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Molecular Cytogenetic Applications in Diagnostics and Research: An Overview

  • Nedime Serakinci
  • Steen KølvraaEmail author
Protocol
Part of the Springer Protocols Handbooks book series (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.

Keywords

Chromosome Aberration Painting Probe Williams Beuren Syndrome Kallmann Syndrome Chorionic Villous Sampling 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 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 – 147CrossRefPubMedGoogle Scholar
  2. Brock D (1982) Current reviews in obstetrics and gynecology, vol 2. Churchill Livingstone, EdinburghGoogle Scholar
  3. 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 – 86CrossRefPubMedGoogle Scholar
  4. 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 – 105CrossRefPubMedGoogle Scholar
  5. 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 – 307CrossRefPubMedGoogle Scholar
  6. 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 – 222CrossRefPubMedGoogle Scholar
  7. 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 – 235CrossRefPubMedGoogle Scholar
  8. 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 – 616CrossRefPubMedGoogle Scholar
  9. 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 – 279CrossRefPubMedGoogle Scholar
  10. Clay H, Ramakrishnan L (2005) Multiplex fluorescent in situ hybridization in zebrafish embryos using tyramide signal amplification. Zebrafish 2:105 – 111CrossRefPubMedGoogle Scholar
  11. 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 – 151CrossRefPubMedGoogle Scholar
  12. 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 – 1174CrossRefPubMedGoogle Scholar
  13. 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 – 253CrossRefPubMedGoogle Scholar
  14. Dirks RW, Molenaar C, Tanke HJ (2003) Visualizing RNA molecules inside the nucleus of living cells. Methods 29:51 – 57CrossRefPubMedGoogle Scholar
  15. Gall JG, Pardue ML (1969) Formation and detection of RNA-DNA hybrid molecules in cytologi-cal preparations. Proc Natl Acad Sci USA 63:378 – 383CrossRefPubMedGoogle Scholar
  16. John HA, Birnstiel ML, Jones KW (1969) RNA-DNA hybrids at the cytological level. Nature 223:582 – 587CrossRefPubMedGoogle Scholar
  17. 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 – 821CrossRefPubMedGoogle Scholar
  18. 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 – 265CrossRefPubMedGoogle Scholar
  19. 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 – 147CrossRefPubMedGoogle Scholar
  20. 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 – 921CrossRefPubMedGoogle Scholar
  21. 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 – 6637CrossRefPubMedGoogle Scholar
  22. 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 – 244CrossRefPubMedGoogle Scholar
  23. 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 8:103CrossRefPubMedGoogle Scholar
  24. Luke S, Shepelsky M (1998) FISH: recent advances and diagnostic aspects. Cell Vis 5:49 – 53PubMedGoogle Scholar
  25. 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 – 56CrossRefPubMedGoogle Scholar
  26. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, NCBI (2008) Online Mendelian Inheritance in Man (OMIM). http://www.ncbi.nlm.nih.gov/omim
  27. 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 – 845CrossRefPubMedGoogle Scholar
  28. Nuovo GJ (1995) In situ PCR: protocols and applications. PCR Methods Appl 4:S151 – S167PubMedGoogle Scholar
  29. 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 – 331CrossRefPubMedGoogle Scholar
  30. 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 – 106CrossRefPubMedGoogle Scholar
  31. Pearson PL (2006) Historical development of analysing large-scale changes in the human genome. Cytogenet Genome Res 115:198 – 204CrossRefPubMedGoogle Scholar
  32. 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 – 157Google Scholar
  33. Pinkel D, Straume T, Gray JW (1986b) Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization. Proc Natl Acad Sci USA 83:2934 – 2938CrossRefGoogle Scholar
  34. 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 – 120CrossRefPubMedGoogle Scholar
  35. 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 – 119PubMedGoogle Scholar
  36. 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 – 489CrossRefPubMedGoogle Scholar
  37. Santangelo P, Nitin N, Bao G (2006) Nanostructured probes for RNA detection in living cells. Ann Biomed Eng 34:39 – 50CrossRefPubMedGoogle Scholar
  38. 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 – 497CrossRefPubMedGoogle Scholar
  39. Speicher MR, Gwyn Ballard S, Ward DC (1996) Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 12:368 – 335CrossRefPubMedGoogle Scholar
  40. Sreekantaiah C (2007) FISH panels for hematologic malignancies. Cytogenet Genome Res 118: 284 – 296CrossRefPubMedGoogle Scholar
  41. Sundberg K, Jorgensen FS, Tabor A, Bang J (1995) Experience with early amniocentesis. J Perinat Med 23:149 – 158CrossRefPubMedGoogle Scholar
  42. Swanson A, Strawn E, Lau E, Bick D (2007) Preimplantation genetic diagnosis: technology and clinical applications. Wisconsin Med J 106:145 – 151Google Scholar
  43. 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 – 410CrossRefPubMedGoogle Scholar
  44. Wojcik A, Bruckmann E, Obe G (2004) Insights into the mechanisms of sister chromatid exchange formation. Cytogenet Genome Res 104:304 – 309CrossRefPubMedGoogle Scholar
  45. Yunis JJ, Lewandowski RC (1983) High-resolution cytogenetics. Birth Defects Orig Artic Ser 19: 11 – 37PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  1. 1.Department of Clinical GeneticsVejle County HospitalVejleDenmark

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