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Molecular Karyotyping for Detection of Prognostic Markers in Fine Needle Aspiration Biopsy Samples of Uveal Melanoma

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1102))

Abstract

Uveal melanoma is the most common cancer of the eye in which approximately 50 % of cases develop metastases that are fatal within 2–15 years. Thus it is critical to identify prognostic markers to select high-risk patients into an adjuvant treatment. Chromosomal copy number alterations have been associated with poor prognosis. Historically the gold standard for identifying chromosomal aberrations had been fluorescent in situ hybridization. But in recent years other techniques have been developed that allow very rapid molecular analysis for estimation of chromosomal copy number with finer resolution. These include microsatellite analysis, multiple ligation-dependent probe amplification, and, most recently, genome-wide single-nucleotide polymorphism array analysis. These various procedures have identified loss of all or part of chromosome 3 (monosomy), losses of 1p, 6q, or 8p, or gains of 6p or 8q which, together with tumor location, morphology, and size, can be used to accurately predict the risk of metastasis.

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References

  1. Gaudi SM JL (2011) Molecular bases of cutaneous and uveal melanomas. Pathol Res Int. doi: 10.4061/2011/159421

  2. van den Bosch T, Kilic E, Paridaens D, de Klein A (2010) Genetics of uveal melanoma and cutaneous melanoma: two of a kind? Dermatol Res Pract. doi:10.1155/2010/360136

    PubMed  Google Scholar 

  3. Damato B (2004) Developments in the management of uveal melanoma. Clin Exp Ophthalmol 32:639–647

    Article  Google Scholar 

  4. Shields J, Shields CL (2008) Posterior uveal melanoma. Clinical features. Lippincott, Williams and Wilkins, Philadelphia, PA

    Google Scholar 

  5. Kujala E, Mäkitie T, Kivelä T (2003) Very long-term prognosis of patients with malignant uveal melanoma. Invest Ophthalmol Vis Sci 44:4651–4659

    Article  PubMed  Google Scholar 

  6. Paul EV, Parnell BL, Fraker M (1962) Prognosis of malignant melanomas of the choroid and ciliary body. Int Ophthalmol Clin 12:387–402

    Article  Google Scholar 

  7. Kincaid MC (1998) Uveal melanoma. Cancer Control 5:299–309

    PubMed  Google Scholar 

  8. Damato B, Coupland SE (2009) A reappraisal of the significance of largest basal diameter of posterior uveal melanoma. Eye 23:2152–2162

    Article  PubMed  CAS  Google Scholar 

  9. Damato B, Eleuteri A, Taktak AFG, Coupland SE (2011) Estimating prognosis for survival after treatment of choroidal melanoma. Prog Retin Eye Res 30:285–295

    Article  PubMed  Google Scholar 

  10. Prescher G, Bornfeld N, Becher R (1990) Nonrandom chromosomal abnormalities in primary uveal melanoma. J Natl Cancer Inst 82:1765–1769

    Article  PubMed  CAS  Google Scholar 

  11. Sisley K, Cottam DW, Rennie IG, Parsons MA, Potter AM, Potter CW et al (1992) Non-random abnormalities of chromosomes 3, 6, and 8 associated with posterior uveal melanoma. Genes Chromosomes Cancer 5:197–200

    Article  PubMed  CAS  Google Scholar 

  12. Sisley KR, Rennie IG, Cottam DW, Potter AM, Potter CW, Rees RC (1990) Cytogenetic findings in six posterior uveal melanomas: involvement of chromosomes 3, 6, and 8. Genes Chromosomes Cancer 2:205–209

    Article  PubMed  CAS  Google Scholar 

  13. Prescher G, Bornfeld N, Hirche H, Horsthemke B, Jockel KH, Becher R (1996) Prognostic implications of monosomy 3 in uveal melanoma. Lancet 347:1222–1225

    Article  PubMed  CAS  Google Scholar 

  14. Damato B, Dopierala J, Klaasen A, van Dijk M, Sibbring J, Coupland SE (2009) Multiplex ligation-dependent probe amplification of uveal melanoma: correlation with metastatic death. Invest Ophthalmol Vis Sci 50:3048–3055

    Article  PubMed  Google Scholar 

  15. Damato B, Dopierala JA, Coupland SE (2010) Genotypic profiling of 452 choroidal melanomas with multiplex ligation-dependent probe amplification. Clin Cancer Res 16:6083–6092

    Article  PubMed  CAS  Google Scholar 

  16. Damato B, Duke C, Coupland SE, Hiscott P, Smith PA, Campbell I et al (2007) Cytogenetics of uveal melanoma: a 7-year clinical experience. Ophthalmology 114:1925–1931

    Article  PubMed  Google Scholar 

  17. Kilic E, Naus NC, van Gils W, Klaver CC, van Til ME, Verbiest MM et al (2005) Concurrent loss of chromosome arm 1p and chromosome 3 predicts a decreased disease-free survival in uveal melanoma patients. Invest Ophthalmol Vis Sci 46:2253–2257

    Article  PubMed  Google Scholar 

  18. van den Bosch T, van Beek JGM, Vaarwater J, Verdijk RM, Naus NC, Paridaens D et al (2012) Higher percentage of FISH-determined monosomy 3 and 8q amplification in uveal melanoma cells relate to poor patient prognosis. Invest Ophthalmol Vis Sci 53:2668–2674

    Article  PubMed  Google Scholar 

  19. Cross NA, Ganesh A, Parpia M, Murray AK, Rennie IG, Sisley K (2006) Multiple locations on chromosome 3 are the targets of specific deletions in uveal melanoma. Eye 20:476–481

    Article  PubMed  CAS  Google Scholar 

  20. Parrella P, Fazio VM, Gallo AP, Sidransky D, Merbs SL (2003) Fine mapping of chromosome 3 in uveal melanoma: identification of a minimal region of deletion on chromosomal arm 3p25.1-p25.2. Cancer Res 63:8507–8510

    PubMed  CAS  Google Scholar 

  21. Tschentscher F, Prescher G, Horsman DE, White VA, Rieder H, Anastassiou G et al (2001) Partial deletions of the long and short arm of chromosome 3 point to two tumor suppressor genes in uveal melanoma. Cancer Res 61:3439–3442

    PubMed  CAS  Google Scholar 

  22. Naus NC, Verhoeven ACA, van Drunen E, Slater R, Mooy CM, Paridaens DA et al (2002) Detection of genetic prognostic markers in uveal melanoma biopsies using fluorescence in situ hybridization. Clin Cancer Res 8:534–539

    PubMed  Google Scholar 

  23. Aronow M, Sun Y, Saunthararajah Y, Biscotti C, Tubbs R, Triozzi P et al (2012) Monosomy 3 by FISH in uveal melanoma: variability in techniques and results. Surv Ophthalmol 57:463–473

    Article  PubMed  Google Scholar 

  24. Lake SL, Damato BE, Dopierala J, Baudo MM, Taktak AFG, Coupland SE (2011) Multiplex ligation-dependent probe amplification analysis of uveal melanoma with extraocular extension demonstrates heterogeneity of gross chromosomal abnormalities. Invest Ophthalmol Vis Sci 52:5559–5564

    Article  PubMed  CAS  Google Scholar 

  25. Vaarwater J, van den Bosch T, Mensink HW, van Kempen C, Verdijk RM, Naus NC et al (2012) Multiplex ligation-dependent probe amplification equals fluorescence in-situ hybridization for the identification of patients at risk for metastatic disease in uveal melanoma. Melanoma Res 22:30–37

    Article  PubMed  CAS  Google Scholar 

  26. Lake SL, Coupland SE, Taktak AFG, Damato BE (2010) Whole-genome microarray detects deletions and loss of heterozygosity of chromosome 3 occurring exclusively in metastasizing uveal melanoma. Invest Ophthalmol Vis Sci 51:4884–4891

    Article  PubMed  Google Scholar 

  27. Tschentscher F, Prescher G, Zeschnigk M, Horsthemke B, Lohmann DR (2000) Identification of chromosomes 3, 6, and 8 aberrations in uveal melanoma by microsatellite analysis in comparison to comparative genomic hybridization. Cancer Genet Cytogenet 122:13–17

    Article  PubMed  CAS  Google Scholar 

  28. Shields CL, Ganguly A, Materin MA, Teixeira L, Mashayekhi A, Swanson LA et al (2007) Chromosome 3 analysis of uveal melanoma using fine-needle aspiration biopsy at the time of plaque radiotherapy in 140 consecutive cases: the Deborah Iverson, MD, Lectureship. Arch Ophthalmol 125:1017–1024

    Article  PubMed  Google Scholar 

  29. Ewens KG, Kanetsky PA, Richards-Yutz J, Al-Dahmash S, De Luca, MC, Bianciotto CG et al (2013) Genomic profile of 320 uveal melanoma cases: Chromosome 8p-loss and metastatic outcome. Invest Ophthalmol Vis Sci 54:5721–5729

    Article  PubMed  Google Scholar 

  30. Lin M, Wei LJ, Sellers WR, Lieberfarb M, Wong WH, Li C (2004) dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics 20:1233–1240

    Article  PubMed  CAS  Google Scholar 

  31. Genome-Wide Human SNP Nsp/Sty 6.0 User Guide. http://www.affymetrix.com/support/technical/byproduct.affx?product=genomewidesnp_nsp_sty_assay

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Ganguly, A., Richards-Yutz, J., Ewens, K.G. (2014). Molecular Karyotyping for Detection of Prognostic Markers in Fine Needle Aspiration Biopsy Samples of Uveal Melanoma. In: Thurin, M., Marincola, F. (eds) Molecular Diagnostics for Melanoma. Methods in Molecular Biology, vol 1102. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-727-3_23

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  • DOI: https://doi.org/10.1007/978-1-62703-727-3_23

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-726-6

  • Online ISBN: 978-1-62703-727-3

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