Molecular karyotyping for detection of prognostic markers in fine needle aspiration biopsy samples of uveal melanoma

Methods in Molecular Biology

Volumn 1102, Issue , 2014, Pages 441-458

  Ganguly, Arupa ^a   Richards Yutz, Jennifer ^a   Ewens, Kathryn G ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Chromosome aberrations; FISH; MLPA; MSA; SNP array; Uveal melanoma

Indexed keywords

ARTICLE; CANCER GROWTH; CANCER PROGNOSIS; CHROMOSOME 1; CHROMOSOME 1P; CHROMOSOME 3; CHROMOSOME 5; CHROMOSOME 6; CHROMOSOME 6P; CHROMOSOME 6Q; CHROMOSOME 8; CHROMOSOME 8P; CHROMOSOME 8Q; CHROMOSOME LOSS; CONTROLLED STUDY; FINE NEEDLE ASPIRATION BIOPSY; FLUORESCENCE IN SITU HYBRIDIZATION; GENETIC SCREENING; HUMAN; HUMAN CELL; HUMAN TISSUE; KARYOTYPING; METASTASIS; MICROSATELLITE MARKER; MONOSOMY; MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; UVEA MELANOMA;

BIOPSY, FINE-NEEDLE; DNA, NEOPLASM; HUMANS; KARYOTYPING; MELANOMA; MICROSATELLITE REPEATS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROGNOSIS; TUMOR MARKERS, BIOLOGICAL; UVEA; UVEAL NEOPLASMS;

EID: 84891775611     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-727-3_23     Document Type: Article

References (31)

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
3. Damato B (2004) Developments in the management of uveal melanoma. Clin Exp Ophthalmol 32:639-647
4. Shields J, Shields CL (2008) Posterior uveal melanoma. Clinical features. Lippincott, Williams and Wilkins, Philadelphia, PA
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
6. Paul EV, Parnell BL, Fraker M (1962) Prognosis of malignant melanomas of the choroid and ciliary body. Int Ophthalmol Clin 12:387-402
7. Kincaid MC (1998) Uveal melanoma. Cancer Control 5:299-309
8. Damato B, Coupland SE (2009) A reappraisal of the significance of largest basal diameter of posterior uveal melanoma. Eye 23:2152-2162
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
10. Prescher G, Bornfeld N, Becher R (1990) Nonrandom chromosomal abnormalities in primary uveal melanoma. J Natl Cancer Inst 82:1765-1769
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
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
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
14. Damato B, Dopierala J, Klaasen A, van Dijk M, Sibbring J, Coupland SE (2009) Multiplex ligation-dependent probe amplifi cation of uveal melanoma: Correlation with metastatic death. Invest Ophthalmol Vis Sci 50:3048-3055
15. Damato B, Dopierala JA, Coupland SE (2010) Genotypic profiling of 452 choroidal melanomas with multiplex ligation-dependent probe amplifi cation. Clin Cancer Res 16:6083-6092
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
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
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 amplifi cation in uveal melanoma cells relate to poor patient prognosis. Invest Ophthalmol Vis Sci 53:2668-2674
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
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
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
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 fl uorescence in situ hybridization. Clin Cancer Res 8:534-539
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
24. Lake SL, Damato BE, Dopierala J, Baudo MM, Taktak AFG, Coupland SE (2011) Multiplex ligation-dependent probe amplifi cation analysis of uveal melanoma with extraocular extension demonstrates heterogeneity of gross chromosomal abnormalities. Invest Ophthalmol Vis Sci 52:5559-5564
25. Vaarwater J, van den Bosch T, Mensink HW, van Kempen C, Verdijk RM, Naus NC et al (2012) Multiplex ligation-dependent probe amplifi cation equals fl uorescence in-situ hybridization for the Identification of patients at risk for metastatic disease in uveal melanoma. Melanoma Res 22:30-37
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
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
28. Shields CL, Ganguly A, Materin MA, Teixeira L, Mashayekhi A, Swanson LA et al (2007) Chromosome 3 analysis of uveal melanoma using fi ne-needle aspiration biopsy at the time of plaque radiotherapy in 140 consecutive cases: The Deborah Iverson, MD, Lectureship. Arch Ophthalmol 125:1017-1024
29. Ewens KG, Kanetsky PA, Richards-Yutz J, Al-Dahmash S, De Luca, MC, Bianciotto CG et al (2013) Genomic profi le of 320 uveal melanoma cases: Chromosome 8p-loss and metastatic outcome. Invest Ophthalmol Vis Sci 54:5721-5729
30. Lin M, Wei LJ, Sellers WR, Lieberfarb M, Wong WH, Li C (2004) dChipSNP: Signifi -cance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics 20:1233-1240
31. Genome-Wide Human SNP Nsp/Sty 6.0 User Guide. http://www.affymetrix.com/ support/ technical/by product affx? p r oduct=genomewidesnp-nsp-sty-assay