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Fluorescence In Situ Hybridization

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Molecular Biomethods Handbook

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References

  1. Rudkin GT, Stollar BD (1977) High resolution detection of DNA-RNA hybrids in situ by indirect immunofluorescence. Nature 265:472–473

    Article  PubMed  CAS  Google Scholar 

  2. Lichter P, Cremer T, Borden J, Manuelidis L, Ward DC (1988) Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Hum Genet 80:224–234

    Article  PubMed  CAS  Google Scholar 

  3. Jang W, Yonescu R, Knutsen T, Brown T, Reppert T, Sirotkin K, Schuler GD, Ried T, Kirsch IR (2006) Linking the human cytogenetic map with nucleotide sequence: the CCAP clone set. Cancer Genet Cytogenet 168:89–97

    Article  PubMed  CAS  Google Scholar 

  4. Knutsen T, Gobu V, Knaus R, Padilla-Nash H, Augustus M, Strausberg RL, Kirsch IR, Sirotkin K, Ried T (2005) The interactive online SKY/M-FISH & CGH database and the Entrez cancer chromosomes search database: linkage of chromosomal aberrations with the genome sequence. Genes Chromosomes Cancer 44:52–64

    Article  PubMed  CAS  Google Scholar 

  5. Oliveira AM, French CA (2005) Applications of fluorescence in situ hybridization in cytopathology: a review. Acta Cytol 49:587–594

    Article  PubMed  Google Scholar 

  6. 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  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  8. Speicher MR, Gwyn Ballard S, Ward DC (1996) Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 12:368–375

    Article  PubMed  CAS  Google Scholar 

  9. Chudoba I, Plesch A, Lorch T, Lemke J, Claussen U, Senger G (1999) High resolution multicolor-banding: a new technique for refined FISH analysis of human chromosomes. Cytogenet Cell Genet 84:156–160

    Article  PubMed  CAS  Google Scholar 

  10. Bayani J, Squire JA (2000) Chapter 22 cell biology of chromosomes and Nuclei. In: Current protocols in cell biology (Morgan, K.). John Wiley & Sons, Inc, Bethesda

    Google Scholar 

  11. Schwarzacher T, Heslop-Harrison P (2000) Practical in situ hybridization. Springer-Verlag, New York

    Google Scholar 

  12. Hungerford DA, Donnely A, Nowel A, Beck S (1959) The chromosome constitution of a human phenotypic intersex. Am J Hum Gen 11:215

    CAS  Google Scholar 

  13. Moorhead PS, Nowell PC, Mellman WJ, Battips DM, Hungerford DA (1960) Chromosome preparations of leukocytes cultured from human peripheral blood. Exp Cell Res 20:613–616

    Article  PubMed  CAS  Google Scholar 

  14. Barch MJ (1991) The ACT cytogenetics laboratory manual, 2nd edn Raven Press, New York

    Google Scholar 

  15. Henegariu O, Heerema NA, Lowe Wright L, Bray-Ward P, Ward DC, Vance GH (2001) Improvements in cytogenetic slide preparation: controlled chromosome spreading, chemical aging and gradual denaturing. Cytometry 43:101–109

    Article  PubMed  CAS  Google Scholar 

  16. Speel EJ (1999) Robert Feulgen Prize Lecture 1999. Detection and amplification systems for sensitive, multiple-target DNA and RNA in situ hybridization: looking inside cells with a spectrum of colors. Histochem Cell Biol 112:89–113

    Article  PubMed  CAS  Google Scholar 

  17. Squire J, Meurs EF, Chong KL, McMillan NA, Hovanessian AG, Williams BR (1993) Localization of the human interferon-induced, ds-RNA activated p68 kinase gene (PRKR) to chromosome 2p21–p22. Genomics 16:768–770

    Article  PubMed  CAS  Google Scholar 

  18. Matsuda Y, Harada YN, Natsuume-Sakai S, Lee K, Shiomi T, Chapman VM (1992) Location of the mouse complement factor H gene (cfh) by FISH analysis and replication R-banding. Cytogenet Cell Genet 61:282–285

    Article  PubMed  CAS  Google Scholar 

  19. Milatovich A, Hsieh CL, Bonaminio G, Tecott L, Julius D, Francke U (1992) Serotonin receptor 1c gene assigned to X chromosome in human (band q24) and mouse (bands D-F4). Hum Mol Genet 1:681–684

    Article  PubMed  CAS  Google Scholar 

  20. Liu J, Tsai YL, Zheng XZ, Baramki TA, Yazigi RA, Katz E (1998) Potential use of repeated fluorescence in situ hybridization in the same human blastomeres for preimplantation genetic diagnosis. Fertil Steril 70:729–733

    Article  PubMed  CAS  Google Scholar 

  21. Verlinsky Y, Cieslak J, Ivakhnenko V, Evsikov S, Wolf G, White M, Lifchez A, Kaplan B, Moise J, Valle J, Ginsberg N, Strom C, Kuliev A (1997) Prepregnancy genetic testing for age-related aneuploidies by polar body analysis. Genet Test 1:231–235

    Article  PubMed  Google Scholar 

  22. Daniel A, Wu Z, Darmanian A, Malafiej P, Tembe V, Peters G, Kennedy C, Ades L (2004) Issues arising from the prenatal diagnosis of some rare trisomy mosaics – the importance of cryptic fetal mosaicism. Prenat Diagn 24:524–536

    Article  PubMed  Google Scholar 

  23. Romana SP, Tachdjian G, Druart L, Cohen D, Berger R, Cherif D (1993) A simple method for prenatal diagnosis of trisomy 21 on uncultured amniocytes. Eur J Hum Genet 1:245–251

    PubMed  CAS  Google Scholar 

  24. Leana-Cox J, Jenkins L, Palmer CG, Plattner R, Sheppard L, Flejter WL, Zackowski J, Tsien F, Schwartz S (1994) Molecular cytogenetic analysis of inv dup(15) chromosomes, using probes specific for the Prader-Willi/Angelman syndrome region: clinical implications. Am J Hum Genet 54:748–756

    PubMed  CAS  Google Scholar 

  25. Pettenati MJ, Hayworth R, Cox K, Rao PN (1994) Prenatal detection of cri du chat syndrome on uncultured amniocytes using fluorescence in situ hybridization (FISH). Clin Genet 45:17–20

    Article  PubMed  CAS  Google Scholar 

  26. Driscoll DA (2001) Prenatal diagnosis of the 22q11.2 deletion syndrome. Genet Med 3:14–18

    Article  PubMed  CAS  Google Scholar 

  27. Weksberg R, Stachon AC, Squire JA, Moldovan L, Bayani J, Meyn S, Chow E, Bassett AS (2006) Molecular characterization of deletion break-points in adults with 22q11 deletion syndrome. Hum Genet 6:837–845

    Google Scholar 

  28. Rowley JD (1973) Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature 243:290–293

    Article  PubMed  CAS  Google Scholar 

  29. Landstrom AP, Tefferi A (2006) Fluorescent in situ hybridization in the diagnosis, prognosis, and treatment monitoring of chronic myeloid leukemia. Leuk Lymphoma 47:397–402

    Article  PubMed  CAS  Google Scholar 

  30. Hanna W (2001) Testing for HER2 status. Oncology 61 Suppl 2:22–30

    Google Scholar 

  31. Hicks DG, Tubbs RR (2005) Assessment of the HER2 status in breast cancer by fluorescence in situ hybridization: a technical review with interpretive guidelines. Hum Pathol 36:250–261

    Article  PubMed  CAS  Google Scholar 

  32. Slamon DJ, Clark GM, Wong SG, Levin WJ, Ullrich A, McGuire WL (1987) Human breast cancer: correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 235:177–182

    Article  PubMed  CAS  Google Scholar 

  33. Ross JS, Fletcher JA, Bloom KJ, Linette GP, Stec J, Symmans WF, Pusztai L, Hortobagyi GN (2004) Targeted therapy in breast cancer: the HER-2/neu gene and protein. Mol Cell Proteomics 3:379–398

    Article  PubMed  CAS  Google Scholar 

  34. Balmain A, Gray J, Ponder B (2003) The genetics and genomics of cancer. Nat Genet 33 Suppl:238–244

    Article  PubMed  CAS  Google Scholar 

  35. Speicher MR, Carter NP (2005) The new cytogenetics: blurring the boundaries with molecular biology. Nat Rev Genet 6:782–792

    Article  PubMed  CAS  Google Scholar 

  36. Bayani J, Brenton JD, Macgregor PF, Beheshti B, Albert M, Nallainathan D, Karaskova J, Rosen B, Murphy J, Laframboise S, Zanke B, Squire JA (2002) Parallel analysis of sporadic primary ovarian carcinomas by spectral karyotyp-ing, comparative genomic hybridization, and expression microarrays. Cancer Res 62:3466–3476

    PubMed  CAS  Google Scholar 

  37. Zielenska M, Bayani J, Pandita A, Toledo S, Marrano P, Andrade J, Petrilli A, Thorner P, Sorensen P, Squire JA (2001) Comparative genomic hybridization analysis identifies gains of 1p35 approximately p36 and chromosome 19 in oste-osarcoma. Cancer Genet Cytogenet 130:14–21

    Article  PubMed  CAS  Google Scholar 

  38. Bayani J, Pandita A, Squire JA (2005) Molecular cytogenetic analysis in the study of brain tumors: findings and applications. Neurosurg Focus 19:E1

    Article  PubMed  Google Scholar 

  39. Bayani J, Selvarajah S, Maire G, Vukovic B, A1-Romaih K, Zielenska M, Squire JA (2006) Genomic mechanisms and measurement of structural and numerical instability in cancer cells. Semin Cancer Biol 1:5–18

    Google Scholar 

  40. Bayani JM, Squire JA (2002) Applications of SKY in cancer cytogenetics. Cancer Invest 20:373–386

    Article  PubMed  Google Scholar 

  41. Bayani J, Zielenska M, Pandita A, A1-Romaih K, Karaskova J, Harrison K, Bridge JA, Sorensen P, Thorner P, Squire JA (2003) Spectral karyotyping identifies recurrent complex rearrangements of chromosomes 8, 17, and 20 in osteosarcomas. Genes Chromosomes Cancer 36:7–16

    Article  PubMed  CAS  Google Scholar 

  42. Beheshti B, Karaskova J, Park PC, Squire JA, Beatty BG (2000) Identification of a high frequency of chromosomal rearrangements in the centromeric regions of prostate cancer cell lines by sequential giemsa banding and spectral karyotyping. Mol Diagn 5:23–32

    PubMed  CAS  Google Scholar 

  43. Singh SK, Hawkins C, Clarke ID, Squire JA, Bayani J, Hide T, Henkelman RM, Cusimano MD, Dirks, PB (2004) Identification of human brain tumor initiating cells. Nature 432:396–401

    Article  PubMed  CAS  Google Scholar 

  44. Squire JA, Arab S, Marrano P, Bayani J, Karaskova J, Taylor M, Becker L, Rutka J, Zielenska M (2001) Molecular cytogenetic analysis of glial tumors using spectral karyotyping and comparative genomic hybridization. Mol Diagn 6:93–108

    Article  PubMed  CAS  Google Scholar 

  45. Lim G, Karaskova J, Beheshti B, Vukovic B, Bayani J, Selvarajah S, Watson SK, Lam WL, Zielenska M, Squire JA (2005) An integrated mBAND and submegabase resolution tiling set (SMRT) CGH array analysis of focal amplification, microdeletions, and ladder structures consistent with breakage-fusion-bridge cycle events in osteosarcoma. Genes Chromosomes Cancer 42:392–403

    Article  PubMed  CAS  Google Scholar 

  46. Lim G, Karaskova J, Vukovic B, Bayani J, Beheshti B, Bernardini M, Squire JA, Zielenska M (2004) 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 line MG-63. Cancer Genet Cytogenet 153:158–164

    Article  PubMed  CAS  Google Scholar 

  47. Selvarajah S, Yoshimoto M, Park PC, Maire G, Paderova J, Bayani J, Lim G, Al-Romaih K, Squire JA, Zielenska M (2006) The breakage-fusion-bridge (BFB) cycle as a mechanism for generating genetic heterogeneity in osteosarcoma. Chromosoma 6:459–467

    Article  Google Scholar 

  48. Vukovic B, Beheshti B, Park PC, Lim G, Bayani J, Zielenska M, Squire JA Correlating breakage-fusion-bridge events with the over-all chromosomal instability and in vitro karyotypic evolution in prostate cancer. Cytogenet Genome Res 1–2:1–11

    Google Scholar 

  49. Squire JA, Thorner P, Marrano P, Parkinson D, Ng YK, Gerrie B, Chilton-Macneill S, Zielenska M (1996) Identification of MYCN copy number heterogeneity by direct FISH analysis of neuroblastoma preparations. Mol Diagn 1:281–289

    Article  PubMed  CAS  Google Scholar 

  50. Tsao MS, Sakurada A, Cutz JC, Zhu CQ, Kamel-Reid S, Squire J, Lorimer I, Zhang T, Liu N, Daneshmand M, Marrano P, da Cunha Santos G, Lagarde A, Richardson F, Seymour L, Whitehead M, Ding K, Pater J, Shepherd FA (2005) Erlotinib in lung cancer – molecular and clinical predictors of outcome. N Engl J Med 353:133–144

    Article  PubMed  CAS  Google Scholar 

  51. Yoshimoto M, Cutz JC, Nuin PA, Joshua AM, Bayani J, Evans AJ, Zielenska M, Squire JA (2006) Interphase FISH analysis of PTEN in histologic sections shows genomic deletions in 68% of primary prostate cancer and 23% of high-grade pros-tatic intra-epithelial neoplasias. Cancer Genet Cytogenet 169:128–137

    Article  PubMed  CAS  Google Scholar 

  52. Kolomietz E, Al-Maghrabi J, Brennan S, Karaskova J, Minkin S, Lipton J, Squire JA (2001) Primary chromosomal rearrangements of leukemia are frequently accompanied by extensive submicroscopic deletions and may lead to altered prognosis. Blood 97:3581–3588

    Article  PubMed  CAS  Google Scholar 

  53. Yoshimoto M, Joshua AM, Chilton-Macneill S, Bayani J, Selvarajah S, Evans AJ, Zielenska M, Squire JA (2006) Three-color FISH analysis of TMPRSS2/ERG fusions in prostate cancer indicates that genomic microdeletion of chromosome 21 is associated with rearrangement. Neoplasia 8:465–469

    Article  PubMed  CAS  Google Scholar 

  54. Kelloff GJ, Lippman SM, Dannenberg AJ, Sigman CC, Pearce HL, Reid BJ, Szabo E, Jordan VC, Spitz MR, Mills GB, Papadimitrakopoulou VA, Lotan R, Aggarwal BB, Bresalier RS, Kim J, Arun B, Lu KH, Thomas ME, Rhodes HE, Brewer MA, Follen M, Shin DM, Parnes HL, Siegfried JM, Evans AA, Blot WJ, Chow WH, Blount PL, Maley CC, Wang KK, Lam S, Lee JJ, Dubinett SM, Engstrom PF, Meyskens FL, Jr, O 'Shaughnessy J, Hawk ET, Levin B, Nelson WG, Hong WK (2006) Progress in chemoprevention drug development: the promise of molecular biomarkers for prevention of intraepithelial neoplasia and cancer – a plan to move forward. Clin Cancer Res 12:3661–3697

    Article  PubMed  CAS  Google Scholar 

  55. Braunschweig T, Chung JY, Hewitt SM (2005) Tissue microarrays: bridging the gap between research and the clinic. Expert Rev Proteomics 2:325–336

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments:

The authors wish to acknowledge all current and former members of the Squire and Zielenska Laboratories for their technical contributions (http://www.utoronto.ca/cancyto/). This work has been supported through funds from the National Cancer Institute of Canada (NCIC) and the Terry Fox Foundation, The Prostate Cancer Research Foundation of Canada (PCRFC), The Ontario Cancer Research Network (OCRN), The Canadian Foundation for Innovation (CFI), The James Fund for Neuroblastoma Research and The Princess Margaret Ovarian Cancer Foundation.

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Bayani, J., Squire, J.A. (2008). Fluorescence In Situ Hybridization. In: Walker, J.M., Rapley, R. (eds) Molecular Biomethods Handbook. Springer Protocols Handbooks. Humana Press. https://doi.org/10.1007/978-1-60327-375-6_17

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  • DOI: https://doi.org/10.1007/978-1-60327-375-6_17

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