and W. Hiddemann", journal = "Genes, Chromosomes {\&} Cancer", keywords = "Isis mFISH", pages = "20- 29", title = "Loss of genetic material is more common than gain in acute myolid leukemia with complex aberrant karyotype: a detailed analysis of 125 cases using conventional chromosome analysis and fluorescence in situ hybridization including 24-color FISH", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12203786{\&}dopt=Abstract", volume = "35", year = "2002", } @article{00293, author = "B.C. Heng and K.J. Vinoth and H. Liu and M.P. Hande and T. Cao", journal = "Int J Med Sci", keywords = "Isis mFISH", pages = "124- 129", title = "Low temperature tolerance of human embryonic stem cells.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=16906221{\&}query_hl=19{\&}itool=pubmed_docsum", volume = "3", year = "2006", } @article{Boehm2008, author = "Bernhard O. Boehm and Peter M{\"o}ller and Josef H{\"o}gel and Bernhard R. Winkelmann and Wilfried Renner and Silke Rosinger and Ursula Seelhorst and Britta Wellnitz and Winfried M{\"a}rz and Julia Melzner and Silke Br{\"u}derlein", journal = "Diabetes", keywords = "Isis Telomere", month = "Nov", number = "11", pages = "2950--2957", title = "Lymphocytes of type 2 diabetic women carry a high load of stable chromosomal aberrations: a novel risk factor for disease-related early death.", url = "http://dx.doi.org/10.2337/db08-0274", volume = "57", year = "2008", } @article{00061, author = "F. Speleman and O. Delattre and M. Peter and E. Hauben and N. Van Roy and E. Van Marck", journal = "Mod Pathol.", pages = "496- 499", title = "Malignant Melanoma of the Soft Parts (Clear-Cell Sarcoma): Confirmation of EWS and ATF-1 Gene Fusion Caused by a t(12/22) Translocation.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9160316{\&}dopt=Abstract", volume = "10", year = "1997", } @article{Gospodinov2011, author = "Anastas Gospodinov and Thomas Vaissiere and Dragomir B. Krastev and Ga?lle Legube and Boyka Anachkova and Zdenko Herceg", abstract = "Chromatin modifications/remodeling are important mechanisms by which cells regulate various functions through providing accessibility to chromatin DNA. Recent studies implicated INO80, a conserved chromatin-remodeling complex, in the process of DNA repair. However, the precise underlying mechanism by which this complex mediates repair in mammalian cells remains enigmatic. Here, we studied the effect of silencing of the Ino80 subunit of the complex on double-strand break repair in mammalian cells. Comet assay and homologous recombination repair reporter system analyses indicated that Ino80 is required for efficient double-strand break repair. Ino80 association with chromatin surrounding double-strand breaks suggested the direct involvement of INO80 in the repair process. Ino80 depletion impaired focal recruitment of 53BP1 but did not impede Rad51 focus formation, suggesting that Ino80 is required for the early steps of repair. Further analysis by using bromodeoxyuridine (BrdU)-labeled single-stranded DNA and replication protein A (RPA) immunofluorescent staining showed that INO80 mediates 5'-3' resection of double-strand break ends.", journal = "Mol Cell Biol", keywords = "CometImager", month = "Dec", number = "23", pages = "4735--4745", title = "Mammalian Ino80 mediates double-strand break repair through its role in DNA end strand resection.", url = "http://dx.doi.org/10.1128/MCB.06182-11", volume = "31", year = "2011", } @article{00133, author = "H. Scherthan and M. Jerratsch and B. Li and S. Smith and M. Hult{\'e}n and T. Lock and de Lange, T.", journal = "Mol Biol Cell", pages = "4189- 4203", title = "Mammalian meiotic telomeres: protein composition and redistribution in relation to nuclear pores", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11102517{\&}dopt=Abstract", volume = "11", year = "2000", } @article{Rothkamm2013, author = "Kai Rothkamm and Stephen Barnard and Elizabeth A. Ainsbury and Jenna Al-Hafidh and Joan-Francesc Barquinero and Carita Lindholm and Jayne Moquet and Marjo Per?l? and Sandrine Roch-Lef?vre and Harry Scherthan and Hubert Thierens and Anne Vral and Veerle Vandersickel", abstract = "The identification of severely exposed individuals and reassurance of the 'worried well' are of prime importance for initial triage following a large scale radiation accident. We aim to develop the {\~a}-H2AX foci assay into a rapid biomarker tool for use in accidents. Here, five laboratories established a standard operating procedure and analysed 100 ex vivo {\~a}-irradiated, 4 or 24h incubated and overnight-shipped lymphocyte samples from four donors to generate {\~a}-H2AX reference data, using manual and/or automated foci scoring strategies. In addition to acute, homogeneous exposures to 0, 1, 2 and 4Gy, acute simulated partial body (4Gy to 50\% of cells) and protracted exposures (4Gy over 24h) were analysed. Data from all laboratories could be satisfactorily fitted with linear dose response functions. Average yields observed at 4h post exposure were 2-4 times higher than at 24h and varied considerably between laboratories. Automated scoring caused larger uncertainties than manual scoring and was unable to identify partial exposures, which were detectable in manually scored samples due to their overdispersed foci distributions. Protracted exposures were detectable but doses could not be accurately estimated with the {\~a}-H2AX assay. We conclude that the {\~a}-H2AX assay may be useful for rapid triage following a recent acute radiation exposure. The potentially higher speed and convenience of automated relative to manual foci scoring needs to be balanced against its compromised accuracy and inability to detect partial body exposures. Regular re-calibration or inclusion of reference samples may be necessary to ensure consistent results between laboratories or over long time periods.", journal = "Mutat Res", keywords = "Metafer MetaCyte foci", month = "May", title = "Manual versus automated gamma-H2AX foci analysis across five European laboratories: Can this assay be used for rapid biodosimetry in a large scale radiation accident?", url = "http://dx.doi.org/10.1016/j.mrgentox.2013.04.012", year = "2013", } @article{00111, author = "I. Chudoba and Y. Franke and G. Senger and G. Sauerbrei and S. Demuth and V. Beensen and A. Neumann and I. Hansmann and U. Claussen", journal = "European Journal of Human Genetics", pages = "533- 540", title = "Maternal UDP 20 in a hyperactive child with severe growth retardation", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10439958{\&}dopt=Abstract", volume = "7", year = "1999", } @article{Hada2010, author = "M. Hada and B. Gersey and P. B. Saganti and R. Wilkins and F. A. Cucinotta and H. Wu", abstract = "Human risks from chronic exposures to both low- and high-LET radiation are of intensive research interest in recent years. In the present study, human epithelial cells were exposed in vitro to gamma-rays at a dose rate of 17mGy/h or secondary neutrons of 25mGy/h. The secondary neutrons have a broad energy spectrum that simulates the Earth's atmosphere at high altitude, as well as the environment inside spacecrafts like the Russian MIR station and the International Space Station (ISS). Chromosome aberrations in the exposed cells were analyzed using the multicolor banding in situ hybridization (mBAND) technique with chromosome 3 painted in 23 colored bands that allows identification of both inter- and intrachromosome exchanges including inversions. Comparison of present dose responses between gamma-rays and neutron irradiations for the fraction of cells with damaged chromosome 3 yielded a relative biological effectiveness (RBE) value of 26+/-4 for the secondary neutrons. Our results also revealed that secondary neutrons of low dose rate induced a higher fraction of intrachromosome exchanges than gamma-rays, but the fractions of inversions observed between these two radiation types were indistinguishable. Similar to the previous findings after acute radiation exposures, most of the inversions observed in the present study were accompanied by other aberrations. The fractions of complex type aberrations and of unrejoined chromosomal breakages were also found to be higher in the neutron-exposed cells than after gamma-rays. We further analyzed the location of the breaks involved in chromosome aberrations along chromosome 3, and observed hot spots after gamma-ray, but not neutron, exposures.", journal = "Mutat Res", keywords = "Isis mBAND", month = "Mar", title = "mBAND analysis of chromosome aberrations in human epithelial cells induced by gamma-rays and secondary neutrons of low dose rate.", url = "http://dx.doi.org/10.1016/j.mrgentox.2010.03.009", year = "2010", } @article{00243, author = "I. Chudoba and G. Hickmann and T. Friedrich and A. Jauch and P. Kozlowski and G. Senger", journal = "Cytogenet Genome Res", keywords = "Isis mBAND", pages = "390- 393", title = "mBAND: a high resolution multicolor banding technique for the detection of complex intrachromosomal aberrations", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15162070", volume = "104", year = "2004", } @article{00132, author = "H. Scherthan and M. Jerratsch and S. Dhar and Y.A. Wang and S.P. Goff and T.K. Pandita", journal = "Mol. Cell Biol.", pages = "7773- 7783", title = "Meiotic telomere distribution and sertoli cell nuclear architecture are altered in Atm- and Atm-p53-deficient mice", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11003672{\&}dopt=Abstract", volume = "20", year = "2000", } @article{00136, author = "E. Trelles-Sticken and M.E. Dresser and H. Scherthan", journal = "J. Cell Biol.", pages = "95- 106", title = "Meiotic telomere protein Ndj1p is required for meiosis-specific telomere distribution, bouquet formation and efficient homologue pairing", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11018056{\&}dopt=Abstract", volume = "151", year = "2000", } @article{Bolognesi11, author = "Claudia Bolognesi and Cristina Balia and Paola Roggieri and Francesco Cardinale and Paolo Bruzzi and Francesca Sorcinelli and Florigio Lista and Raffaele D'Amelio and Enzo Righi", abstract = "In the case of a large-scale nuclear or radiological incidents a reliable estimate of dose is an essential tool for providing timely assessment of radiation exposure and for making life-saving medical decisions. Cytogenetics is considered as the "gold standard" for biodosimetry. The dicentric analysis (DA) represents the most specific cytogenetic bioassay. The micronucleus test (MN) applied in interphase in peripheral lymphocytes is an alternative and simpler approach. A dose-effect calibration curve for the MN frequency in peripheral lymphocytes from 27 adult donors was established after in vitro irradiation at a dose range 0.15-8 Gy of 137Cs gamma rays (dose rate 6 Gy min-1). Dose prediction by visual scoring in a dose-blinded study (0.15-4.0 Gy) revealed a high level of accuracy (R = 0.89). The scoring of MN is time consuming and requires adequate skills and expertise. Automated image analysis is a feasible approach allowing to reduce the time and to increase the accuracy of the dose estimation decreasing the variability due to subjective evaluation. A good correlation (R = 0.705) between visual and automated scoring with visual correction was observed over the dose range 0-2 Gy. Almost perfect discrimination power for exposure to 1-2 Gy, and a satisfactory power for 0.6 Gy were detected. This threshold level can be considered sufficient for identification of sub lethally exposed individuals by automated CBMN assay.", journal = "Radiation Measurements", keywords = "Radiation Micronuclei Metafer MNScore", number = "2", pages = "169 - 175", title = "Micronucleus test for radiation biodosimetry in mass casualty events: Evaluation of visual and automated scoring", url = "http://www.sciencedirect.com/science/article/B6TVS-51GHX11-2/2/d9bfe8b341e244472f4b83fc95d44692", volume = "46", year = "2011", } @article{00075, author = "M. Bentz and A. Plesch and S. Stigenbauer and H. D{\"o}hner and P. Lichter", journal = "Genes Chromosomes Cancer", keywords = "Isis CGH", pages = "1- 4", title = "Minimal Sizes of Deletions Detected by Comperative Genomic Hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9491330{\&}dopt=Abstract", volume = "21", year = "1998", } @article{Douet-Guilbert2012, author = "N. Douet-Guilbert and E. {De Braekeleer} and A. Basinko and A. Herry and N. Gueganic and C. Bovo and K. Trillet and A. {Dos Santos} and M. J. {Le Bris} and F. Morel and J. R. Eveillard and C. Berthou and M. {De Braekeleer}", journal = "Leukemia", keywords = "24XCyte Probes Probe", month = "Jul", number = "7", pages = "1695--1697", title = "Molecular characterization of deletions of the long arm of chromosome 5 (del(5q)) in 94 MDS/AML patients.", url = "http://dx.doi.org/10.1038/leu.2012.9", volume = "26", year = "2012", } @article{00239, author = "P.M. De Angelis and B. Fjell and K.L. Kravik and T. Haug and S.H. Tunheim and W. Reichelt and M. Beigi and O.P. Clausen and E. Galteland and T. Stokke", journal = "Int J Oncol", keywords = "Isis CGH", pages = "1279- 1288", title = "Molecular characterizations of derivatives of HCT116 colorectal cancer cells that are resistant to the chemotherapeutic agent 5-fluorouracil.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=15067352{\&}query_hl=5{\&}itool=pubmed_docsum", volume = "24", year = "2004", } @article{00187, author = "H. Van Limbergen and B. Poppe and A. Janssens and R. De Bock and A. De Paepe and L. Noens and F. Speleman", journal = "Leukemia", pages = "344- 351", title = "Molecular cytogenetic analysis of 10/11 rearrangements in acute myeolid leukemia.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11896537{\&}dopt=Abstract", volume = "16", year = "2002", } @article{00165, author = "H. Van Limbergen and H.B. Beverloo and van Drunen, E. and A. Janssens and K. H{\"a}hlen and B. Poppe and N. Van Roy and P. Marynen and de Paepe, A. and R. Slater and F. Speleman", journal = "Genes, Chromosomes {\&} Cancer", keywords = "Isis mBAND", pages = "274- 282", title = "Molecular cytogenetic and clinical findings in ETV6/ABL1-positive leukemia", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11170285{\&}dopt=Abstract", volume = "30", year = "2001", } @article{Carreira2009, author = "Isabel M Carreira and Joana B Melo and Carlos Rodrigues and Liesbeth Backx and Joris Vermeesch and Anja Weise and Nadezda Kosyakova and Guiomar Oliveira and Eunice Matoso", abstract = "ABSTRACT: BACKGROUND: Inverted duplications (inv dup) of a terminal chromosome region are a particular subset of rearrangements that often results in partial tetrasomy or partial trisomy when accompanied by a deleted chromosome. Associated mosaicism could be the consequence of a post-zygotic event or could result from the correction of a trisomic conception. Tetrasomies of distal segments of the chromosome 3q are rare genetic events and their phenotypic manifestations are diverse. To our knowledge, there are only 12 cases reported with partial 3q tetrasomy. Generally, individuals with this genomic imbalance present mild to severe developmental delay, facial dysmorphisms and skin pigmentary disorders. RESULTS: We present the results of the molecular cytogenetic characterization of an unbalanced mosaic karyotype consisting of mos 46,XY,add(12)(p13.3) [56]/46,XY [44] in a previously described 11 years old autistic boy, re-evaluated at adult age. The employment of fluorescence in situ hybridization (FISH) and multicolor banding (MCB) techniques identified the extra material on 12p to be derived from chromosome 3, defining the additional material on 12p as an inv dup(3)(qter --> q26.3::q26.3 --> qter). Subsequently, array-based comparative genomic hybridization (aCGH) confirmed the breakpoint at 3q26.31, defining the extra material with a length of 24.92 Mb to be between 174.37 and 199.29 Mb. CONCLUSION: This is the thirteenth reported case of inversion-duplication 3q, being the first one described as an inv dup translocated onto a non-homologous chromosome. The mosaic terminal inv dup(3q) observed could be the result of two proposed alternative mechanisms. The most striking feature of this case is the autistic behavior of the proband, a characteristic not shared by any other patient with tetrasomy for 3q26.31 --> 3qter. The present work further illustrates the advantages of the use of an integrative cytogenetic strategy, composed both by conventional and molecular techniques, on providing powerful information for an accurate diagnosis. This report also highlights a chromosome region potentially involved in autistic disorders.", journal = "Mol Cytogenet", keywords = "Isis", pages = "16", title = "Molecular cytogenetic characterisation of a mosaic add(12)(p13.3) with an inv dup(3)(q26.31 --> qter) detected in an autistic boy.", url = "http://dx.doi.org/10.1186/1755-8166-2-16", volume = "2", year = "2009", } @article{00130, author = "A. Heller and J. Seidel and A. H{\"u}bler and H. Strake and V. Beensen and G. Senger and M. Rocchi and J. Wirth and I. Chudoba and U. Claussen and T. Liehr", journal = "J. Med. Genet.", pages = "529- 532", title = "Molecular Cytogenetic Characterisation of Partial Trisomy 9q in a Case with Pyloric Stenosis and a Review", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10882757{\&}dopt=Abstract", volume = "37", year = "2000", } @article{00118, author = "H. Starke and I. Schreyer and C. K{\"a}hler and W. Fiedler and V. Beensen and A. Heller and A. Neitzel and U. Claussen and T. Liehr", journal = "Prenat. Diagn.", pages = "1169- 1174", title = "Molecular Cytogenetic Characterization of a Prenatally Detected Supernumerary Minute Marker Chromosome 8", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10590438{\&}dopt=Abstract", volume = "19", year = "1999", } @article{00291, author = "C. Karst and V. Trifonov and S.A. Romanenko and U. Claussen and K. Mrasek and S. Michel and P. Avner and T. Liehr", journal = "Int. J. Molecular Medicine", keywords = "Isis mBAND", pages = "209- 213", title = "Molecular cytogenetic characterization of the mouse cell line WMP2 by spectral karyotyping and multicolor banding applying murine probes.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=16391817{\&}query_hl=7{\&}itool=pubmed_docsum", volume = "17", year = "2006", } @article{00047, author = "K. Fischer and S. Fr{\"o}hling and s.W. Scherer and J. McAllister Brown and C. Scholl and S. Stilgenbauer and L.-C. Tsui and P. Lichter and H. D{\"o}hner", journal = "Blood", pages = "2036- 2041", title = "Molecular Cytogenetic Delineation of Deletions and Translocations Involving Chromosome Band 7q22 in Myeloid Leukemias", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9058725{\&}dopt=Abstract", volume = "89", year = "1997", } @article{00204, author = "B. Kaluzewski and M. Constantinou and E. Zajac", journal = "J. Appl. Genet.", keywords = "Isis CGH mFISH", pages = "539- 546", title = "Molecular cytogenetic techniques in detecting subtle chromosomal imbalances", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=14617835{\&}query_hl=1{\&}itool=pubmed_docsum", volume = "44", year = "2003", } @article{00230, author = "T. Liehr and G. Hickmann and P. Kozlowski and U. Claussen and H. Starke", journal = "Chromosome Research", keywords = "Ikaros Isis mFISH mBAND", pages = "239- 244", title = "Molecular-cytogenetic characterization of the origin and the presence of pericentromeric euchromatin on minute supernumerary marker chromosomes (SMCs)", volume = "12", year = "2004", } @article{00062, author = "F. Speleman and B. Dermaut and C.R. De Potter and M. Van Gele and N. Van Roy and A. De Paepe and G. Laureys", journal = "Genes Chromosomes Cancer", pages = "192- 194", title = "Monosomy 22 in a Mixed Germ Cell-Sex Cord-Stromal Tumor of the Ovary", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9219001{\&}dopt=Abstract", volume = "19", year = "1997", } @article{00053, author = "W. Krone and H. Kehrer-Sawatzki and A. Siegel and H. R{\"o}ck and H. G{\"o}tz", journal = "Cytogenetics and Cell Genetics", pages = "96- 102", title = "Monosomy 6 in human cultured fibroblast-like cells after long-term stimulation with acidic fibroblast growth factor (FGF1)", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9371397{\&}dopt=Abstract", volume = "78", year = "1997", } @article{00098, author = "B. Rautenstrauss and T. Liehr and C. Fuchs and A. Bevot and A. Bornemann and E. Postler and R. Meyermann and S. Uhlhaas and W. Friedl and R. Michaelis", journal = "International Journal of Molecular Medicine", pages = "333- 337", title = "Mosaicism for Charcot-Marie-Tooth disease type 1A: Onset in childhood suggests somatic reversion in early developmental stages", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9852234{\&}dopt=Abstract", volume = "1", year = "1998", } @article{00010, author = "T. Liehr and B. Rautenstrauss and H. Grehl and K.D. Bathke and A. Ekici and A. Rauch and H.-D. Rott", journal = "Human Genetics", keywords = "Isis", pages = "22- 28", title = "Mosaicism for the Charcot-Marie-Tooth disease type 1A duplication suggests somatic reversion", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8682501{\&}dopt=Abstract", volume = "98", year = "1996", } @article{00049, author = "A.H.N. Hopman and S. Claessen and E.J.M. Speel", journal = "Histochem Cell Biol", pages = "291- 298", title = "Multi-color brightfield in situ hybridisation on tissue sections", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9387920{\&}dopt=Abstract", volume = "108", year = "1997", } @article{00175, author = "T. Liehr and A. Nietzel and H. Starke and A. Heller and A. Weise and K. Mrasek and U. Claussen", journal = "Cytogenet Genome Res.", keywords = "Isis mBAND", pages = "43- 50", title = "Multicolor chromosome banding (MCB) with YAC/BAC-based probes and region-specific microdissection DNA libraries", volume = "97", year = "2002", } @article{00186, author = "J.I. Mart{\'i}n-Subero and I. Chudoba and L. Harder and S. Gesk and W. Grote and F.J. Novo and M.J. Calasanz and R. Siebert", journal = "Am J Pathol", keywords = "Isis mFISH", pages = "413- 420", title = "Multicolor FICTION. Expanding the possibilities of combined morphologic, immunophenotypic and genetic single cell analyses", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12163366{\&}dopt=Abstract", volume = "161", year = "2002", } @article{00247, author = "T. Liehr and H. Starke and A. Weise and H. Lehrer and U. Claussen", journal = "Histol Histopathol", keywords = "Isis mFISH mBAND", pages = "229- 237", title = "Multicolour FISH probe sets and their applications", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=14702191{\&}dopt=Abstract", volume = "19", year = "2004", } @article{00269, author = "A. Letessier and M.-J. Mozziconacci and A. Murati and J. Juriens and J. Adelaide and D. Birnbaum and M. Chaffanet", journal = "British Journal of Cancer", keywords = "Isis mBAND", pages = "382- 388", title = "Multicolour-banding fluorescence in situ hybridization (mbanding-FISH) to identify recurrent chromosomal alterations in breast tumour cell lines.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15655561", volume = "92", year = "2005", } @article{Ketelslegers2008, author = "Hans B Ketelslegers and Ralph W H Gottschalk and Gudrun Koppen and Greet Schoeters and Willy F Baeyens and van Larebeke, Nicolas A and van Delft, Joost H M and Jos C S Kleinjans", abstract = "Cancer has been suggested to result from interactions between genetic and environmental factors, and certain subgroups in the general population may be at increased risk because of their relatively higher susceptibility to environmental carcinogens. The current study, part of a large biomonitoring study conducted in Flanders from 2002 to 2006 (The Flanders Environment and Health Survey), aims to determine these susceptible subpopulations based on multiple genotypic differences between individuals. A random selection of 429 adolescents and 361 adults was genotyped for 36 polymorphisms in 23 genes selected because of their known role in carcinogen metabolism, DNA repair, and oxidative stress. In both age groups, relationships between endogenous exposure to organochloride substances (polychlorinated biphenyl, hexachlorobenzene, dichlorodiphenyl dichloroethane), metals (cadmium, lead), and urinary metabolites (1-hydroxypyrene, trans-trans muconic acid) versus genotoxic effects (Comet assay and micronuclei in lymphocytes, and urinary 8-hydroxydeoxyguanosine) were investigated. In addition, in the study among adults, the relationship of these exposures with several tumor markers (prostate-specific antigen, carcinoembryonic antigen, and p53) was tested. The impact of the genotype on established exposure-effect relationships was evaluated. Eight exposure-effect relationships were found, including three novel associations, with an impact of various genotypes, predominantly affecting biotransformation and oxidative stress response. This study shows that at least part of the interindividual differences in relationships between carcinogen exposure and genotoxic effect can be explained by genotypic differences, enabling the identification of more susceptible subgroups for environmental cancer risks. This may be of relevance for environmental health policy setting.", journal = "Cancer Epidemiol Biomarkers Prev", keywords = "Metafer MNScore", month = "Aug", number = "8", pages = "1902--1912", title = "Multiplex genotyping as a biomarker for susceptibility to carcinogenic exposure in the FLEHS biomonitoring study.", url = "http://dx.doi.org/10.1158/1055-9965.EPI-08-0045", volume = "17", year = "2008", } @article{00052, author = "H. Kehrer-Sawatzki and M. Udart and W. Krone and R. Baden and R. Fahsold and G. Thomas and B. Schmucker and G. Assum", journal = "Human Genetics", pages = "67- 74", title = "Mutational analysis and expression studies of the neurofibromatosis type 2 (NF2) gene in a patient with a ring chromosome 22 and NF2", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9225971{\&}dopt=Abstract", volume = "100", year = "1997", } @article{00312, author = "A. Rauch and C.T. Thiel and D. Schindler and U. Wick and Y.J. Crow and A.B. Ekici and van Essen, A.J. and T.O. Goecke and L. Al-Gazali and .H. Chrzanowska and C. Zweier and H.G. Brunner and K. Becker and C.J. Curry and B. Dallapiccola and K. Devriendt and A. D{\"o}rfler and E. Kinning and A. Megarbane and et al.", journal = "Science", keywords = "Isis", pages = "816- 819", title = "Mutations in the pericentrin (PCNT) gene cause primordial dwarfism", url = "http://www.ncbi.nlm.nih.gov/pubmed/18174396?ordinalpos=8{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", volume = "319", year = "2008", } @article{Quentin2011, author = "Samuel Quentin and Wendy Cuccuini and Raphael Ceccaldi and Olivier Nibourel and Corinne Pondarre and Marie-Pierre Pag?s and Nadia Vasquez and Catherine {Dubois d'Enghien} and J{\'e}r{\^o}me Larghero and {Peffault de Latour}, R{\'e}gis and Vanderson Rocha and Jean-Hugues Dalle and Pascale Schneider and Mauricette Michallet and G{\'e}rard Michel and Andr{\'e} Baruchel and Fran{\c{c}}ois Sigaux and Eliane Gluckman and Thierry Leblanc and Dominique Stoppa-Lyonnet and Claude Preudhomme and G{\'e}rard Soci{\'e} and Jean Soulier", abstract = "Fanconi anemia (FA) is a genetic condition associated with bone marrow (BM) failure, myelodysplasia (MDS), and acute myeloid leukemia (AML). We studied 57 FA patients with hypoplastic or aplastic anemia (n = 20), MDS (n = 18), AML (n = 11), or no BM abnormality (n = 8). BM samples were analyzed by karyotype, high-density DNA arrays with respect to paired fibroblasts, and by selected oncogene sequencing. A specific pattern of chromosomal abnormalities was found in MDS/AML, which included 1q+ (44.8\%), 3q+ (41.4\%), -7/7q (17.2\%), and 11q- (13.8\%). Moreover, cryptic RUNX1/AML1 lesions (translocations, deletions, or mutations) were observed for the first time in FA (20.7\%). Rare mutations of NRAS, FLT3-ITD, MLL-PTD, ERG amplification, and ZFP36L2-PRDM16 translocation, but no TP53, TET2, CBL, NPM1, and CEBP? mutations were found. Frequent homozygosity regions were related not to somatic copy-neutral loss of heterozygosity but to consanguinity, suggesting that homologous recombination is not a common progression mechanism in FA. Importantly, the RUNX1 and other chromosomal/genomic lesions were found at the MDS/AML stages, except for 1q+, which was found at all stages. These data have implications for staging and therapeutic managing in FA patients, and also to analyze the mechanisms of clonal evolution and oncogenesis in a background of genomic instability and BM failure.", journal = "Blood", keywords = "Metafer MSearch Ikaros Isis", month = "Apr", number = "15", pages = "e161--e170", title = "Myelodysplasia and leukemia of Fanconi anemia are associated with a specific pattern of genomic abnormalities that includes cryptic RUNX1/AML1 lesions.", url = "http://dx.doi.org/10.1182/blood-2010-09-308726", volume = "117", year = "2011", } @article{Botchkarev1998a, author = "V. A. Botchkarev and N. V. Botchkarev and K. M. Albers and van der Veen, C. and G. R. Lewin and R. Paus", abstract = "Hair follicle epithelium and nervous system share a common ectodermal origin, and some neurotrophins can modulate keratinocyte proliferation and apoptosis. It is therefore reasonable to ask whether growth factors that control neural development are also involved in the regulation of hair follicle morphogenesis. Focusing on neurotrophin-3 (NT-3) and its high-affinity-receptor [tyrosine kinase C (TrkC)], we show that hair placode keratinocytes express TrkC mRNA and immunoreactivity early during murine hair follicle morphogenesis. In later stages of hair follicle development, TrkC mRNA, TrkC-, and NT-3-immunoreactivity are seen in keratinocytes of the proximal hair bulb as well as in dermal papilla fibroblasts. Compared with the corresponding wild-type animals, early stages of hair follicle morphogenesis are significantly accelerated in newborn NT-3 overexpressing mice, whereas these are retarded in newborn heterozygous NT-3 knockout (+/-) mice. These observations suggest that NT-3 is an important growth modulator during morphogenesis and remodeling of neuroectodermal-mesenchymal interaction systems like the hair follicle.", journal = "J Invest Dermatol", keywords = "Isis", month = "Aug", number = "2", pages = "279--285", title = "Neurotrophin-3 involvement in the regulation of hair follicle morphogenesis.", url = "http://dx.doi.org/10.1046/j.1523-1747.1998.00277.x", volume = "111", year = "1998", } @article{Jensen2008, author = "KC Jensen and DA Turbin and S Leung and MA Miller and K Johnson and B Norris and T Hastie and S McKinney and TO Nielsen and DG Huntsman and CB Gilks and RB West", abstract = "BACKGROUND: HER2 gene amplification and/or protein overexpression in breast cancer is associated with a poor prognosis and predicts response to anti-HER2 therapy. We examine the natural history of breast cancers in relationship to increased HER2 copy numbers in a large population-based study. PATIENTS AND METHODS: HER2 status was measured by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) in approximately 1,400 breast cancer cases with greater than 15 years of follow-up. Protein expression was evaluated with two different commercially-available antibodies. RESULTS: We looked for subgroups of breast cancer with different clinical outcomes, based on HER2 FISH amplification ratio. The current HER2 ratio cut point for classifying HER2 positive and negative cases is 2.2. However, we found an increased risk of disease-specific death associated with FISH ratios of >1.5. An 'intermediate' group of cases with HER2 ratios between 1.5 and 2.2 was found to have a significantly better outcome than the conventional 'amplified' group (HER2 ratio >2.2) but a significantly worse outcome than groups with FISH ratios less than 1.5. CONCLUSION: Breast cancers with increased HER2 copy numbers (low level HER2 amplification), below the currently accepted positive threshold ratio of 2.2, showed a distinct, intermediate outcome when compared to HER2 unamplified tumors and tumors with HER2 ratios greater than 2.2. These findings suggest that a new cut point to determine HER2 positivity, at a ratio of 1.5 (well below the current recommended cut point of 2.2), should be evaluated.", journal = "Breast Cancer Res Treat", keywords = "Metafer MetaCyte Metafer-PV", number = "3", pages = "453-9", title = "New cutpoints to identify increased HER2 copy number: analysis of a large, population-based cohort with long-term follow-up", url = "http://dx.doi.org/10.1007/s10549-007-9887-y", volume = "112", year = "2008", } @article{00258, author = "C. Schunck and T. Johannes and D. Varga and T. L{\"o}rch and A. Plesch", journal = "Cytogenet Genome Res", keywords = "Metafer MSearch DCScore CometScan MicroNuclei", pages = "383- 389", title = "New developments in automated cytogenetic imaging: unattended scoring of dicentric chromosomes, micronuclei, single cell electrophoresis, and fluorescence signals.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15162069", volume = "104", year = "2004", } @article{00093, author = "C. Lange and T. Liehr and M. Goen and E. Gebhart and B. Fleckenstein and A. Ensser", journal = "Genomics", pages = "340- 350", title = "New Eukaryotic Semaphorins with Close Homology to Semaphorins of DNA Viruses", volume = "51", year = "1998", } @article{00029, author = "T. Haferlach and M. Winkemann and L. Ramm-Pettersen and M. Meeder and R. Schoch and K. Weber-Matthiesen and B. Schlegelberger and C. Schoch and W.-D. Ludwig and W. Hiddemann and H. L{\"o}ffler", journal = "British Journal of Haematology", keywords = "Isis", pages = "452- 459", title = "New insights into the biology of Philadelphia-chromosome-positive acute lymphoblastic leukemia using a combination of May-Gr{\"u}nwald-Giemsa staining and fluorescence in situ hybridization at the single cell level", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9375772{\&}dopt=Abstract", volume = "99", year = "1997", } @article{00268, author = "A. Weise and H. Starke and K. Mrasek and U. Claussen and T. Liehr", journal = "Cytogenetic and Genomic Research", keywords = "Isis mBAND", pages = "217- 222", title = "New insights into the evolution of chromosome 1.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15545733", volume = "108", year = "2005", } @article{00324, author = "G.B. C{\^o}t{\'e}", abstract = "Automated fluorescent in situ hybridization scanners are more rapid and accurate than people and are becoming more popular. However, the methods used by these machines to score and interpret fluorescent in situ hybridization signals in nuclei are still those used by human observers. A new approach is presented to make the software classify the fluorescent patterns in additional relevant categories, thus avoiding the rejection of relevant information and consequent bias. The statistical interpretation of the fluorescent pattern distributions is carried out with a maximum likelihood estimation of the most likely proportions of various cell lines in the sample, and thus determines the diagnosis and the level of mosaicism in a single step. This approach is faster and more accurate than those used by human observers. It requires the scanning of fewer nuclei, less efforts for validation, and it makes the interpretation of results much simpler.", journal = "Diagn Mol Pathol", keywords = "Metafer MetaCyte", pages = "119- 124", title = "Nuclear FISH. Automation, analysis, and interpretation.", url = "http://www.ncbi.nlm.nih.gov/pubmed/19430291?ordinalpos=1{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDoc", volume = "18", year = "2009", } @article{00115, author = "T. Liehr and U. Claussen and E. Gebhart", journal = "Biomolecular Engineering", pages = "65- 69", title = "Nucleus extration from single mounted tissue sections", volume = "15", year = "1999", } @article{00003, author = "K. Weber-Matthiesen and J. Deerberg and M. Poetsch and W. Grote and B. Schlegelberger", journal = "Blood", keywords = "Isis", pages = "1464- 1468", title = "Numerical chromosome aberrations are present within the CD30+ Hodgkin and Reed-Sternberg cells in 100% of analyzed cases of Hodgkin's disease", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=7632954{\&}dopt=Abstract", volume = "86", year = "1995", } @article{00103, author = "V. Jay and J. Squire and J. Bayant and A.M. Alkhani and J.T. Rutka and M. Zielenska", journal = "Pathology", keywords = "Isis CGH", pages = "337- 344", title = "Oncogene Amplification in Medulloblastoma: Analysis of a Case by Comparative Genomic Hybridization and Fluorescence in situ Hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10643003{\&}dopt=Abstract", volume = "31", year = "1999", } @article{00037, author = "W. El-Rifai and M.L. Larramendy and A.M. Bj{\"o}rkqvist and S. Hemmer and S. Knuutila", journal = "Laboratory Investigation", keywords = "Isis CGH", pages = "699- 700", title = "Optimation of Comparative Genomic Hybridization Using Fluorochrome Conjugated to dCTP and dUTP", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9426409{\&}dopt=Abstract", volume = "77", year = "1997", } @article{00123, author = "J. Yan and E. Guilbault and J. Mass{\'e} and M. Bronsard and P. DeGrandpr{\'e} and J.-C. Forest and R. Drouin", journal = "Clinical Genetics", keywords = "Isis", pages = "309- 318", title = "Optimization of the fluorescence in situ hybridization (FISH) technique for high detection efficiency of very small proportions of target interphase nuclei", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11076056{\&}dopt=Abstract", volume = "58", year = "2000", } @article{00081, author = "E. Wolff and S. Girod and T. Liehr and U. Vorderw{\"u}lbecke and J. Ries and H. Steiniger and E. Gebhart", journal = "Oral Oncol.", keywords = "Isis CGH", pages = "186- 190", title = "Oral squamous cell carcinoma are characterized by a rather uniform pattern of genomic imbalaces detected by comparative genomic hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9692052{\&}dopt=Abstract", volume = "34", year = "1998", } @article{00018, author = "N. Arnold and L. H{\"a}gele and L. Walz and W. Schempp and J. Pfisterer and T. Bauknecht and M. Kiechle", journal = "Genes, Chromosomes {\&} Cancer", keywords = "Isis CGH", pages = "46- 54", title = "Overpresentation of 3q and 8q material and loss of 18q material are the currrent findings in the advanced human ovarian cancer", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9162197{\&}dopt=Abstract", volume = "16", year = "1996", } @article{Krueger2012, author = "Christel Krueger and Michelle R. King and Felix Krueger and Miguel R. Branco and Cameron S. Osborne and Kathy K. Niakan and Michael J. Higgins and Wolf Reik", abstract = "Although somatic homologous pairing is common in Drosophila it is not generally observed in mammalian cells. However, a number of regions have recently been shown to come into close proximity with their homologous allele, and it has been proposed that pairing might be involved in the establishment or maintenance of monoallelic expression. Here, we investigate the pairing properties of various imprinted and non-imprinted regions in mouse tissues and ES cells. We find by allele-specific 4C-Seq and DNA FISH that the Kcnq1 imprinted region displays frequent pairing but that this is not dependent on monoallelic expression. We demonstrate that pairing involves larger chromosomal regions and that the two chromosome territories come close together. Frequent pairing is not associated with imprinted status or DNA repair, but is influenced by chromosomal location and transcription. We propose that homologous pairing is not exclusive to specialised regions or specific functional events, and speculate that it provides the cell with the opportunity of trans-allelic effects on gene regulation.", journal = "PLoS One", keywords = "Alleles; Animals; Chromosomes, Mammalian, genetics; Embryonic Stem Cells; Gene Expression Regulation; Genomic Imprinting; In Situ Hybridization, Fluorescence; KCNQ1 Potassium Channel, genetics; Mice, genetics; MetaCyte; Metafer", number = "7", pages = "e38983", title = "Pairing of homologous regions in the mouse genome is associated with transcription but not imprinting status.", url = "http://dx.doi.org/10.1371/journal.pone.0038983", volume = "7", year = "2012", } @article{00206, author = "A. Nietzel and B. Albrecht and H. Starke and A. Heller and G. Gillessen-Kaesbach and U. Claussen and T. Liehr", journal = "J Med Genet", keywords = "Isis mBAND", pages = "0- 0", title = "Partial hexasomy 15pter-->15q13 including SNRPN and D15S10: first molecular cytogenetically proven case report.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12624157{\&}dopt=Abstract", volume = "40", year = "2003", } @article{00160, author = "A. Dufke and C. Walczak and T. Liehr and H. Starke and V. Trifonov and N. Rubtsov and M. Sch{\"o}ning and H. Enders and T. Eggermann", journal = "European Journal of Human Genetics", pages = "572- 576", title = "Partial tetrasomy 12pter-12p12.3 in a girl with Pallister-Killian syndrome: extraodinary finding of an analphoid, inverted duplicated marker", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11528501{\&}dopt=Abstract", volume = "9", year = "2001", } @article{00210, author = "M. Prakash Hande and T.V. Azizova and C.R. Geard and L.E. Burak and C.R. Mitchell and V.F. Khokhryakov and E.K. Vasilenko and D.J. Brenner", journal = "Am. J. Hum. Genet.", keywords = "Isis mBAND mFISH", pages = "1162- 1170", title = "Past exposure to densely ionizing radiation leaves a unique permanent signature in the genome", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12679897{\&}dopt=Abstract", volume = "72", year = "2003", } @article{00198, author = "K. Rothkamm and I. Kr{\"u}ger and L.H. Thompson and M. L{\"o}brich", journal = "Mol Cel Biol", keywords = "Isis", pages = "5706- 5715", title = "Pathways of DNA double-strand break repair during the mammalian cell cycle", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12897142{\&}dopt=Abstract", volume = "23", year = "2003", } @article{Magerl2001, author = "M. Magerl and D. J. Tobin and S. M{\"u}ller-R{\"o}ver and E. Hagen and G. Lindner and I. A. McKay and R. Paus", abstract = "In this study, we have correlated cutaneous apoptosis and proliferation in neonatal mice during hair follicle morphogenesis. We have applied a novel triple- staining technique that uses Ki67 immunoreactivity as a marker of proliferation as well as TUNEL and Hoechst 33342 staining as apoptosis markers. We have also assessed the immunoreactivity of interleukin-1 beta-converting enzyme, caspase 1, a key enzyme in the execution of apoptosis, and of P-cadherin, which has been suggested as a key adhesion receptor in segregating proliferating keratinocytes. The TUNEL data were systematically compared with high resolution light microscopy and transmission electron microscopy data. Virtually all keratinocytes of the developing hair bud were strongly Ki67(+), suggesting that the hair bud is not an epidermal invagination but primarily the product of localized keratinocyte proliferation. As hair follicle development advanced, three distinct foci of proliferation became apparent: the distal outer root sheath around the hair canal, the mid outer root sheath, and the proximal hair matrix. Of these proliferating hair follicle keratinocytes only defined subsets expressed P-cadherin. TUNEL(+) cells in the hair follicle were not found before stage 5 of murine hair follicle morphogenesis. During the early stages of hair follicle development, interleukin-1 beta-converting enzyme immunoreactivity was present on all keratinocytes, but virtually disappeared from the proximal hair follicle epithelium later on. High resolution light microscopy/transmission electron microscopy revealed scattered and clustered apoptotic keratinocytes in all epithelial hair follicle compartments throughout hair follicle development, including its earliest stages. This highlights striking differences in the demarcation of apoptotic hair follicle keratinocytes between the TUNEL technique and high resolution light microscopy/transmission electron microscopy and suggests a role for apoptosis in sculpting the hair follicle even during early hair follicle development.", journal = "J Invest Dermatol", keywords = "Isis", month = "Jun", number = "6", pages = "947--955", title = "Patterns of proliferation and apoptosis during murine hair follicle morphogenesis.", url = "http://dx.doi.org/10.1046/j.0022-202x.2001.01368.x", volume = "116", year = "2001", } @article{Ahmed2012, author = "Emad A. Ahmed and Diane Agay and Gerrit Schrock and Michel Drouet and Viktor Meineke and Harry Scherthan", abstract = "Exposure to high doses of ionizing radiation (IR) can lead to localized radiation injury of the skin and exposed cells suffer dsDNA breaks that may elicit cell death or stochastic changes. Little is known about the DNA damage response after high-dose exposure of the skin. Here, we investigate the cellular and DNA damage response in acutely irradiated minipig skin.IR-induced DNA damage, repair and cellular survival were studied in 15 cm(2) of minipig skin exposed in vivo to ~50 Co-60 {\~a} rays. Skin biopsies of control and 4 h up to 96 days post exposure were investigated for radiation-induced foci (RIF) formation using {\~a}-H2AX, 53BP1, and active ATM-p immunofluorescence. High-dose IR induced massive {\~a}-H2AX phosphorylation and high 53BP1 RIF numbers 4 h, 20 h after IR. As time progressed RIF numbers dropped to a low of 3-fold elevated at all subsequent time points. Replicating basal cells (Ki67+) were reduced 3 days post IR followed by increased proliferation and recovery of epidermal cellularity after 28 days.Acute high dose irradiation of minipig epidermis impaired stem cell replication and induced elevated apoptosis from 3 days onward. DNA repair cleared the high numbers of DBSs in skin cells, while RIFs that persisted in ", journal = "PLoS One", keywords = "Isis", number = "6", pages = "e39521", title = "Persistent DNA damage after high dose in vivo gamma exposure of minipig skin.", url = "http://dx.doi.org/10.1371/journal.pone.0039521", volume = "7", year = "2012", } @article{Kaplan2010, author = "Henry G Kaplan and Judith A Malmgren and Mary Atwood and Lynn C Goldstein", abstract = "Human epidermal growth factor receptor 2 (HER2)/neu, topoisomerase II alpha (TOP2A), and polysomy 17 may predict tumor responsiveness to doxorubicin (DOX) therapy.We identified neoadjuvant DOX/cyclophosphamide treated breast cancer patients in our registry from 1997 to 2008 with sufficient tissue for testing (n = 34). Fluorescence in situ hybridization (FISH) testing was done on deparaffinized tissue sections pretreated using vendor's standard protocol modification, and incubated with US Food and Drug Administration approved Abbott Diagnostics Vysis PathVysion™ probe set, including Spectrum-Green-conjugated probe to ?-satellite DNA located at the centromere of chromosome 17 (17p11.1-q11.1) and a Spectrum-Orange-conjugated probe to the TOP2A gene. Morphometric analysis was performed using a MetaSystems image analysis system. Manual counting was performed on all samples in which autofluorescence and/or artifact prevented the counting of sufficient numbers of cells. A ratio >2.0 was considered positive for TOP2A amplification. Polysomy 17 (PS17) presence was defined as signals of ?2.5. Outcomes were pathological complete response (pCR), partial response (PR), and nonresponse (NR).Of 34 patients tested, one was TOP2A amplified (hormone receptor negative/HER2 negative, partial responder). The subset of TOP2A nonamplified, HER2 negative, and PS17 absent (n = 23) patients had treatment response: pCR = 2 (9\%), PR = 14 (61\%), and NR = 7 (30\%). Including the two PS17 present and HER2-positive patients (n = 33), 76\% of TOP2A nonamplified patients had pCR or PR.We observed substantial treatment response in patients lacking three postulated predictors that would be difficult to attribute to cyclophosphamide alone. Patients who are HER2 negative and lack TOP2A amplification and PS17 should not be excluded from receiving DOX-containing regimens.", journal = "Cancer Manag Res", keywords = "Her2 Metafer MetaCyte", pages = "213--218", title = "Positive response to neoadjuvant cyclophosphamide and doxorubicin in topoisomerase II nonamplified/HER2/neu negative/polysomy 17 absent breast cancer patients.", url = "http://dx.doi.org/10.2147/CMR.S12849", volume = "2", year = "2010", } @article{00101, author = "M. Valtavaara and C. Szpirer and J. Szpirer and R. Myllyl{\"a}", journal = "Journal of Biological Chemistry", pages = "12881- 12886", title = "Primary Structure, Tissue Distribution, and Chromosomal Localization of a Novel Isoform of Lysyl Hydroxylase (Lysyl Hydroxylase 3)*", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9865788{\&}dopt=Abstract", volume = "273", year = "1998", } @article{00143, author = "P.M. De Angelis and T. Stokke and M. Beigi and O. Mj{\aa}land and O.P.F. Clausen", journal = "Int J Colorectal Dis", keywords = "Isis CGH", pages = "38- 45", title = "Prognostic significance of recurrent chromosomal aberrations detected by comparative genomic hybridization in sporadic colorectal cancer.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=11317696{\&}query_hl=1{\&}itool=pubmed_docsum", volume = "16", year = "2001", } @article{00271, author = "Z. Zemanova and K. Michalova and L. Sindelarova and P. Smisek and J. Brezinova and S. Ransdorfova and V. Vavra and A. Dohnalova and J. Stary", journal = "Leukemia Research", keywords = "Isis mFISH", pages = "273- 281", title = "Prognostic value of structural chromosomal rearrangements and small cell clones with high hyperdiploidy in children with acute lymphoblastic leukemia.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15661262", volume = "29", year = "2005", } @article{00229, author = "E. Zamorano-Ponce and J. Fern{\'a}ndez and G. Vargas and P. Rivera and M.A. Carballo", journal = "Toxicol. Lett.", keywords = "CometImager", pages = "85- 90", title = "Protective activity of cedron (Aloysia triphylla) infusion over genetic damage induced by cisplatin evaluated by the Comet assay technique", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15294350{\&}query_hl=1", volume = "152", year = "2004", } @article{00194, author = "A. Schaeferhenrich and W. Sendt and J. Scheele and A. Kuechler and T. Liehr and U. Claussen and A. Rapp and K.-O. Greulich and B.L. Pool-Zobel", journal = "Food and Chemical Toxicology", keywords = "Ikaros Isis mFISH", pages = "655- 664", title = "Putative colon cancer risk factors damage global DNS and TP53 in primary human colon cells isolated from surgical samples", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12659718{\&}dopt=Abstract", volume = "41", year = "2003", } @article{00222, author = "S. Perner and S. Br{\"u}derlein and C. Hasel and I. Waibel and A. Holdenried and N. Ciloglu and H. Chopurian and K.V. Nielsen and A. Plesch and J. H{\"o}gel and P. M{\"o}ller", journal = "Am J Pathol", keywords = "Isis Telomere", pages = "1751- 1756", title = "Quantifying telomere lengths of human individual chromosome arms by centromere-calibrated fluorescence in-situ hybridization and digital imaging", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=14578175{\&}dopt=Abstract", volume = "163", year = "2003", } @article{00129, author = "G. M{\'e}hes and T. L{\"o}rch and P.F. Ambros", journal = "Cytometry", keywords = "RCDetect", pages = "357- 362", title = "Quantitative analysis of disseminated tumor cells in the bone marrow by automated fluorescence image analysis", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11135289{\&}dopt=Abstract", volume = "42", year = "2000", } @article{Andres2010, author = "Christine Andres and Sonja Meyer and Olayinka A Dina and Jon D Levine and Tim Hucho", abstract = "Dorsal root ganglia (DRG)-neurons are commonly characterized immunocytochemically. Cells are mostly grouped by the experimenter's eye as "marker-positive" and "marker-negative" according to their immunofluorescence intensity. Classification criteria remain largely undefined. Overcoming this shortfall, we established a quantitative automated microscopy (QuAM) for a defined and multiparametric analysis of adherent heterogeneous primary neurons on a single cell base.The growth factors NGF, GDNF and EGF activate the MAP-kinase Erk1/2 via receptor tyrosine kinase signalling. NGF and GDNF are established factors in regeneration and sensitization of nociceptive neurons. If also the tissue regenerating growth factor, EGF, influences nociceptors is so far unknown. We asked, if EGF can act on nociceptors, and if QuAM can elucidate differences between NGF, GDNF and EGF induced Erk1/2 activation kinetics. Finally, we evaluated, if the investigation of one signalling component allows prediction of the behavioral response to a reagent not tested on nociceptors such as EGF.We established a software-based neuron identification, described quantitatively DRG-neuron heterogeneity and correlated measured sample sizes and corresponding assay sensitivity. Analysing more than 70,000 individual neurons we defined neuronal subgroups based on differential Erk1/2 activation status in sensory neurons. Baseline activity levels varied strongly already in untreated neurons. NGF and GDNF subgroup responsiveness correlated with their subgroup specificity on IB4(+)- and IB4(-)-neurons, respectively. We confirmed expression of EGF-receptors in all sensory neurons. EGF treatment induced STAT3 translocation into the nucleus. Nevertheless, we could not detect any EGF induced Erk1/2 phosphorylation. Accordingly, intradermal injection of EGF resulted in a fundamentally different outcome than NGF/GDNF. EGF did not induce mechanical hyperalgesia, but blocked PGE2-induced sensitization.QuAM is a suitable if not necessary tool to analyze activation of endogenous signalling in heterogeneous cultures. NGF, GDNF and EGF stimulation of DRG-neurons shows differential Erk1/2 activation responses and a corresponding differential behavioral phenotype. Thus, in addition to expression-markers also signalling-activity can be taken for functional subgroup differentiation and as predictor of behavioral outcome. The anti-nociceptive function of EGF is an intriguing result in the context of tissue damage but also for understanding pain resulting from EGF-receptor block during cancer therapy.", journal = "Mol Pain", keywords = "Animals; Cells; Epidermal Growth Factor, pharmacology; Ganglia, Spinal; Glial Cell Line-Derived Neurotrophic Factor, pharmacology; Intercellular Signaling Peptides and Proteins, pharmacology; Male; Microscopy, methods; Nerve Growth Factor, MetaCyte", pages = "98", title = "Quantitative automated microscopy (QuAM) elucidates growth factor specific signalling in pain sensitization.", url = "http://dx.doi.org/10.1186/1744-8069-6-98", volume = "6", year = "2010", } @article{00277, author = "M. Bollmann and H. Heller and A. B{\'a}nkfalvi and H. Griefingholt and R. Bollmann", journal = "BJU International", keywords = "Metafer MetaCyte", pages = "1219- 1225", title = "Quantitative molecular urinary cytology by fluorescence in situ hybridization: a tool for tailoring surveillance of patients with superficial bladder cancer?", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15892805{\&}query_hl=1", volume = "95", year = "2005", } @article{00280, author = "D. Varga and I. Michel and B. Patino-Garcia and T. Paiss and W. Vogel and C. Maier", journal = "Cytogenet. Genome Res.", keywords = "Metafer MSearch MicroNuclei", pages = "41- 45", title = "Radiosensitivity detected by the micronucleus test is not generally increased in sporadic prostate cancer patients.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search{\&}DB=PubMed", volume = "111", year = "2005", } @article{00182, author = "C. Popovici and C. Basset and F. Bertucci and B. Orsetti and J. Ad{\'e}laide and M.-J. Mozziconacci and N. Conte and A. Murati and C. Ginestier and E. Charafe-Jauffret and S.P. Ethier and M. Lafage-Pochitalof and C. Theillet and D. Birnbaum and M. Chaffanet", journal = "Genes Chromosomes Cancer", keywords = "Isis mFISH mBAND", pages = "204- 218", title = "Reciprocal translocations in breast tumor cell lines: cloning of a t(3;20) that targets the FHIT gene", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12353263{\&}dopt=Abstract", volume = "35", year = "2002", } @article{00148, author = "K. Mrasek and A. Heller and N. Rubtsov and V. Trifonov and H. Starke and M. Rocchi and U. Claussen and T. Liehr", journal = "Cytogenet. Cell Genet.", keywords = "Isis mBAND mFISH", pages = "242- 248", title = "Reconstruction of the female Gorilla gorilla karyotype using 25-color FISH and multicolor banding (MCB)", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11528119{\&}dopt=Abstract", volume = "93", year = "2001", } @article{00008, author = "E. Gebhart and P. Hofbeck and Y. Hofman and R. Lerch and G. Schmitt and T. Liehr", journal = "Applied Cytogenetics", keywords = "Isis", pages = "146- 148", title = "Recovering of Archival Tumor Cytogenetic Slides for Two-Color-Interphase FISH", volume = "22", year = "1996", } @article{00169, author = "M. Fojtov{\'a} and J. Fulne{\&}#269;kov{\'a} and J. Fajkus and A. Kova{\&}#345;{\'i}k", journal = "J Exp Bot", keywords = "Isis", pages = "2151- 2158", title = "Recovery of tobacco cells from cadmium stress is accompanied by DNA repair and increased telomerase activity.", url = "http://jxb.oxfordjournals.org/cgi/content/full/53/378/2151", volume = "53", year = "2002", } @article{00036, author = "A.-M. Bj{\"o}rkqvist and L. Tammilehto and S. Anttila and K. Mattson and S. Knuutila", journal = "Br J Cancer", keywords = "Isis CGH", pages = "523- 527", title = "Recurrent DNA copy number changes in lq, 4q9 6q9 9p, 13q9 14q and 22q detected by comparative genomic hybridization in malignant mesothelioma", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9052404{\&}dopt=Abstract", volume = "75", year = "1997", } @article{00035, author = "G. Armengol and M. Tarkkanen and M. Virolainen and A. Forus and J. Valle and T. B{\"o}hling and S. Asko Seljavaara and C. Blomqvist and I. Elomaa and E. Karaharju and A.H. Kivioja and M.A. Siimes and E. Tukiainen and M.R. Caballin and O. Myklebost and S. Knuutila", journal = "Br J Cancer", keywords = "Isis CGH", pages = "1403- 1409", title = "Recurrent gains of lq 8 and 12 in the Ewing family of tumours by comparative genomic hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9166930{\&}dopt=Abstract", volume = "75", year = "1997", } @article{Varela2012, author = "Christine Varela and J{\'e}r{\^o}me Alexandre Denis and J{\'e}r{\^o}me Polentes and Maxime Feyeux and Sophie Aubert and Benoite Champon and Genevi{\`e}ve Pi{\'e}tu and Marc Peschanski and Nathalie Lefort", abstract = "Human pluripotent stem cells offer a limitless source of cells for regenerative medicine. Neural derivatives of human embryonic stem cells (hESCs) are currently being used for cell therapy in 3 clinical trials. However, hESCs are prone to genomic instability, which could limit their clinical utility. Here, we report that neural differentiation of hESCs systematically produced a neural stem cell population that could be propagated for more than 50 passages without entering senescence; this was true for all 6 hESC lines tested. The apparent spontaneous loss of evolution toward normal senescence of somatic cells was associated with a jumping translocation of chromosome 1q. This chromosomal defect has previously been associated with hematologic malignancies and pediatric brain tumors with poor clinical outcome. Neural stem cells carrying the 1q defect implanted into the brains of rats failed to integrate and expand, whereas normal cells engrafted. Our results call for additional quality controls to be implemented to ensure genomic integrity not only of undifferentiated pluripotent stem cells, but also of hESC derivatives that form cell therapy end products, particularly neural lines.", journal = "J Clin Invest", keywords = "Isis Ikaros mBAND mFISH", month = "Feb", number = "2", pages = "569--574", title = "Recurrent genomic instability of chromosome 1q in neural derivatives of human embryonic stem cells.", url = "http://dx.doi.org/10.1172/JCI46268", volume = "122", year = "2012", } @article{Lange2010, author = "Kathrin Lange and Dorothea Gadzicki and Brigitte Schlegelberger and Gudrun G{\"o}hring", abstract = "Chromosome aberrations are important prognostic markers in multiple myeloma (MM), but their identification may be hampered by complexity of the karyotypes. Using multicolor fluorescence in situ hybridization (mFISH), we found cryptic aberrations in 7 of 10 patients with a complex karyotype. Moreover, in addition to typical aberrations involving 1q, 13q, 14q and 17p and structural aberrations in chromosomes 1, 6, 9 and 19, (iso)dicentric chromosomes and whole-arm translocations were detected. These chromosome aberrations were generated by breaks in heterochromatic regions indicating an increased breakage of these regions, which may predispose to the generation of chromosome aberrations in multiple myeloma.", journal = "Leuk Res", keywords = "Adult; Aged; Aged, 80 and over; Chromosome Aberrations; Chromosomes, Human, genetics; Female; Humans; In Situ Hybridization, Fluorescence; Karyotyping; Male; Middle Aged; Multiple Myeloma; Isis mFISH Ikaros", month = "Aug", number = "8", pages = "1002--1006", title = "Recurrent involvement of heterochromatic regions in multiple myeloma-a multicolor FISH study.", url = "http://dx.doi.org/10.1016/j.leukres.2009.10.027", volume = "34", year = "2010", } @article{00023, author = "L. Messiaen and B.P. Leroy and S. De Bie and K. De Pauw and N. Van Roy and F. Speleman and G. Van Camp and A. De Paepe", journal = "European Journal of Human Genetics", pages = "34- 38", title = "Refined Genetic and Physical Mapping of BPES Type II", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8800926{\&}dopt=Abstract", volume = "4", year = "1996", } @article{00141, author = "T. Liehr and L.T. Reiter and J.R. Lupski and T. Murakami and U. Claussen and B. Rautenstrauss", journal = "Mammalian Genome", keywords = "Isis", pages = "326- 328", title = "Regional localization of 10 mariner transposon-like ESTs by means of FISH - evicence for a correlation with fragile sites", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11309667{\&}dopt=Abstract", volume = "12", year = "2001", } @article{00030, author = "F. Pr{\"o}ls and T. Liehr and B. Loser and B. Rautenstrauss", journal = "Mammalian Genome", keywords = "Isis", pages = "94- 95", title = "Regional localization of Flic 1, a calcyclin/S100A6-like gene, to rat Chromosome 7q22-31 by means of FISH", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9434963{\&}dopt=Abstract", volume = "9", year = "1997", } @article{00014, author = "F. Pr{\"o}ls and T. Liehr and M. Marx and B. Rautenstrauss", journal = "Mammalian Report", keywords = "Isis", pages = "867- 868", title = "Regional localization of rat microvascular endothelial differentiation gene 1 (Mdg1) to Chromosome 6q16-23 by means of FISH", volume = "7", year = "1996", } @article{Kraeft2004, author = "Stine-Kathrein Kraeft and Andras Ladanyi and Kevin Galiger and Anna Herlitz and Andrew C. Sher and Danielle E. Bergsrud and Gaelle Even and Stephanie Brunelle and Lyndsay Harris and Ravi Salgia and Tom Dahl and John Kesterson and Lan Bo Chen", abstract = "The purpose of this study was to assess the feasibility of using rare event imaging system (REIS)-assisted analysis to detect occult tumor cells (OTCs) in peripheral blood (PB). The study also sought to determine whether REIS-assisted OTC detection presents a clinically viable alternative to manual microscopic detection to establish the true significance of OTC from solid epithelial tumors.We recently demonstrated proof of concept using a fluorescence-based automated microscope system, REIS, for OTC detection from the PB. For this study, the prototype of the system was adopted for high-throughput and high-content cellular analysis.The performance of the improved REIS was examined using normal blood (n = 10), normal blood added to cancer cells (n = 20), and blood samples obtained from cancer patients (n = 80). Data from the screening of 80 clinical slides from breast and lung cancer patients, by manual microscopy and by the REIS, revealed that as many as 14 of 35 positive slides (40\%) were missed by manual screening but positively identified by REIS. In addition, REIS-assisted scanning reliably and reproducibly quantified the total number of cells analyzed in the assay and categorized positive cells based on their marker expression profile.REIS-assisted analysis provides excellent sensitivity and reproducibility for OTC detection. This approach may enable an improved method for screening of PB samples and for obtaining novel information about disease staging and about risk evaluation in cancer patients.", journal = "Clin Cancer Res", keywords = "Metafer RCDetect", month = "May", number = "9", pages = "3020--3028", title = "Reliable and sensitive identification of occult tumor cells using the improved rare event imaging system.", volume = "10", year = "2004", } @article{00212, author = "A. Kuechler and M. Dreidax and S.U. Pigorsch and T. Liehr and U. Claussen and T.G. Wendt and J. Dunst", journal = "Strahlenther Onkol", keywords = "Isis mFISH", pages = "493- 498", title = "Residual chromosomal damage after radiochemotherapy with and without Amifostine detected by 24-color FISH", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12835887{\&}dopt=Abstract", volume = "7", year = "2003", } @article{Becker2009, author = "Daniela Becker and Thilo Els{\"a}sser and Torsten Tonn and Erhard Seifried and Marco Durante and Sylvia Ritter and Claudia Fournier", abstract = "To characterise the radiation response of human hematopoietic stem and progenitor cells (HSPC) with respect to X and carbon ion irradiation.HSPC from peripheral blood of healthy donors treated with granulocyte-colony stimulating factor (G-CSF) were enriched for the transmembrane glycoprotein CD34 (cluster of differentiation) and irradiated with X rays or carbon ions (29 keV/microm monoenergetic beam and 60-85 keV/microm spread-out Bragg peak), mimicking radiotherapy conditions. Apoptotic cell death, cell cycle progression and the frequency of chromosomal aberrations were determined.After radiation exposure no inhibition in the progression of the cell cycle was detected. However, an enhanced frequency of apoptotic cells and an increase in aberrant cells were observed, both effects being more pronounced for carbon ions than X rays, resulting in a relative biological effectiveness (RBE) of 1.4-1.7. The fraction of complex-type aberrations was higher following carbon ion exposure.RBE values of carbon ions are low, as expected for radiosensitive cells. The observed frequencies of apoptotic cells and chromosome aberrations in HSPC are similar to those reported for human peripheral blood lymphocytes suggesting that at least with respect to apoptosis and chromosomal aberrations mature lymphocytes reflect the respective radiation responses of their proliferating progenitors.", journal = "Int J Radiat Biol", keywords = "Apoptosis; Isis; mFISH", month = "Nov", number = "11", pages = "1051--1059", title = "Response of human hematopoietic stem and progenitor cells to energetic carbon ions.", url = "http://dx.doi.org/10.3109/09553000903232850", volume = "85", year = "2009", } @article{00019, author = "J. Szymanska and N. Mandahl and F. Mertens and M. Tarkkanen and E. Karaharju and S. Knuutila", journal = "Genes Chromosomes Cancer", keywords = "Isis CGH", pages = "31- 34", title = "Ring chromosomes in parosteal osteosarcoma contain sequences from 12q13-15. A combined cytogenetic and comparative genomic hybridization study", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9162194{\&}dopt=Abstract", volume = "16", year = "1996", } @article{00260, author = "M. Tenopoulou and P.-T. Doulias and A. Barbouti and U. Brunk and D. Galaris", journal = "Biochem J", keywords = "CometImager", pages = "703- 710", title = "Role of compartmentalized redox-active iron in hydrogen peroxide-induced DNA damage and apoptosis.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=15579135{\&}query_hl=12{\&}itool=pubmed_docsum", volume = "387", year = "2005", } @article{00199, author = "J.B. Johnston and A.F. Kabore and J. Strutinsky and X. Hu and J.T. Paul and D.M. Kropp and B. Kuschak and A. Begleiter and S.P. Gibson", journal = "Oncogene", keywords = "Isis", pages = "8356- 8369", title = "Role of the TRAIL/APO2-L death receptors in chloranbucil- and fludarabine-induced apoptosis in chronic lymphocytic leukemia", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=14614459", volume = "22", year = "2003", } @article{00196, author = "N. Shouman and B. Pabst and M. Arslan-Kirchner and A. Eckardt and R. Sch{\"o}nweiler and M. Ptok and Y. Mehraein and J. Schmidtke and K. Miller", journal = "Int. J. Oral and Maxillofacial Surgery", keywords = "Isis", pages = "198- 200", title = "Search for deleteion 22q11.2 in interphase nuclei of buccal mucosa of patients ascertained by isolated cleft palate: a new diagnostic approach", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12729782{\&}dopt=Abstract", volume = "32", year = "2003", } @article{00016, author = "Y. Zhang and M. Poetsch and K. Weber-Matthiesen and K. Rhode and M. Winkemann and T. Haferlach and W. Gassmann and W.-D. Ludwig and W. Grote and H. L{\"o}ffler and B. Schlegelberger", journal = "British Journal of Haematology", keywords = "Isis", pages = "673- 680", title = "Secondary acute leukaemias with 11q23 rearrangement: clinical, cytogenetic, FISH and FICTION studies", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8616034{\&}dopt=Abstract", volume = "92", year = "1996", } @article{00262, author = "C. Arce and D. Cortes-Padilla and D.G. Huntsman and M.A. Miller and A. Duennas-Gonzalez and A. Alvarado and V. P{\'e}rez and D. Gallardo-Rinc{\'o}n and F. Lara-Medina", journal = "World J Surg Oncol.", keywords = "Isis", pages = "35- 42", title = "Secretory carcinoma of the breast containing the ETV6-NTRK3 fusion gene in a male: case report and review of the literature", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15963235{\&}query_hl=3{\&}itool=pubmed_docsum", volume = "17", year = "2005", } @article{00048, author = "L. Fr{\"o}nicke and B.P. Chowdhary and H. Scherthan", journal = "Cytogenetics and Cell Genetics", pages = "223- 227", title = "Segmental homology among cattle (Bos taurus), Indian muntjac (Muntiacus muntjak vaginalis), and Chinese muntjac (M. reevesi) karyotypes", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9284921{\&}dopt=Abstract", volume = "77", year = "1997", } @article{00040, author = "M. Van Gele and N. Van Roy and A. Jauch and G. Laureys and Y. Benoit and V. Schelfhout and C.R. De Potter and P. Brock and A. Uyttebroeck and R. Sciot and E. Schuuring and R. Versteeg and F. Speleman", journal = "Eur J Cancer", keywords = "Isis CGH", pages = "1979- 1982", title = "Sensitive and Reliable Detection of Genomic Imbalances in Human Neuroblastomas using Comparative Genomic Hybridisation Analysis", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9516837{\&}dopt=Abstract", volume = "33", year = "1997", } @article{00060, author = "E.J.M. Speel and F.C.S. Ramaekers and A.H.N. Hopman", journal = "Journal of Histochemistry {\&} Cytochemistry", pages = "1439- 1446", title = "Sensitive Multicolor Fluorescence In Situ Hybridization Using Catalyzed Reporter Deposition (CARD) Amplification", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9313806{\&}dopt=Abstract", volume = "45", year = "1997", } @article{00313, author = "A. Kowalska and B. Brunner and E. Bozsaky and Q.-R. Chen and C. Stock and T. L{\"o}rch and J. Khan and P.F. Ambros", journal = "Cytogenet Genome Res", keywords = "Isis CGH Warp", pages = "1- 6", title = "Sequence based high resolution chromosomal CGH.", url = "http://www.ncbi.nlm.nih.gov/pubmed/18544918?ordinalpos=1{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", volume = "121", year = "2008", } @article{alpar10, author = "Don{\'a}t Alp{\'a}r and Gergely Nagy and Carsten Hohoff and B{\'e}la Kajt{\'a}r and Katalin Bartyik and Judit Hermesz and P{\'a}l J{\'a}ks{\'o} and Hajnalka Andrikovics and L{\'a}szl{\'o} Kereskai and L{\'a}szl{\'o} Pajor", abstract = "A 12-year-old male with pre-B-cell acute lymphoblastic leukemia with cryptic BCR/ABL rearrangement underwent sex-mismatched allogeneic bone marrow transplantation (allo-BMT). Contradictory results were provided by various chimerism analyses 3 months later. Y-chromosome-specific quantitative polymerase chain reaction and sex chromosome-specific interphase fluorescence in situ hybridization (i-FISH) showed complete donor chimerism. Analysis of autosomal short tandem repeats (A-STR), BCR/ABL i-FISH test, and X-STR haplotype indicated relapse. Metaphase-FISH and combined BCR/ABL and sex chromosome-specific i-FISH patterns revealed loss of the Y-chromosome and duplication of the X-chromosome in the host cells. Sex chromosome changes after allo-BMT can cause significant difficulties in chimerism analysis.", journal = "Pediatric Blood {\&} Cancer", keywords = "Metafer MetaCyte MSearch", month = "12/2010", number = "6", pages = "1239-1242", title = "Sex chromosome changes after sex-mismatched allogeneic bone marrow transplantation can mislead the chimerism analysis", url = "http://onlinelibrary.wiley.com/doi/10.1002/pbc.22617/abstract", volume = "6", year = "2010", } @article{00294, author = "S. Mayer and S. Br{\"u}derlein and S. Perner and I. Waibel and A. Holdenried and N. Ciloglu and C. Hasel and T. Mattfeldt and K.V. Nielsen and P. M{\"o}ller", journal = "Cytogenet. Genome Res.", keywords = "Isis Telomere", pages = "194- 201", title = "Sex-specific telomere length profiles and age-dependent erosion dynamics of individual chromosome arms in humans.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=16484772{\&}query_hl=1{\&}itool=pubmed_docsum", volume = "112", year = "2006", } @article{Horstmann2005, author = "M. Horstmann and M. Durante and C. Johannes and R. Pieper and G. Obe", abstract = "Chromosome aberration analysis in astronauts has been used to provide direct, biologically motivated estimates of equivalent doses and risk associated to cosmic radiation exposure during space flight. However, the past studies concentrated on measurements of dicentrics and translocations, while chromosome intrachanges (inversions) have never been measured in astronauts' samples. Recent data reported in the literature suggest that densely ionizing radiation can induce a large fraction of intrachanges, thus leading to the suspicion that interchanges grossly underestimate the cosmic radiation-induced cytogenetic damage in astronauts. We have analyzed peripheral blood lymphocytes from 11 astronauts involved in short- or long-term space flights in low-Earth orbit using high-resolution multicolor banding to assess the frequency of intrachromosomal exchanges in both pre- and post-flight samples. We did not detect any inversions in chromosome 5 from a total of 2800 cells in astronauts' blood. In addition, no complex type exchanges were found in a total of 3590 astronauts' lymphocytes analyzed by multifluor fluorescence in situ hybridisation. We conclude that, within the statistical power of this study, the analysis of interchanges for biological dosimetry in astronauts does not significantly underestimate the space radiation-induced cytogenetic damage, and complex-type exchanges or intrachanges have limited practical use for biodosimetry at very low doses.", journal = "Radiat Environ Biophys", keywords = "Isis mBAND", month = "Dec", number = "3", pages = "219--224", title = "Space radiation does not induce a significant increase of intrachromosomal exchanges in astronauts' lymphocytes.", url = "http://dx.doi.org/10.1007/s00411-005-0017-0", volume = "44", year = "2005", } @article{00011, author = "I.-D. Adler and J. Bishop and X. Lowe and T.E. Schmid and G. Schriever-Schwemm and W. Xu and A.J. Wyrobek", journal = "Mutation Research", keywords = "Isis", pages = "259- 268", title = "Spontaneous rates of sex chromosomal aneuploidies in sperm and offspring of mice: a validation of the detection of aneuploid sperm by fluorescence in situ hybridization", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9015144{\&}dopt=Abstract", volume = "372", year = "1996", } @article{00254, author = "M. Hausmann and C. Cremer and G. Linares-Cruz and T.C. Nebe and K. Peters and A. Plesch and J. Tham and M. Vetter and M. Werner", journal = "Cellular Oncology", keywords = "Metafer MetaCyte", pages = "119- 124", title = "Standardisation of FISH-procedures: summary of the second discussion workshop.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15371647", volume = "26", year = "2004", } @article{00282, author = "K. Swerts and P.F. Ambros and C. Brouzes and J.M.F. Navarro and N. Gross and D. Rampling and R. Schumacher-K. and A.R. Sementa and R. Ladenstein and K. Beiske", journal = "J. Histochem. Cytochem.", keywords = "Metafer RCDetect", pages = "1433- 1440", title = "Standardization of the immunocytochemical detection of neuroblastoma cells in bone marrow.", url = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed{\&}Cmd=ShowDetailView{\&}TermToSearch=15956022{\&}ordinalpos=15{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Re", volume = "53", year = "2005", } @article{00327, author = "A. Vaurijoux and G. Gruel and F. Pouzoulet and E. Gr{\'e}goire and C. Martin and S. Roch-Lef{\`e}vre and Pa. Voisin and Ph. Voisin and L. Roy", journal = "Radiation Research", keywords = "Metafer MSearch AutoCapt DCScore", pages = "541- 548", title = "Strategy for population triage based on dicentric analysis.", url = "http://www.ncbi.nlm.nih.gov/pubmed/19580489?ordinalpos=1{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDoc", volume = "171", year = "2009", } @article{Brezinová2007, author = "J Brezinov{\'a} and Z Zemanov{\'a} and S Ransdorfov{\'a} and L Pavlistov{\'a} and L Babick{\'a} and L Houskov{\'a} and J Melicherc{\'i}kov{\'a} and M Siskov{\'a} and J Cerm{\'a}k and K Michalov{\'a}", journal = "Cancer Genet Cytogenet", keywords = "Isis mBAND", number = "1", pages = "10-6", title = "Structural aberrations of chromosome 7 revealed by a combination of molecular cytogenetic techniques in myeloid malignancies", url = "http://dx.doi.org/10.1016/j.cancergencyto.2006.09.003", volume = "173", year = "2007", } @article{00135, author = "H. Tillmann and S. Stein and T. Liehr and K. Escherich", journal = "Gene", pages = "241- 251", title = "Structure and chromosomal localization of the human and mouse muscle fructose-1,6-biphosphatase genes", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10773464{\&}dopt=Abstract", volume = "247", year = "2000", } @article{00275, author = "U. Wick and E. Gebhart", journal = "Int J Mol Med", keywords = "Isis Telomere", pages = "463- 469", title = "Studies on the action of mitomycin C and bleomycin on telomere lengths of human lymphocyte chromosomes.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=16077956{\&}query_hl=5{\&}itool=pubmed_docsum", volume = "16", year = "2005", } @article{00211, author = "B. Christensen and S. Kolvraa and L. Lykke-Hansen and T. L{\"o}rch and D. Gohel and S. Smidt-Jensen and J. Bang and J. Philip", journal = "Fetal Diagn Ther", keywords = "Isis Metafer RCDetect", pages = "376- 384", title = "Studies on the isolation and identification of fetal nucleated red blood cells in the circulation of pregnant women before and after Chorion Villus sampling", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12913351{\&}dopt=Abstract", volume = "18", year = "2003", } @article{00144, author = "J. Nishio and H. Iwasaki and M. Ishiguro and Y. Ohjimi and S. Yo and T. Isayama and M. Naito and M. Kikuchi", journal = "Genes Chromosomes Cancer", keywords = "Isis CGH", pages = "305- 309", title = "Supernumerary ring chromosome in a Bednar tumor (pigmented dermatofibrosarcoma protuberans) is composed of interspersed sequences from chromosomes 17 and 22: a fluorescence in situ hybridization and comparative genomic hybridization analysis", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11170290{\&}dopt=Abstract", volume = "30", year = "2001", } @article{00088, author = "H. Iwasaki and Y. Ohjimi and M. Ishiguro and T. Isayama and C. Fujita and et al, Y. Kaneko", journal = "Virchows Arch", pages = "521- 528", title = "Supernumerary ring chromosomes and nuclear blebs in some low-grade malignant soft tissue tumours: atypical lipomatous tumours and dermatofibrosarcoma protuberans", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9672193{\&}dopt=Abstract", volume = "432", year = "1998", } @article{00250, author = "A.E. Carpenter and D.M. Sabatini", journal = "Nature Reviews - Genetics", keywords = "Metafer", pages = "11- 22", title = "Systematic genome-wide screens of gene function.", url = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed{\&}Cmd=ShowDetailView{\&}TermToSearch=14708012{\&}ordinalpos=7{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Res", volume = "5", year = "2004", } @article{Wang2009, author = "G Wang and A Auerbach and M Wei and N Dow and TS Barry and L Hodge and D Schaffer and LH Sobin and NS Aguilera", abstract = "Gastric extranodal marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue (MZL-MALT) is speculated to be immune mediated and is notable for responding to treatment by Helicobacter pylori eradication. However, the gastric MZL-MALT with t(11;18)(q21;q21) has been shown to be resistant to treatment by H. pylori eradication. We studied the molecular, immunohistochemical, and histological aspects of 48 cases of gastric MZL-MALT and used a reverse transcription real-time PCR assay to assess the presence of a t(11;18)(q21;q21) in formalin-fixed, paraffin-embedded tissue. Florescence in situ hybridization for t(11:18)(q21;q21) was used to confirm the real-time PCR results. Three distinct morphological subtypes were recognized: monocytoid, small lymphocytic, and plasmacytoid. Morphology, immunophenotype, and immunoglobulin heavy chain (IgH) gene rearrangement were correlated with the results of the t(11:18)(q21;q21) assay. Of the 48 analyzed cases, 15 (31%) were positive for t(11;18)(q21;q21) and 33 (69%) were monoclonal for IgH gene rearrangement. Of the 15, 13 (87%) cases with t(11;18)(q21;q21) translocation showed IgH gene rearrangement by PCR. Of the 33 t(11;18)(q21;q21)-negative cases tested, 20 cases (61%) showed IgH gene rearrangement. The 15 t(11;18)(q21;q21) translocation-positive cases had either monocytoid (12 of 15) or small lymphocytic morphology (3 of 15). Aberrant expression of CD43 was observed in 8 of 15 (53%) t(11;18)(q21;q21)-positive cases and 21 of 31 (68%) t(11;18)(q21;q21)-negative cases. Our data show that t(11;18)(q21;q21)-positive MZL-MALTs frequently show monocytoid morphology, less often small lymphocytic morphology, and not purely plasmacytoid morphology. Identification of a t(11;18)(q21;q21) by reverse transcription real-time PCR is highly specific for MZL-MALT and helps in the diagnosis of MZL-MALT. Studying the correlation between this translocation and morphological features may increase our understanding of the role of this translocation in the pathogenesis and the clinical behavior of gastric MZL-MALT.", journal = "Mod Pathol", keywords = "Metafer MetaCyte", number = "1", pages = "79-86", title = "t(11;18)(q21;q21) in extranodal marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue in stomach: a study of 48 cases", url = "http://dx.doi.org/10.1038/modpathol.2008.155", volume = "22", year = "2009", } @article{00157, author = "R. Huber and U. Kulka and Th. L{\"o}rch and H. Braselmann and D. Engert and M. Figel and M. Bauchinger", journal = "Mutation Research", keywords = "Metafer2", pages = "51- 57", title = "Technical Report: application of the Metafer2 fluorescence scanning system for the analysis of radiation-induced chromosome aberrations measured by FISH-chromosome painting", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11377243{\&}dopt=Abstract", volume = "492", year = "2001", } @article{00082, author = "R. Huber and Th. L{\"o}rch and U. Kulka and H. Braselmann and M. Bauchinger", journal = "Mutation Research", keywords = "Metafer", pages = "27- 32", title = "Technical report: automated classification of first and second cycle metaphases.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9804877{\&}dopt=Abstract", volume = "419", year = "1998", } @article{00264, author = "J.M. Watson and P. Bulankova and K. Riha and D.E. Shippen and B. Vyskot", journal = "Plant J", keywords = "Isis", pages = "662- 674", title = "Telomerase-independent cell survival in Arabidopsis thaliana.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=16115064{\&}query_hl=3{\&}itool=pubmed_DocSum", volume = "43", year = "2005", } @article{Muntoni2009, author = "Alessandra Muntoni and Axel A. Neumann and Mark Hills and Roger R. Reddel", abstract = "Alternative lengthening of telomeres (ALT) is a telomere length maintenance mechanism based on recombination, where telomeres use other telomeric DNA as a template for DNA synthesis. About 10\% of all human tumors depend on ALT for their continued growth, and understanding its molecular details is critically important for the development of cancer treatments that target this mechanism. We have previously shown that telomeres of ALT-positive human cells can become lengthened via inter-telomeric copying, i.e. by copying the telomere of another chromosome. The possibility that such telomeres could elongate by using other sources of telomeric DNA as copy templates has not been investigated previously. In this study, we have determined whether a telomere can become lengthened by copying its own sequences, without the need for using another telomere as a copy template. To test this, we transduced an ALT cell line with a telomere-targeting construct and obtained clones with a single tagged telomere. We showed that the telomere tag can be amplified without the involvement of other telomeres, indicating that telomere elongation can also occur by intra-telomeric DNA copying. This is the first direct evidence that the ALT mechanism involves more than one method of telomere elongation.", journal = "Hum Mol Genet", keywords = "Metafer MSearch", month = "Mar", number = "6", pages = "1017--1027", title = "Telomere elongation involves intra-molecular DNA replication in cells utilizing alternative lengthening of telomeres.", url = "http://dx.doi.org/10.1093/hmg/ddn436", volume = "18", year = "2009", } @article{Lange2010a, author = "Kathrin Lange and Lisa Holm and Kirsten Vang Nielsen and Andreas Hahn and Winfried Hofmann and Hans Kreipe and Brigitte Schlegelberger and Gudrun G{\"o}hring", abstract = "Telomere shortening and chromosomal instability are believed to play an important role in the development of myeloid neoplasia. So far, published data are only available on the average telomere length in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), but not on the telomere length of individual chromosomes. We used a new technique, telomere/centromere-fluorescence in situ hybridization (T/C-FISH), which combines fluorescence R-banding and FISH using a probe against the telomere repeats to measure the telomere length of each chromosome arm in 78 patients with MDS. In line with the previous results, patients with MDS showed significantly shorter telomeres than those of healthy controls. Telomere lengths did not differ significantly between distinct morphological subtypes of MDS. However, there was a significant difference in telomere length between patients with an isolated monosomy 7 and patients with a normal karyotype (P ", journal = "Genes Chromosomes Cancer", keywords = "Anemia, genetics; Isis Telomere Ikaros", month = "Mar", number = "3", pages = "260--269", title = "Telomere shortening and chromosomal instability in myelodysplastic syndromes.", url = "http://dx.doi.org/10.1002/gcc.20737", volume = "49", year = "2010", } @article{00218, author = "G. Houge and T. Liehr and J. Schoumans and G.O. Ness and K. Solland and H. Starke and U. Claussen and P. Stromme and B. Akre and S. Vermeulen", journal = "American Journal of Medical Genetics", keywords = "Isis mFISH mBAND", pages = "235- 240", title = "Ten years follow up of a boy with a complex chromosomal rearrangement: going from a >5 to 15 breakpoint CCR", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12673653{\&}dopt=Abstract", volume = "118", year = "2003", } @article{00161, author = "T. Liehr and V. Beensen and H. Starke and R. Hauschild and E. Hempell and V. Fritsche and C. Hoppe and G. Gro{\ss}wendt and M. Prechtel and M. Ziegler and U. Claussen and von Eggeling, F.", journal = "Clin. Genet.", pages = "83- 85", title = "Tetrasomy 21 due to a de novo Robertsonian translocation t(14/21) and an additional free trisomy 21", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11531976{\&}dopt=Abstract", volume = "60", year = "2001", } @article{Kim2008, author = "Juwon Kim and Tae Sung Park and Jaewoo Song and Kyung-A. Lee and Sang-Guk Lee and June-Won Cheong and Jong Rak Choi", abstract = "Trisomy 8 is one of the most frequent numerical chromosomal abnormalities observed in hematological malignancies, whereas tetrasomy 8 is a clonal aberration seen mainly in myeloid disorders such as acute myelod leukemia (AML) and myelodysplastic syndromes. In contrast to trisomy 8, tetrasomy 8 is a rare chromosomal aberration, in that only 17 reported AML cases with isolated tetrasomy 8 have been documented. Interestingly, the majority of reported cases were associated with monocytic-lineage leukemias. According to recent reports, tetrasomy 8 is regarded as a poor prognostic factor, and most patients having this abnormality relapsed and died within 1 yr. Here, we report a patient with acute monoblastic leukemia having tetrasomy 8 and a very aggressive disease course.", journal = "Korean J Lab Med", keywords = "Aneuploidy; Chromosomes; Humans;MetaCyte; Ikaros; Karyotyping; Leukemia", month = "Aug", number = "4", pages = "262--266", title = "Tetrasomy 8 in a patient with acute monoblastic leukemia.", url = "http://dx.doi.org/10.3343/kjlm.2008.28.4.262", volume = "28", year = "2008", } @article{00004, author = "T. Haferlach and M. Winkemann and H. L{\"o}ffler and R. Schoch and W. Gassmann and C. Fonatsch and M. Poetsch and K. Weber-Matthiesen and B. Schlegelberger", journal = "Blood", keywords = "Isis", pages = "2459- 2463", title = "The abnormal eosinophils are part of the leukemia cell population in Acute Myelomonocytic Leukemia with abnormal eosinophils (AML M4Eo) and carry the pericentric inversion 16: A combination of May- Gr{\"u}nwald-Giemsa staining and FISH", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8630411{\&}dopt=Abstract", volume = "87", year = "1995", } @article{00009, author = "T. Haferlach and M. Winkemann and H. L{\"o}ffler and R. Schoch and W. Gassmann and C. Fonatsch and C. Schoch and M. Poetsch and K. Weber-Matthiesen and B. Schlegelberger", journal = "Blood", keywords = "Isis", pages = "2459- 2463", title = "The Abnormal Eosinophils Are Part of the Leukemic Cell Population in Acute Myelomonocytic Leukemia With Abnormal Eosinophils (AML M4Eo) and Carry the Pericentric Inversion 16: A Combination of May-Gr{\"u}nwald-Giemsa Staining and FISH", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8630411{\&}dopt=Abstract", volume = "87", year = "1996", } @article{Ji2009, author = "Zhiying Ji and Luoping Zhang and Weihong Guo and Cliona M McHale and Martyn T Smith", abstract = "Both occupational exposure to the leukemogen benzene and in vitro exposure to its metabolite hydroquinone (HQ) lead to the induction of numerical and structural chromosome changes. Several studies have shown that HQ can form DNA adducts, disrupt microtubule assembly and inhibit DNA topoisomerase II (topo II) activity. As these are potential mechanisms underlying endoreduplication (END), a phenomenon that involves DNA amplification without corresponding cell division, we hypothesized that HQ could cause END. We measured END in the human lymphoblastoid cell line, TK6, treated with HQ (0-20 microM) and etoposide (0-0.2 microM) for 48 h. Etoposide was used as a positive control as it is a topo II poison and established human leukemogen that has previously been shown to induce END in Chinese hamster ovary cells. Both HQ and etoposide significantly induced END in a dose-dependent manner (P(trend) s.", journal = "Mutagenesis", keywords = "Metafer MSearch", month = "Jul", number = "4", pages = "367--372", title = "The benzene metabolite, hydroquinone and etoposide both induce endoreduplication in human lymphoblastoid TK6 cells.", url = "http://dx.doi.org/10.1093/mutage/gep018", volume = "24", year = "2009", } @article{00292, author = "S. Selvarajah and M. Yoshimoto and P.C. Park and G. Maire and J. Paderova and J. Bayani and G. Lim and K. Al-Romaih and J.A. Squire and M. Zielenska", journal = "Chromosoma", keywords = "Isis mBAND", pages = "459- 467", title = "The breakage-fusion-bridge (BFB) cycle as a mechanism for generating genetic heterogeneity in osteosarcoma.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=16897100{\&}query_hl=21{\&}itool=pubmed_docsum", volume = "115", year = "2006", } @article{00273, author = "P. Duesberg and R. Li and A. Fabarius and R. Hehlmann", journal = "Cellular Oncology", keywords = "Isis mFISH", pages = "293- 318", title = "The chromosomal basis of cancer.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=16373963{\&}query_hl=1{\&}itool=pubmed_docsum", volume = "27", year = "2005", } @article{Carrell2008(b), author = "Douglas T. Carrell", abstract = "Severe male infertility has been shown to be associated with improper meiotic recombination and elevated sperm chromosome aneuploidy. Elevated sperm aneuploidy increases the risk of embryo lethality or fetal anomalies. Although difficulties in interpreting aneuploidy data still exist, advances in fluorescent in situ hybridization (FISH) technology have facilitated the study of sperm from patients with severe spermatogenesis defects, which has demonstrated the prudence of evaluating sperm chromosome aneuploidy in men with severe male factor infertility, such as nonobstructive azoospermia or severe ultrastructure defects, especially in cases of previous repeated in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) failure. Testing is also advisable in men with chromosome translocations and unexplained recurrent pregnancy loss, and it may be beneficial in patients with unexplained, repeated IVF failure. Automated FISH imaging and analysis technology is now available and is beneficial in reducing technician time analyzing sperm aneuploidy. Emerging technologies, such comparative genomic hybridization, may be beneficial in further improving the quality of data derived from aneuploidy analysis and reducing the cost of the assay.", journal = "J Androl", keywords = "Metafer MetaCyte", number = "2", pages = "124--133", title = "The clinical implementation of sperm chromosome aneuploidy testing: pitfalls and promises.", url = "http://dx.doi.org/10.2164/jandrol.107.003699", volume = "29", year = "2008", } @article{00172, author = "J. Lemke and J. Claussen and S. Michel and I. Chudoba and P. M{\"u}hlig and M. Westermann and K. Sperling and N. R{\'u}btsov and U.-W. Grummt and P. Ullmann and K. Kromeyer-Hauschil and T. Liehr and U. Claussen", journal = "Am J Hum Genet", keywords = "Isis mBAND", pages = "1051- 1059", title = "The DNA-based structure of human chromosome 5 in interphase", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12370837{\&}dopt=Abstract", volume = "71", year = "2002", } @article{00007, author = "G. Van Camp and P. Coucke and F. Speleman and N. Van Roy and E.C. Beyer and B.A. Oostra and P.J. Willems", journal = "Genomics", pages = "402- 403", title = "The Gene for Human Gap Junction Protein connexin37 (GJA4) Maps to Chromosome 1p35.1, in the Vicinity of D1S195", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8586454{\&}dopt=Abstract", volume = "30", year = "1995", } @article{Kosyakova2009, author = "Nadezda Kosyakova and Anja Weise and Kristin Mrasek and Uwe Claussen and Thomas Liehr and Heike Nelle", abstract = "ABSTRACT: BACKGROUND: Chromosome banding is widely used in cytogenetics. However, the biological nature of hierarchically organized splitting of chromosomal bands of human chromosomes is an enigma and has not been, as yet, studied. RESULTS: Here we present for the first time the hierarchically organized splitting of chromosomal bands in their sub-bands for all human chromosomes. To do this, array-proved multicolor banding (aMCB) probe-sets for all human chromosomes were applied to normal metaphase spreads of three different G-band levels. We confirmed for all chromosomes to be a general principle that only Giemsa-dark bands split into dark and light sub-bands, as we demonstrated previously by chromosome stretching. Thus, the biological band splitting is in > 50\% of the sub-bands different than implemented by the ISCN nomenclature suggesting also a splitting of G-light bands. Locus-specific probes exemplary confirmed the results of MCB. CONCLUSION: Overall, the present study enables a better understanding of chromosome architecture. The observed difference of biological and ISCN band-splitting may be an explanation why mapping data from human genome project do not always fit the cytogenetic mapping.", journal = "Mol Cytogenet", keywords = "Isis mBAND", pages = "4", title = "The hierarchically organized splitting of chromosomal bands for all human chromosomes.", url = "http://dx.doi.org/10.1186/1755-8166-2-4", volume = "2", year = "2009", } @article{00328, author = "A. Rossnerova and M. Spatova and P. Rossner and I. Solansky and R.J. Sram", abstract = "The measurement of micronuclei (MN) in human peripheral blood lymphocytes is frequently used in molecular epidemiology as one of the preferred methods for assessing chromosomal damage resulting from environmental mutagen exposure. In the present study, we evaluated the effect of exposure to carcinogenic polycyclic aromatic hydrocarbons (c-PAHs), volatile organic compounds (VOC) and smoking on the frequency of MN in a group of 56 city policemen living and working in Prague. The average age of the participants was 34+/-6 years. The study was conducted on the same subjects in February and May 2007. The concentrations of air pollutants were obtained from personal and stationary monitoring. A statistically significant decrease in the levels of pollutants was observed in May when compared with February, with the exception of toluene levels measured by stationary monitoring. The frequency of MN was determined by the automatic image scoring (MetaSystems Metafer 4, version 3.2.1) of DAPI-stained slides. The results of the image analysis indicated a significant difference in the frequency of MN (mean levels 7.32+/-3.42 and 4.67+/-2.92, for February and May, respectively). Our study suggests that automatic image analysis of MN is a highly sensitive method for evaluating the effect of c-PAHs and confirms that there are no differences between smokers and nonsmokers. These results demonstrate the ability of c-PAHs to increase MN frequency, even if the exposure to c-PAHs occurred up to 60 days before the collection of biological material. Our work is the first human biomonitoring study focused on the measurement of MN by automated image analysis for assessing chromosomal damage as a result of environmental mutagen exposure.", journal = "Mutation Research", keywords = "Metafer MSearch MicroNuclei", number = "2", pages = "42-47", title = "The impact of air pollution on the levels of micronuclei measured by automated image analysis.", url = "http://www.ncbi.nlm.nih.gov/pubmed/19409399?ordinalpos=6{\&}itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDoc", volume = "669", year = "2009", } @article{00326, author = "G. Davis and D. Farrell and C. Felix", journal = "Poster", keywords = "Metafer MSearch AutoCapt", pages = "0- 0", title = "The impact of the Metasystems Metafer scanning system on the oncology service, genetic services, Wellington, New Zealand.", year = "2009", } @article{Vral2011, author = "Anne Vral and Michael Fenech and Hubert Thierens", abstract = "Biological dosimetry, based on the analysis of micronuclei (MN) in the cytokinesis-block micronucleus (CBMN) assay can be used as an alternative method for scoring dicentric chromosomes in the field of radiation protection. Biological dosimetry or Biodosimetry, is mainly performed, in addition to physical dosimetry, with the aim of individual dose assessment. Many studies have shown that the number of radiation-induced MN is strongly correlated with dose and quality of radiation. The CBMN assay has become, in the last years, a thoroughly validated and standardised technique to evaluate in vivo radiation exposure of occupational, medical and accidentally exposed individuals. Compared to the gold standard, the dicentric assay, the CBMN assay has the important advantage of allowing economical, easy and quick analysis. The main disadvantage of the CBMN assay is related to the variable micronucleus (MN) background frequency, by which only in vivo exposures in excess of 0.2-0.3 Gy X-rays can be detected. In the last years, several improvements have been achieved, with the ultimate goals (i) of further increasing the sensitivity of the CBMN assay for low-dose detection by combining the assay with a fluorescence in situ hybridisation centromere staining technique, (ii) of increasing the specificity of the test for radiation by scoring nucleoplasmic bridges in binucleated cells and (iii) of making the assay optimally suitable for rapid automated analysis of a large number of samples, viz. in case of a large-scale radiation accident. The development of a combined automated MN-centromere scoring procedure remains a challenge for the future, as it will allow systematic biomonitoring of radiation workers exposed to low-dose radiation.", journal = "Mutagenesis", keywords = "Metafer MNScore Micronuclei", month = "Jan", number = "1", pages = "11--17", title = "The micronucleus assay as a biological dosimeter of in vivo ionising radiation exposure.", url = "http://dx.doi.org/10.1093/mutage/geq078", volume = "26", year = "2011", } @article{Thierens2009, author = "H Thierens and A Vral", abstract = "The cytokinesis-block micronucleus assay in peripheral blood lymphocytes is a standardised and validated technique for biodosimetry. Automated scoring of micronuclei allows large scale applications as in population triage in case of radiation accidents or malevolent use of radioactive sources. The dose detection limit (95% confidence) of the micronucleus assay for individual dose assessment is restricted to 0.2 Gy but can be decreased to 0.1 Gy by scoring centromeres in micronuclei using fluorescence in situ hybridization (FISH). In the past the micronucleus assay was applied for a number of large scale biomonitoring studies of nuclear power plant workers and hospital workers. Baseline micronucleus frequencies depend strongly on age and gender. The assay was also already used for biodosimetry of radiation accidents. In a multiple endpoint biodosimetry study for dose assessment of a worker exposed accidentally in 2003 to X-rays, a good agreement was obtained between dose estimates resulting from the micronucleus assay, the scoring of dicentrics and translocations. Automated scoring of micronuclei in combination with centromere signals, allowing systematic biodosimetry of exposed populations, remains a challenge for the future.", journal = "Ann Ist Super Sanita", number = "3", pages = "260-4", title = "The micronucleus assay in radiation accidents", url = "http://www.ncbi.nlm.nih.gov/pubmed/19861730?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum{\&}ordinalpos=1", volume = "45", year = "2009", } @article{00108, author = "O. Bartsch and W. Kre{\ss} and A. Wagner and E. Seemanova", journal = "Cytogenet Cell Genet", pages = "310- 314", title = "The Novel contiguous gene syndrome of myotubular myopathy (MTM1), male hypogenitalism and deletion in Xq28:report of the first family case", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10449925{\&}dopt=Abstract", volume = "85", year = "1999", } @article{00249, author = "J. Cermak and M. Belickova and H. Krejcova and K. Michalova and S. Zilovcova and Z. Zemanova and H. Brezinova and Z. Sieglova", journal = "Leukemia Research", keywords = "Isis mFISH mBAND", pages = "371- 379", title = "The presence of clonal cell subpopulations in peripheral blood and bone marrow of patients with refractory cytopenia with multilieage dysplasia but not in patients with refractory anemia may reflect a multistep pathogenesis of myelodysplasia.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=15725470", volume = "29", year = "2004", } @article{00263, author = "S. Sommer and I. Buraczewska and M. Wojewodzka and E. Bouzyk and I. Szumiel and A. Wojcik", journal = "Int. J. Radiat. Biol.", keywords = "Isis", pages = "741- 749", title = "The radiation sensitivity of human chromosomes 2, 8, and 14 in peripheral blood lymphocytes of seven donors.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=16449081{\&}query_hl=32{\&}itool=pubmed_docsum", volume = "81", year = "2005", } @article{00056, author = "S.J.M. O'Connor and P.D. Forsyth and S. Dalal and P.A. Evans and M.A. Short and C. Shiach and A.S. Jack and G.J. Morgan", journal = "British Journal of Haematology", pages = "597- 604", title = "The rapid diagnosis of acute promyelocytic leukaemia using PML (5E10) monoclonal antibody", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9401072{\&}dopt=Abstract", volume = "99", year = "1997", } @article{00050, author = "H. Kehrer-Sawatzki and J. H{\"a}ussler and W. Krone and H. Bode and D.E. Jenne and K.U. Mehnert and U. T{\"u}mmers and G. Assum", journal = "Human Genetics", pages = "237- 247", title = "The second case of a t(17/22) in a family with neurofibromatosis type 1: sequence analysis of the breakpoint regions", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9048928{\&}dopt=Abstract", volume = "99", year = "1997", } @article{00091, author = "M. Jokela and M. M{\"a}kiniemi and S. Lehtonen and C. Szpirer and U. Hellmann and J.E. Syv{\"a}oja", journal = "Nucleic Acids Res", pages = "730- 734", title = "The small subunit of the human nad mouse DANN polymerase e are homologous to the second largest subunit of the yeast Saccharommyces cerevisiae DNA polymerase e", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9443964{\&}dopt=Abstract", volume = "26", year = "1998", } @article{00113, author = "D. Gisselson and M. H{\"o}glund and F. Mertens and B. Johansson and P. Dal Cin and den Berghe, H. Van and W. C. Earnshaw and F. Mitelman and N. Mandahl", journal = "Human Genetics", pages = "315- 325", title = "The structure and dynamics of ring chromosomes in human neoplastic and non-neoplastic cells", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10369161{\&}dopt=Abstract", volume = "104", year = "1999", } @article{00110, author = "A. Blixt and M. Mahlapuu and C. Bjursell and C. Darnfors and T. Johannesson and S. Enerb{\"a}ck and P. Carlsson", journal = "Genomics", pages = "387- 390", title = "The Two-Exon Gene of the Human Forkhead Transcription Factor FREAC-2 (FKHL6) is located at 6p25.3", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9799607{\&}dopt=Abstract", volume = "53", year = "1999", } @article{Mackinnon2011, author = "Ruth N. Mackinnon and Ilse Chudoba", abstract = "Multicolour fluorescence in situ hybridisation (M-FISH) and multicolour banding (M-BAND) are advanced chromosome painting techniques combining multiple chromosome- or region-specific paints in one step. M-FISH identifies all chromosomes or chromosome arms at once, whereas M-BAND identifies the different regions of a single chromosome. The use of either or both can improve the accuracy of karyotyping and help identify cryptic chromosome rearrangements. These probes are prepared by pooling multiple chromosome- or chromosome region-specific DNA libraries, each labelled with a unique combination of fluorochromes. Commercial probes are available, avoiding the need for probe preparation. In the protocol described here, a commercial probe is used. Well-spread metaphases are prepared according to standard techniques, followed by alkaline denaturation and application of the denatured probe. After an incubation period, the slides are washed. A fluorescence microscope with filter sets specific to the fluorescent labels is used for analysis, together with specialised image analysis software. The software interprets the combination of fluorochromes to identify each chromosome and produce a false colour image specific for each chromosome or region. The single colour galleries - which show the hybridisation patterns of the individual fluorochromes - are useful to help interpret and confirm the false colour images produced by the software, including ambiguous signals.", journal = "Methods Mol Biol", keywords = "24XCyte, XCyte, mBAND, mFISH, Probes", pages = "203--218", title = "The use of M-FISH and M-BAND to define chromosome abnormalities.", url = "http://dx.doi.org/10.1007/978-1-61779-074-4_15", volume = "730", year = "2011", } @article{00002, author = "J. Weber and W. Scheid and H. Traut", journal = "Mutation Research", keywords = "Metafer2", pages = "31- 34", title = "Time-saving in biological dosimetry by using the automatic metaphase finder Metafer2", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=1380117{\&}dopt=Abstract", volume = "272", year = "1992", } @article{Klein2010, author = "Andreas Klein and Nan Li and Joshua M Nicholson and Amanda A McCormack and Adolf Graessmann and Peter Duesberg", abstract = "Cancers are clones of autonomous cells defined by individual karyotypes, much like species. Despite such karyotypic evidence for causality, three to six synergistic mutations, termed oncogenes, are generally thought to cause cancer. To test single oncogenes, they are artificially activated with heterologous promoters and spliced into the germ line of mice to initiate cancers with collaborating spontaneous oncogenes. Because such cancers are studied as models for the treatment of natural cancers with related oncogenes, the following must be answered: 1) which oncogenes collaborate with the transgenes in cancers; 2) how do single transgenic oncogenes induce diverse cancers and hyperplasias; 3) what maintains cancers that lose initiating transgenes; 4) why are cancers aneuploid, over- and underexpressing thousands of normal genes? Here we try to answer these questions with the theory that carcinogenesis is a form of speciation. We postulate that transgenic oncogenes initiate carcinogenesis by inducing aneuploidy. Aneuploidy destabilizes the karyotype by unbalancing teams of mitosis genes. This instability thus catalyzes the evolution of new cancer species with individual karyotypes. Depending on their degree of aneuploidy, these cancers then evolve new subspecies. To test this theory, we have analyzed the karyotypes and phenotypes of mammary carcinomas of mice with transgenic SV40 tumor virus- and hepatitis B virus-derived oncogenes. We found that (1) a given transgene induced diverse carcinomas with individual karyotypes and phenotypes; (2) these karyotypes coevolved with newly acquired phenotypes such as drug resistance; (3) 8 of 12 carcinomas were transgene negative. Having found one-to-one correlations between individual karyotypes and phenotypes and consistent coevolutions of karyotypes and phenotypes, we conclude that carcinogenesis is a form of speciation and that individual karyotypes maintain cancers as they maintain species. Because activated oncogenes destabilize karyotypes and are dispensable in cancers, we conclude that they function indirectly, like carcinogens. Such oncogenes would thus not be valid models for the treatment of cancers.", journal = "Cancer Genet Cytogenet", keywords = "Isis mFISH", month = "Jul", number = "2", pages = "79--99", title = "Transgenic oncogenes induce oncogene-independent cancers with individual karyotypes and phenotypes.", url = "http://dx.doi.org/10.1016/j.cancergencyto.2010.04.008", volume = "200", year = "2010", } @article{00015, author = "K. Weber-Matthiesen and J. Deerberg-Wittram and A. Rosenwald and M. Poetsch and W. Grote and B. Schlegelberger", journal = "American Journal of Pathology", keywords = "Isis", pages = "463- 468", title = "Translocation t(2/5) is not a primary event in Hodgkin's disease. Simultaneous immunophenotyping and interphase cytogenetics", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=8701985{\&}dopt=Abstract", volume = "2", year = "1996", } @article{00102, author = "T. Liehr and H. Starke and V. Beensen and C. K{\"a}hler and M. Harbich and E. Brude and M. Ziegler and U. Claussen", journal = "Int. J. Mol. Med.", keywords = "Isis", pages = "11- 14", title = "Translocation trisomy dup(21p) and free trisomy 21 can be distinguished by interphase-FISH", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9864379{\&}dopt=Abstract", volume = "3", year = "1999", } @article{Beyne-Rauzy2004, author = "Odile Beyne-Rauzy and Christian Recher and Nicole Dastugue and C{\'e}cile Demur and G{\'e}raldine Pottier and Guy Laurent and Laure Sabatier and V{\'e}ronique Mansat-De Mas", abstract = "Previous studies have documented that Tumor necrosis factor alpha (TNFalpha) is a potent negative regulator of normal hematopoiesis. However, the mechanism by which TNFalpha acts at the cellular level is not totally understood. Although apoptotic cell killing appears to be the most common cellular effect of TNFalpha, other studies suggest that this cytokine may elicit other cellular responses such as prolonged growth inhibition. In this context, we have investigated whether TNFalpha may induce senescence in hematopoietic cells, which display intrinsic defect in the apoptotic machinery. The present study described that, in the leukemic KG1 cells, TNFalpha induced no apoptosis but a senescence state characterized by prolonged growth arrest, increased beta-galactosidase activity, p21WAF-1 induction, decreased telomerase activity, telomeric disturbances (shortening, losses, fusions), and additional chromosomal aberrations. Telomerase inhibition correlated with reduced levels of hTERT transcripts. GM-CSF prevented TNFalpha effects and allowed leukemic cells to recover growth capacity. Finally, our study shows for the first time that, at least in some hematopoietic cells, TNFalpha may induce senescence with important functional consequences, including sustained growth inhibition and genetic instability, and that this cellular response is efficiently regulated by hematopoietic growth factors.", journal = "Oncogene", keywords = "24XCyte;Isis;mFISH", month = "Sep", number = "45", pages = "7507--7516", title = "Tumor necrosis factor alpha induces senescence and chromosomal instability in human leukemic cells.", url = "http://dx.doi.org/10.1038/sj.onc.1208024", volume = "23", year = "2004", } @article{00205, author = "S. Scheil and S. Hagen and S. Br{\"u}derlein and I. Leuschner and W. Behnisch and P. M{\"o}ller", journal = "Int. J. Cancer", keywords = "Isis CGH mFISH mBAND Ikaros", pages = "347- 352", title = "Two novel in vitro human hepatoblastoma models, HepU1 and HepU2, are highly characteristic of fetal-embryonal differentiation in hepatoblastoma", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=12704668{\&}dopt=Abstract", volume = "105", year = "2003", } @article{00027, author = "M. Deichmann and M. Bentz and R. Haas", journal = "Journal of Virological Methods", keywords = "Isis", pages = "19- 25", title = "Ultra-sensitive FISH is a useful tool for studying chronic HIV-1 infection", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9128858{\&}dopt=Abstract", volume = "65", year = "1997", } @article{Silva2009, author = "Maria Luiza Macedo Silva and do Socorro Pombo-de-Oliveira, Maria and Susana C Raimondi and Hasmik Mkrtchyan and Eliana Abdelhay and de Figueiredo, Amanda Faria and de Souza, Mariana Tavares and Daniela Ribeiro Ney Garcia and de Ventura, Eliane Maria Soares and de Sousa, Adriana Martins and Thomas Liehr", abstract = "ABSTRACT: BACKGROUND: Children with Down syndrome (DS) have an increased risk of childhood acute leukemia, especially acute megakaryoblastic leukemia (AMKL) also called acute myeloid leukemia (AML) type M7. Here four yet unreported infants with such malignancies are reported. RESULTS: An unbalanced translocation involving chromosome 1 was identified by GTG banding in all cases. These were characterized in more detail by molecular cytogenetic approaches. Additional molecular analysis revealed in three of the four cases mutations in exon 2 of the GATA binding protein 1 (globin transcription factor 1), located in Xp11.23. CONCLUSION: Our results corroborate that abnormalities of chromosome 1 are common in DS-associated AMKL. Whether this chromosomal region contains gene(s) involved in hematopoietic malignant transformation remains to be determined.", journal = "Mol Cytogenet", keywords = "Isis mBAND", pages = "7", title = "Unbalanced chromosome 1 abnormalities leading to partial trisomy 1q in four infants with Down syndrome and acute megakaryocytic leukemia.", url = "http://dx.doi.org/10.1186/1755-8166-2-7", volume = "2", year = "2009", } @article{00174, author = "V.S. Lestou and R.D. Gascoyne and C. Salski and J.M. Connors and D.E. Horsman", journal = "Genes, Chromosomes {\&} Cancer", keywords = "Isis mBAND", pages = "201- 210", title = "Uncovering novel inter- and intrachromosomal chromosome I aberrations in follicular lymphomas by using an innovative multicolor banding technique", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11979554{\&}dopt=Abstract", volume = "34", year = "2002", } @article{00154, author = "P.F. Ambros and G. M{\'e}hes and C. Hattinger and I.M. Ambros and A. Luegmayr and R. Ladenstein and H. Gadner", journal = "Leukemia", keywords = "Metafer RCDetect", pages = "275- 277", title = "Unequivocal identification of disseminated tumor cells in the bone marrow by combining immunological and genetic approaches--functional and prognostic information.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=11236944{\&}query_hl=5{\&}itool=pubmed_docsum", volume = "15", year = "2001", } @article{00057, author = "S. Salomaa and A.V. Sevan'kaev and A.A. Zhloba and E. Kumpusalo and S. M{\"a}kinen and C. Lindholm and L. Kumpusalo and S. Kolmakow and A. Nissinen", journal = "International Journal of Radiation Biology", pages = "51- 59", title = "Unstable and stable chromosomal aberrations in lymphocytes of people exposed to Chernobyl fallout Bryansk, Russia", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9020963{\&}dopt=Abstract", volume = "71", year = "1997", } @article{Gagos2008, author = "Sarantis Gagos and George Papaioannou and Maria Chiourea and Sophie Merk-Loretti and Charles-Edward Jefford and Panagiota Mikou and Irmgard Irminger-Finger and Anna Liossi and Jean-Louis Blouin and Sophie Dahoun", abstract = "ABSTRACT: Malignant melanomas are characterized by increased karyotypic complexity, extended aneuploidy and heteroploidy. We report a melanoma metastasis to the peritoneal cavity with an exceptionally stable, abnormal pseudodiploid karyotype as verified by G-Banding, subtelomeric, centromeric and quantitative Fluorescence in Situ Hybridization (FISH). Interestingly this tumor had no detectable telomerase activity as indicated by the Telomere Repeat Amplification Protocol. Telomeric Flow-FISH and quantitative telomeric FISH on mitotic preparations showed that malignant cells had relatively short telomeres. Microsatellite instability was ruled out by the allelic pattern of two major mononucleotide repeats. Our data suggest that a combination of melanoma specific genomic imbalances were sufficient and enough for this fatal tumor progression, that was not accompanied by genomic instability, telomerase activity, or the engagement of the alternative recombinatorial telomere lengthening pathway.", journal = "Mol Cytogenet", keywords = "Isis Telomere", pages = "20", title = "Unusually stable abnormal karyotype in a highly aggressive melanoma negative for telomerase activity.", url = "http://dx.doi.org/10.1186/1755-8166-1-20", volume = "1", year = "2008", } @article{Pajor2011, author = "Gabor Pajor and Laszlo Somogyi and Bela Melegh and Donat Alpar and Bela Kajtar and Laszlo Farkas and Maria Kneif and Daniel Bollmann and Laszlo Pajor and Norbert Sule", abstract = "Urovysion multitarget fluorescence in situ hybridization (FISH) assay is a promising tool for detection of bladder cancer, however, there is still no consensus regarding abnormal signal pattern and cut-off level, and the recommended targeting carries limitations similar to urine cytology. Aim of this study was to explore diagnostic benefits of a recently introduced method featuring target specific genotyping, as well as to investigate the feasibility of locally and statistically determined cut-off, compared with conventional evaluation scheme. Histology, cytology, and comparative FISH approaches were performed on 42 patients with high clinical suspicion for urothelial carcinoma (UC). FISH parallels were (1) Urovysion-alone (according to manufacturer's instruction); (2) Targeted-Urovysion (cytokeratin7 immunophenotyping followed by Urovysion), both of which evaluated by both conventional and statistical evaluation scheme. For statistical evaluation cut-offs and sufficient sample size were determined on controls and ratio of positive cells was recorded, whereas conventional evaluation relied on manufacturer's recommendations. The specificity of cytology, Urovysion-alone in general and targeted-Urovysion in general appeared 86\%, 86\%, and 100\%, respectively. In the same comparison, overall sensitivity was 60\%, 80\%, and 93\%, respectively. In superficial cases sensitivity was 48\% for cytology, 72\% for Urovysion-alone and 91\% for targeted-Urovysion, while no prominent differences were seen in muscle invasive cases. The ratio of FISH positive cells was proportionate with both stage and grade, however, targeted genotyping could separate high grade/high stage cases more effectively. In conclusion, CK7 targeting raises diagnostic efficiency of Urovysion, and could be an ideal tool for identifying tumor cells in ambiguous cases or when other tumors are present. Statistical evaluation produces accuracy comparable with results of conventional evaluation, and with laboratories setting cut-offs individually but according harmonized protocol, it could aid method standardization. Furthermore, by providing additional quantitative information about tumor characteristics, is likely to have therapy relevant value in the future.", journal = "Cytometry A", keywords = "Metafer MetaCyte UroVysion", month = "May", number = "5", pages = "375--382", title = "Urovysion: Considerations on modifying current evaluation scheme, including immunophenotypic targeting and locally set, statistically derived diagnostic criteria.", url = "http://dx.doi.org/10.1002/cyto.a.21065", volume = "79", year = "2011", } @article{Carrell2008, author = "DT Carrell and BR Emery", abstract = "OBJECTIVE: To determine the precision and accuracy of an automated cell counting system when applied to counting aneuploidies in sperm samples. DESIGN: Prospective pilot study. SETTING: Andrology clinic and research laboratory in a university teaching hospital. PATIENT(S): Ten anonymous sperm donors of known fertility and two patients seeking infertility treatment. INTERVENTION(S): Semen samples were processed for detection of aneuploidies for chromosomes 13, 18, 21, X, and Y with use of fluorescent in situ hybridization. The detection of chromosome aneuploidy was performed both by manual counting and by the use of an automated cell counting system with manual review of aneuploid sperm. MAIN OUTCOME MEASURE(S): Semen samples were judged for the percent aneuploidy for chromosomes 13, 18, 21, X, and Y when counted manually or with the use of the automated cell counting system and review by a technician. RESULT(S): The sperm aneuploidy rates determined by the automated cell counting system and careful review were comparable with those obtained by manual counting by a trained technician. CONCLUSION(S): These preliminary data demonstrate that automated cell counting devices may be useful in increasing productivity in aneuploidy detection in sperm and may become an alternative to the labor-intensive manual counting by technicians.", journal = "Fertil Steril", keywords = "Metafer MetaCyte", number = "2", pages = "434-7", title = "Use of automated imaging and analysis technology for the detection of aneuploidy in human sperm", url = "http://dx.doi.org/10.1016/j.fertnstert.2007.06.095", volume = "90", year = "2008", } @article{Rosenberger2011, author = "Albert Rosenberger and Ute R{\"o}ssler and Sabine Hornhardt and Wiebke Sauter and Heike Bickeb{\"o}ller and H-Erich Wichmann and Maria Gomolka", abstract = "The COMET assay is recognized as a rapid and sensitive method in quantifying radiation induced DNA damage. We investigated the distorting influence of endogenous, assay-inherent factors onto base (single cell level) and primary outcome measures (experimental/slide level), such as olive tail moment (OTM) and percentage DNA in the tail (\%tail-DNA). From 2003 to 2008, we performed the assay on lymphocytes isolated from the blood samples of 355 lung cancer patients, 170 controls, and 610 relatives, as well as one single reference individual, repeated 170 times. In total, the data from 10,016 single experiments containing around 1,750,000 cells have been included in this study. This is the first time that the endogenous variability of the COMET assay has been validated systematically on such a huge data set over a 5 year period. Assuming that the reference sample reflects assay specific white noise, we estimated a proportion of 7-95\% of the variability of the outcome measures due to assay variation (white noise) depending on parameter, exposure level, and study group. The proportion of white noise was largest for the initial radiation damage. The specific endogenous factors considered attribute to 14.8\% of the total variability in the primary outcome measurements of the OTM and 6.9\% of the \%tail-DNA. OTM turns out to be a sensitive parameter to detect variation, but is also more susceptible to disturbance caused by endogenous factors than \%tail-DNA. To reduce the experimental variability in COMET assays, we recommend a highly standardized operation protocol as well as inspecting and/or adjusting the primary outcome measures according to endogenous factors before calculating secondary outcome measures, e.g. DNA repair capacity (DRC) or testing statistical inference. A human reference (HR) sample is also useful to inspect homogeneity in the temporal progression of long lasting investigations, but not for calibrating primary outcome measurements.", journal = "DNA Repair (Amst)", keywords = "Metafer CometScan Comet Assay Validation", month = "Mar", number = "3", pages = "322--337", title = "Validation of a fully automated COMET assay: 1.75 million single cells measured over a 5 year period.", url = "http://dx.doi.org/10.1016/j.dnarep.2010.12.003", volume = "10", year = "2011", } @article{Furrer2013, author = "Daniela Furrer and Simon Jacob and Chantal Caron and Fran{\c{c}}ois Sanschagrin and Louise Provencher and Caroline Diorio", abstract = "ABSTRACT: Amplification of the human epidermal growth factor receptor 2 (HER2) is a prognostic marker for poor clinical outcome and a predictive marker for therapeutic response to targeted therapies in breast cancer patients. With the introduction of anti-HER2 therapies, accurate assessment of HER2 status has become essential. Fluorescence in situ hybridization (FISH) is a widely used technique for the determination of HER2 status in breast cancer. However, the manual signal enumeration is time-consuming. Therefore, several companies have developed automated image analysis software like MetaSystems. Some of these signal enumeration software employ the so called "tile-sampling classifier", a programming algorithm through which the software quantifies fluorescent signals in images on the basis of square tiles of fixed dimensions. Considering that the size of tile does not always correspond to the size of a single tumor cell nucleus, some users argue that this analysis method might not completely reflect the biology of cells. For that reason, MetaSystems has developed a new classifier which is able to recognize nuclei within tissue sections in order to determine the HER2 amplification status on nuclei basis. We call this new programming algorithm "nucleisampling classifier". In this study, we evaluated the accuracy of the "nuclei-sampling classifier" in determining HER2 gene amplification by FISH in nuclei of breast cancer cells. To this aim, we randomly selected from our cohort 64 breast cancer specimens (32 nonamplified and 32 amplified) and we compared results obtained through manual scoring and through this new classifier. The new classifier automatically recognized individual nuclei. The automated analysis was followed by an optional human correction, during which the user interacted with the software in order to improve the selection of cell nuclei automatically selected. Overall concordance between manual scoring and automated nucleisampling analysis was 98.4\% (100\% for nonamplified cases and 96.9\% for amplified cases). However, after human correction, concordance between the two methods was 100\%. We conclude that the nuclei-based classifier is a new available tool for automated quantitative HER2 FISH signals analysis in nuclei in breast cancer specimen and it can be used for clinical purposes. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1755654848482838.", journal = "Diagn Pathol", keywords = "Metafer MetaCyte Her2", month = "Feb", number = "1", pages = "17", title = "Validation of a new classifier for the automated analysis of the human epidermal growth factor receptor 2 (HER2) gene amplification in breast cancer specimens.", url = "http://dx.doi.org/10.1186/1746-1596-8-17", volume = "8", year = "2013", } @article{00286, author = "J. Reisinger and S. Rumpler and T. Lion and P.F. Ambros", journal = "Int. J. Cancer", keywords = "Isis", pages = "1603- 1608", title = "Visualization of episomal and integrated Epstein-Barr virus DNA by fiber fluorescence in situ hybridization.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=pubmed{\&}dopt=Abstract{\&}list_uids=16217752{\&}query_hl=1{\&}itool=pubmed_docsum", volume = "118", year = "2006", } @article{00032, author = "B. Rautenstrauss and C. Fuchs and T. Liehr and H. Grehl and T. Murakami and J.R. Lupski", journal = "Journal of the Peripheral Nervous System", keywords = "Isis", pages = "319- 322", title = "Visualization of the CMT1A Duplication and HNPP Deletion by FISH on streched Chromosome Fibers", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=10975740{\&}dopt=Abstract", volume = "2", year = "1997", } @article{00028, author = "T. Haferlach and M. Winkemann and C. Nicking and M. Meeder and L. Ramm-Petersen and R. Schoch and M. Nickelsen and K. Weber-Matthiesen and B. Schlegelberger and C. Schoch and W. Gassmann and H. L{\"o}ffler", journal = "British Journal of Hematology", keywords = "Isis", pages = "99- 106", title = "Which compartments are involved in Philadelphia-chromosome positive chronic myeloid leukaemia? An answer at single cell level by combining May-Gr{\"u}newald-Giemsa staining and fluorescence in situ hybridization techniques", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9136947{\&}dopt=Abstract", volume = "97", year = "1997", } @article{Singh2010, author = "Satyendra K Singh and Wenqi Wu and Lihua Zhang and Holger Klammer and Minli Wang and George Iliakis", abstract = "PURPOSE: The backup pathway of nonhomologous end joining (B-NHEJ) enables cells to process DNA double-strand breaks (DSBs) when the DNA-PK-dependent pathway of NHEJ (D-NHEJ) is compromised. Our previous results show marked reduction in the activity of B-NHEJ when LIG4(-/-) mouse embryo fibroblasts (MEFs) cease to grow and enter a plateau phase. The dependence of B-NHEJ on growth state is substantially stronger than that of D-NHEJ and points to regulatory mechanisms or processing determinants that require elucidation. Because the different D-NHEJ mutants show phenotypes distinct in their details, it is necessary to characterize the dependence of their DSB repair capacity on growth state and to explore species-specific responses. METHODS AND MATERIALS: DSB repair was measured in cells of different genetic background from various species using pulsed-field gel electrophoresis, or the formation of {\~a}-H2AX foci, at different stages of growth. RESULTS: Using pulsed-field gel electrophoresis, we report a marked reduction of B-NHEJ during the plateau phase of growth in KU and XRCC4, mouse or Chinese hamster, mutants. Notably, this reduction is only marginal in DNA-PKcs-deficient cells. However, reduced B-NHEJ is also observed in repair proficient, plateau-phase cells after treatment with DNA-PK inhibitors. The reduction of B-NHEJ activity in the plateau phase of growth does not derive from the reduced expression of participating proteins, is detectable by {\~a}-H2AX foci analysis, and leads to enhanced cell killing. CONCLUSIONS: These results further document the marked dependence on growth state of an essential DSB repair pathway and show the general nature of the effect. Molecular characterization of the mechanism underlying this response will help to optimize the administration of DNA repair inhibitors as adjuvants in radiation therapy.", journal = "Int J Radiat Oncol Biol Phys", keywords = "Metafer MetaCyte H2AX foci", month = "Oct", title = "Widespread Dependence of Backup NHEJ on Growth State: Ramifications for the Use of DNA-PK Inhibitors.", url = "http://dx.doi.org/10.1016/j.ijrobp.2010.08.018", year = "2010", } @article{00261, author = "R. Brem and J. Hall", journal = "Nucleic Acids Research", keywords = "CometImager", pages = "2512- 2520", title = "XRCC1 is required for DNA single-strand break repair in human cells.", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list_uids=15867196{\&}query_hl=14{\&}itool=pubmed_docsum", volume = "33", year = "2005", } @article{00090, author = "Q.-W. Jin and E. Trelles-Sticken and H. Sherthan and J. Loidl", journal = "Journal of Cell Biology", pages = "21- 29", title = "Yeast Nuclei Display Prominent Centromere Clustering That Is Reduced in Nondividing Cells and in Meiotic Propahse", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=9531545{\&}dopt=Abstract", volume = "141", year = "1998", } @article{00122, author = "N.B. Rubtsov and T.V. Karamisheva and N.M. Astakhova and T. Liehr and U. Claussen and N.S. Zhdanova", journal = "Cytogenet Cell Genet", keywords = "Isis", pages = "268- 270", title = "Zoo-FISH with region-specific pints for mink chromosome 5q: delineation of inter- and intrachromosomal rearrangements in human, pig, and fox", url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}list_uids=11124531{\&}dopt=Abstract", volume = "90", year = "2000", }