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Molecular Cytogenetic Applications in Diagnostics and Research: An Overview

  • Protocol
Fluorescence In Situ Hybridization (FISH) — Application Guide

Part of the book series: Springer Protocols Handbooks ((SPH))

Molecular cytogenetics is a new branch of chromosome research that is just is just over 25 years old. Current applications of fluorescence in situ hybridization (FISH) in diagnostics and research are summarized in this chapter. An overview of both DNA- and RNA-based in situ hybridization is provided. The application of molecular cytogenetics to inherited and acquired diseases is reviewed, including pre- and postnatal, preimplantation and tumorcytogenetic diagnostics. The use of FISH in gene mapping, mutagenesis, microbiology, interphase cytogenetics and ZOO-FISH is also reviewed, and the overall strengths and limitations of FISH in all of these fields are discussed.

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References

  • Ayala-Torres S, Chen Y, Svoboda T, Rosenblatt J, Van Houten B (2000) Analysis of gene-specific DNA damage and repair using quantitative polymerase chain reaction. Methods 22:135 – 147

    Article  CAS  PubMed  Google Scholar 

  • Brock D (1982) Current reviews in obstetrics and gynecology, vol 2. Churchill Livingstone, Edinburgh

    Google Scholar 

  • Cacheux V, Tachdjian G, Druart L, Oury JF, Serero S, Blot P, Nessmann C (1994) Evaluation of X, Y, 18, and 13/21 alpha satellite DNA probes for interphase cytogenetic analysis of unculured amniocytes by fluorescence in situ hybridization. Prenat Diagn 14:79 – 86

    Article  CAS  PubMed  Google Scholar 

  • Caparros ML, Alexiou M, Webster Z, Brockdorff N (2002) Functional analysis of the highly conserved exon IV of XIST RNA. Cytogenet Genome Res 99:99 – 105

    Article  CAS  PubMed  Google Scholar 

  • Carter NP, Ferguson-Smith MA, Perryman MT, Telenius H, Pelmear AH, Leversha MA, Glancy MT, Wood SL, Cook K, Dyson HM, et al. (1992) Reverse chromosome painting: a method for the rapid analysis of aberrant chromosomes in clinical cytogenetics. J Med Genet 29:299 – 307

    Article  CAS  PubMed  Google Scholar 

  • Caspersson T, Farber S, Foley GE, Kudynowski J, Modest EJ, Simonsson E, Wagh U, Zech L (1968) Chemical differentiation along metaphase chromosomes. Exp Cell Res 49:219 – 222

    Article  CAS  PubMed  Google Scholar 

  • Caspersson T, Castleman KR, Lomakka G, Modest EJ, Moller A, Nathan R, Wall RJ, Zech L (1971) Automatic karyotyping of quinacrine mustard stained human chromosomes. Exp Cell Res 67:233 – 235

    Article  CAS  PubMed  Google Scholar 

  • Caughey AB, Hopkins LM, Norton ME (2006) Chorionic villus sampling compared with amnio-centesis and the difference in the rate of pregnancy loss. Obstet Gynecol 108:612 – 616

    Article  PubMed  Google Scholar 

  • Chin SF, Daigo Y, Huang HE, Iyer NG, Callagy G, Kranjac T, Gonzalez M, Sangan T, Earl H, Caldas C (2003) A simple and reliable pretreatment protocol facilitates fluorescent in situ hybridisation on tissue microarrays of paraffin wax embedded tumour samples. Mol Pathol 56:275 – 279

    Article  CAS  PubMed  Google Scholar 

  • Clay H, Ramakrishnan L (2005) Multiplex fluorescent in situ hybridization in zebrafish embryos using tyramide signal amplification. Zebrafish 2:105 – 111

    Article  CAS  PubMed  Google Scholar 

  • Collins AR, Oscoz AA, Brunborg G, Gaivao I, Giovannelli L, Kruszewski M, Smith CC, Stetina R (2008) The comet assay: topical issues. Mutagenesis 23:143 – 151

    Article  CAS  PubMed  Google Scholar 

  • Cromie GA, Connelly JC, Leach DR (2001) Recombination at double-strand breaks and DNA ends: conserved mechanisms from phage to humans. Mol Cell 8:1163 – 1174

    Article  CAS  PubMed  Google Scholar 

  • Csaki A, Garwe F, Steinbr ü ck A, Maubach G, Festag G, Weise A, Riemann I, K ö nig K, Fritzsche W (2007) A parallel approach for subwavelength molecular surgery using gene-specific positioned metal nanoparticles as laser light antennas. Nano Lett 7:247 – 253

    Article  CAS  PubMed  Google Scholar 

  • Dirks RW, Molenaar C, Tanke HJ (2003) Visualizing RNA molecules inside the nucleus of living cells. Methods 29:51 – 57

    Article  CAS  PubMed  Google Scholar 

  • Gall JG, Pardue ML (1969) Formation and detection of RNA-DNA hybrid molecules in cytologi-cal preparations. Proc Natl Acad Sci USA 63:378 – 383

    Article  CAS  PubMed  Google Scholar 

  • John HA, Birnstiel ML, Jones KW (1969) RNA-DNA hybrids at the cytological level. Nature 223:582 – 587

    Article  CAS  PubMed  Google Scholar 

  • Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258:818 – 821

    Article  CAS  PubMed  Google Scholar 

  • Koch JE, K ø lvraa S, Petersen KB, Gregersen N, Bolund L (1989) Oligonucleotide-priming methods for the chromosome-specific labelling of alpha satellite DNA in situ. Chromosoma 98:259 – 265

    Article  CAS  PubMed  Google Scholar 

  • Koch J, Hindkjaer J, K ø lvraa S, Bolund L (1995) Construction of a panel of chromosome-specific oligonucleotide probes (PRINS-primers) useful for the identification of individual human chromosomes in situ. Cytogenet Cell Genet 71:142 – 147

    Article  CAS  PubMed  Google Scholar 

  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Bl ö cker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran J V, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860 – 921

    Article  CAS  PubMed  Google Scholar 

  • Langer PR, Waldrop AA, Ward DC (1981) Enzymatic synthesis of biotin-labeled polynucleotides: novel nucleic acid affinity probes. Proc Natl Acad Sci USA 78:6633 – 6637

    Article  CAS  PubMed  Google Scholar 

  • Liehr T, Starke H, Heller A, Kosyakova N, Mrasek K, Gross M, Karst C, Steinhaeuser U, Hunstig F, Fickelscher I, Kuechler A, Trifonov V, Romanenko SA, Weise A (2006) Multicolor fluorescence in situ hybridization (FISH) applied to FISH-banding. Cytogenet Genome Res 114:240 – 244

    Article  CAS  PubMed  Google Scholar 

  • Lohmann JS, Stougaard M, Koch J (2007) Detection of short repeated genomic sequences on metaphase chromosomes using padlock probes and target primed rolling circle DNA synthesis. BMC Mol Biol 8:103

    Article  PubMed  Google Scholar 

  • Luke S, Shepelsky M (1998) FISH: recent advances and diagnostic aspects. Cell Vis 5:49 – 53

    CAS  PubMed  Google Scholar 

  • McKenna DJ, Rajab NF, McKeown SR, McKerr G, McKelvey-Martin VJ (2003) Use of the comet-FISH assay to demonstrate repair of the TP53 gene region in two human bladder carcinoma cell lines. Radiat Res 159:49 – 56

    Article  CAS  PubMed  Google Scholar 

  • McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, NCBI (2008) Online Mendelian Inheritance in Man (OMIM). http://www.ncbi.nlm.nih.gov/omim

  • Nederlof PM, van der Flier S, Vrolijk J, Tanke HJ, Raap AK (1992) Fluorescence ratio measurements of double-labeled probes for multiple in situ hybridization by digital imaging microscopy. Cytometry 13:839 – 845

    Article  CAS  PubMed  Google Scholar 

  • Nuovo GJ (1995) In situ PCR: protocols and applications. PCR Methods Appl 4:S151 – S167

    CAS  PubMed  Google Scholar 

  • Ochshorn Y, Bar-Shira A, Jonish A, Yaron Y (2006) Rapid prenatal diagnosis of aneuploidy for chromosomes 21, 18, 13, and X by quantitative fluorescence polymerase chain reaction. Fetal Diagn Ther 21:326 – 331

    Article  PubMed  Google Scholar 

  • Palotie A, Heiskanen M, Laan M, Horelli-Kuitunen N (1996) High-resolution fluorescence in situ hybridization: a new approach in genome mapping. Ann Med 28:101 – 106

    Article  CAS  PubMed  Google Scholar 

  • Pearson PL (2006) Historical development of analysing large-scale changes in the human genome. Cytogenet Genome Res 115:198 – 204

    Article  CAS  PubMed  Google Scholar 

  • Pinkel D, Gray JW, Trask B, van den Engh G, Fuscoe J, van Dekken H (1986a) Cytogenetic analysis by in situ hybridization with fluorescently labeled nucleic acid probes. Cold Spring Harb Symp Quant Biol 51(Pt 1):151 – 157

    CAS  Google Scholar 

  • Pinkel D, Straume T, Gray JW (1986b) Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization. Proc Natl Acad Sci USA 83:2934 – 2938

    Article  CAS  Google Scholar 

  • Ralph S, Petras M, Pandrangi R, Vrzoc M (1996) Alkaline single-cell gel (comet) assay and genotoxicity monitoring using two species of tadpoles. Environ Mol Mutagen 28:112 – 120

    Article  CAS  PubMed  Google Scholar 

  • Rapp A, Hausmann M, Greulich KO (2005) The comet-FISH technique: a tool for detection of specific DNA damage and repair. Methods Mol Biol 291:107 – 119

    CAS  PubMed  Google Scholar 

  • Ravnan JB, Tepperberg JH, Papenhausen P, Lamb AN, Hedrick J, Eash D, Ledbetter DH, Martin CL (2006) Subtelomere FISH analysis of 11,688 cases: an evaluation of the frequency and pattern of subtelomere rearrangements in individuals with developmental disabilities. J Med Genet 43:478 – 489

    Article  CAS  PubMed  Google Scholar 

  • Santangelo P, Nitin N, Bao G (2006) Nanostructured probes for RNA detection in living cells. Ann Biomed Eng 34:39 – 50

    Article  PubMed  Google Scholar 

  • Schr ö ck E, du Manoir S, Veldman T, Schoell B, Wienberg J, Ferguson-Smith MA, Ning Y, Ledbetter DH, Bar-Am I, Soenksen D, Garini Y, Ried T (1996) Multicolor spectral karyotyping of human chromosomes. Science 273:494 – 497

    Article  PubMed  Google Scholar 

  • Speicher MR, Gwyn Ballard S, Ward DC (1996) Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 12:368 – 335

    Article  CAS  PubMed  Google Scholar 

  • Sreekantaiah C (2007) FISH panels for hematologic malignancies. Cytogenet Genome Res 118: 284 – 296

    Article  CAS  PubMed  Google Scholar 

  • Sundberg K, Jorgensen FS, Tabor A, Bang J (1995) Experience with early amniocentesis. J Perinat Med 23:149 – 158

    Article  CAS  PubMed  Google Scholar 

  • Swanson A, Strawn E, Lau E, Bick D (2007) Preimplantation genetic diagnosis: technology and clinical applications. Wisconsin Med J 106:145 – 151

    Google Scholar 

  • Veldman T, Vignon C, Schr ö ck E, Rowley JD, Ried T (1997) Hidden chromosome abnormalities in haematological malignancies detected by multicolour spectral karyotyping. Nat Genet 15: 406 – 410

    Article  CAS  PubMed  Google Scholar 

  • Wojcik A, Bruckmann E, Obe G (2004) Insights into the mechanisms of sister chromatid exchange formation. Cytogenet Genome Res 104:304 – 309

    Article  CAS  PubMed  Google Scholar 

  • Yunis JJ, Lewandowski RC (1983) High-resolution cytogenetics. Birth Defects Orig Artic Ser 19: 11 – 37

    CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Clinical Genetics, Vejle County Hospital, Vejle, Denmark

    Nedime Serakinci & Steen Kølvraa

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  1. Nedime Serakinci
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  2. Steen Kølvraa
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Correspondence to Steen Kølvraa .

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  1. Institut für Humangenetik und Anthropologie, Kollegiengasse 10, Jena, 07743, Germany

    Thomas Liehr

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Serakinci, N., Kølvraa, S. (2009). Molecular Cytogenetic Applications in Diagnostics and Research: An Overview. In: Liehr, T. (eds) Fluorescence In Situ Hybridization (FISH) — Application Guide. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-70581-9_1

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  • DOI: https://doi.org/10.1007/978-3-540-70581-9_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-70580-2

  • Online ISBN: 978-3-540-70581-9

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