A Prognostic Test to Predict the Risk of Metastasis in Uveal Melanoma Based on a 15-Gene Expression Profile

  • J. William Harbour
Part of the Methods in Molecular Biology book series (MIMB, volume 1102)


Uveal (ocular) melanoma is an aggressive cancer that metastasizes in up to half of patients. Uveal melanoma spreads preferentially to the liver, and the metastatic disease is almost always fatal. There are no effective therapies for advanced metastatic disease, so the most promising strategy for improving survival is to detect metastasis at an earlier stage or to treat high-risk patients in an adjuvant setting. An accurate test for identifying high-risk patients would allow for such personalized management as well as for stratification of high-risk patients into clinical trials of adjuvant therapy.

We developed a gene expression profile (GEP) that distinguishes between primary uveal melanomas that have a low metastatic risk (class 1 tumors) and those with a high metastatic risk (class 2 tumors). We migrated the GEP from a high-density microarray platform to a 15-gene, qPCR-based assay that is now performed in a College of American Pathologists (CAP)-accredited Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory on a routine clinical basis on very small samples obtained by fine needle aspiration and on archival formalin-fixed specimens. We collaborated with several centers to show that our specimen collection protocol was easily learned and performed and that it allowed samples to be safely and reliably transported from distant locations with a very low failure rate. Finally, we showed in a multicenter, prospective study that our GEP assay is highly accurate for predicting which patients will develop metastatic disease, and it was significantly superior to the previous gold standard, chromosome 3 testing for monosomy 3. This is the only prognostic test in uveal melanoma ever to undergo such extensive validation, and it is currently being used in a commercial format under the trade name DecisionDx-UM in over 100 centers in the USA and Canada.

Key words

Uveal melanoma Metastasis Prognosis Gene expression profiling Support vector machine Machine learning algorithm 


  1. 1.
    Harbour JW (2003) Clinical overview of uveal melanoma: introduction to tumors of the eye. In: Albert DM, Polans A (eds) Ocular oncology. Marcel Dekker, New York, pp 1–18CrossRefGoogle Scholar
  2. 2.
    Onken MD, Worley LA, Ehlers JP, Harbour JW (2004) Gene expression profiling in uveal melanoma reveals two molecular classes and predicts metastatic death. Cancer Res 64:7205–7209CrossRefPubMedGoogle Scholar
  3. 3.
    Egan KM, Seddon JM, Glynn RJ, Gragoudas ES, Albert DM (1988) Epidemiologic aspects of uveal melanoma. Surv Ophthalmol 32:239–251CrossRefPubMedGoogle Scholar
  4. 4.
    Ramaiya KJ, Harbour JW (2007) Current management of uveal melanoma. Exp Rev Ophthalmol 2:939–946CrossRefGoogle Scholar
  5. 5.
    Diener-West M, Reynolds SM, Agugliaro DJ, Caldwell R, Cumming K, Earle JD, Hawkins BS, Hayman JA, Jaiyesimi I, Jampol LM, Kirkwood JM, Koh WJ, Robertson DM, Shaw JM, Straatsma BR, Thoma J (2005) Development of metastatic disease after enrollment in the COMS trials for treatment of choroidal melanoma: Collaborative Ocular Melanoma Study Group Report No. 26. Arch Ophthalmol 123:1639–1643CrossRefPubMedGoogle Scholar
  6. 6.
    Augsburger JJ, Gamel JW (1990) Clinical prognostic factors in patients with posterior uveal malignant melanoma. Cancer 66:1596–1600CrossRefPubMedGoogle Scholar
  7. 7.
    Gamel JW, McLean IW, Foster WD, Zimmerman LE (1978) Uveal melanomas: correlation of cytologic features with prognosis. Cancer 41:1897–1901CrossRefPubMedGoogle Scholar
  8. 8.
    de la Cruz PO Jr, Spech CS, McLean IW (1990) Lymphocytic infiltration in uveal malignant melanoma. Cancer 65:112–115CrossRefPubMedGoogle Scholar
  9. 9.
    Folberg R, Pe’er J, Gruman LM, Woolson RF, Jeng G, Montague PR, Moninger TO, Yi H, Moore KC (1992) The morphologic characteristics of tumor blood vessels as a marker of tumor progression in primary human uveal melanoma: a matched case-control study. Hum Pathol 23:1298–1305CrossRefPubMedGoogle Scholar
  10. 10.
    Makitie T, Summanen P, Tarkkanen A, Kivela T (2001) Tumor-infiltrating macrophages (CD68(+) cells) and prognosis in malignant uveal melanoma. Invest Ophthalmol Vis Sci 42:1414–1421PubMedGoogle Scholar
  11. 11.
    Kujala E, Makitie T, Kivela T (2003) Very long-term prognosis of patients with malignant uveal melanoma. Invest Ophthalmol Vis Sci 44:4651–4659CrossRefPubMedGoogle Scholar
  12. 12.
    Kath R, Hayungs J, Bornfeld N, Sauerwein W, Hoffken K, Seeber S (1993) Prognosis and treatment of disseminated uveal melanoma. Cancer 72:2219–2223CrossRefPubMedGoogle Scholar
  13. 13.
    Griffin CA, Long PP, Schachat AP (1988) Trisomy 6p in an ocular melanoma. Cancer Genet Cytogenet 32:129–132CrossRefPubMedGoogle Scholar
  14. 14.
    Horsman DE, Sroka H, Rootman J, White VA (1990) Monosomy 3 and isochromosome 8q in a uveal melanoma. Cancer Genet Cytogenet 45:249–253CrossRefPubMedGoogle Scholar
  15. 15.
    Prescher G, Bornfeld N, Becher R (1990) Nonrandom chromosomal abnormalities in primary uveal melanoma. J Natl Cancer Inst 82:1765–1769CrossRefPubMedGoogle Scholar
  16. 16.
    Sisley K, 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 2:205–209CrossRefPubMedGoogle Scholar
  17. 17.
    Wiltshire RN, Elner VM, Dennis T, Vine AK, Trent JM (1993) Cytogenetic analysis of posterior uveal melanoma. Cancer Genet Cytogenet 66:47–53CrossRefPubMedGoogle Scholar
  18. 18.
    Singh AD, Boghosian-Sell L, Wary KK, Shields CL, De Potter P, Donoso LA, Shields JA, Cannizzaro LA (1994) Cytogenetic findings in primary uveal melanoma. Cancer Genet Cytogenet 72:109–115CrossRefPubMedGoogle Scholar
  19. 19.
    Prescher G, Bornfeld N, Friedrichs W, Seeber S, Becher R (1995) Cytogenetics of twelve cases of uveal melanoma and patterns of nonrandom anomalies and isochromosome formation. Cancer Genet Cytogenet 80:40–46CrossRefPubMedGoogle Scholar
  20. 20.
    McNamara M, Felix C, Davison EV, Fenton M, Kennedy SM (1997) Assessment of chromosome 3 copy number in ocular melanoma using fluorescence in situ hybridization. Cancer Genet Cytogenet 98:4–8CrossRefPubMedGoogle Scholar
  21. 21.
    Patel KA, Edmondson ND, Talbot F, Parsons MA, Rennie IG, Sisley K (2001) Prediction of prognosis in patients with uveal melanoma using fluorescence in situ hybridisation. Br J Ophthalmol 85:1440–1444CrossRefPubMedGoogle Scholar
  22. 22.
    Speicher MR, Prescher G, du Manoir S, Jauch A, Horsthemke B, Bornfeld N, Becher R, Cremer T (1994) Chromosomal gains and losses in uveal melanomas detected by comparative genomic hybridization. Cancer Res 54:3817–3823PubMedGoogle Scholar
  23. 23.
    Gordon KB, Thompson CT, Char DH, O’Brien JM, Kroll S, Ghazvini S, Gray JW (1994) Comparative genomic hybridization in the detection of DNA copy number abnormalities in uveal melanoma. Cancer Res 54:4764–4768PubMedGoogle Scholar
  24. 24.
    Ghazvini S, Char DH, Kroll S, Waldman FM, Pinkel D (1996) Comparative genomic hybridization analysis of archival formalin-fixed paraffin-embedded uveal melanomas. Cancer Genet Cytogenet 90:95–101CrossRefPubMedGoogle Scholar
  25. 25.
    Aalto Y, Eriksson L, Seregard S, Larsson O, Knuutila S (2001) Concomitant loss of chromosome 3 and whole arm losses and gains of chromosome 1, 6, or 8 in metastasizing primary uveal melanoma. Invest Ophthalmol Vis Sci 42:313–317PubMedGoogle Scholar
  26. 26.
    Hughes S, Damato BE, Giddings I, Hiscott PS, Humphreys J, Houlston RS (2005) Microarray comparative genomic hybridisation analysis of intraocular uveal melanomas identifies distinctive imbalances associated with loss of chromosome 3. Br J Cancer 93:1191–1196CrossRefPubMedGoogle Scholar
  27. 27.
    Kilic E, van Gils W, Lodder E, Beverloo HB, van Til ME, Mooy CM, Paridaens D, de Klein A, Luyten GP (2006) Clinical and cytogenetic analyses in uveal melanoma. Invest Ophthalmol Vis Sci 47:3703–3707CrossRefPubMedGoogle Scholar
  28. 28.
    Ehlers JP, Worley L, Onken MD, Harbour JW (2008) Integrative genomic analysis of aneuploidy in uveal melanoma. Clin Cancer Res 14:115–122CrossRefPubMedGoogle Scholar
  29. 29.
    Naus NC, van Drunen E, de Klein A, Luyten GP, Paridaens DA, Alers JC, Ksander BR, Beverloo HB, Slater RM (2001) Characterization of complex chromosomal abnormalities in uveal melanoma by fluorescence in situ hybridization, spectral karyotyping, and comparative genomic hybridization. Genes Chromosomes Cancer 30:267–273CrossRefPubMedGoogle Scholar
  30. 30.
    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 122:13–17CrossRefPubMedGoogle Scholar
  31. 31.
    Scholes AG, Damato BE, Nunn J, Hiscott P, Grierson I, Field JK (2003) Monosomy 3 in uveal melanoma: correlation with clinical and histologic predictors of survival. Invest Ophthalmol Vis Sci 44:1008–1011CrossRefPubMedGoogle Scholar
  32. 32.
    Damato B, Dopierala JA, Coupland SE (2010) Genotypic profiling of 452 choroidal melanomas with multiplex ligation-dependent probe amplification. Clin Cancer Res 16:6083–6092CrossRefPubMedGoogle Scholar
  33. 33.
    Onken MD, Worley LA, Person E, Char DH, Bowcock AM, Harbour JW (2007) Loss of heterozygosity of chromosome 3 detected with single nucleotide polymorphisms is superior to monosomy 3 for predicting metastasis in uveal melanoma. Clin Cancer Res 13:2923–2927CrossRefPubMedGoogle Scholar
  34. 34.
    Prescher G, Bornfeld N, Hirche H, Horsthemke B, Jockel KH, Becher R (1996) Prognostic implications of monosomy 3 in uveal melanoma. Lancet 347:1222–1225CrossRefPubMedGoogle Scholar
  35. 35.
    Maat W, Jordanova ES, van Zelderen-Bhola SL, Barthen ER, Wessels HW, Schalij-Delfos NE, Jager MJ (2007) The heterogeneous distribution of monosomy 3 in uveal melanomas: implications for prognostication based on fine-needle aspiration biopsies. Arch Pathol Lab Med 131:91–96PubMedGoogle Scholar
  36. 36.
    Tschentscher F, Husing J, Holter T, Kruse E, Dresen IG, Jockel KH, Anastassiou G, Schilling H, Bornfeld N, Horsthemke B, Lohmann DR, Zeschnigk M (2003) Tumor classification based on gene expression profiling shows that uveal melanomas with and without monosomy 3 represent two distinct entities. Cancer Res 63:2578–2584PubMedGoogle Scholar
  37. 37.
    Worley LA, Onken MD, Person E, Robirds D, Branson J, Char DH, Perry A, Harbour JW (2007) Transcriptomic versus chromosomal prognostic markers and clinical outcome in uveal melanoma. Clin Cancer Res 13:1466–1471CrossRefPubMedGoogle Scholar
  38. 38.
    Petrausch U, Martus P, Tonnies H, Bechrakis NE, Lenze D, Wansel S, Hummel M, Bornfeld N, Thiel E, Foerster MH, Keilholz U (2007) Significance of gene expression analysis in uveal melanoma in comparison to standard risk factors for risk assessment of subsequent metastases. Eye 22:997–1007CrossRefPubMedGoogle Scholar
  39. 39.
    van Gils W, Lodder EM, Mensink HW, Kilic E, Naus NC, Bruggenwirth HT, van Ijcken W, Paridaens D, Luyten GP, de Klein A (2008) Gene expression profiling in uveal melanoma: two regions on 3p related to prognosis. Invest Ophthalmol Vis Sci 49:4254–4262CrossRefPubMedGoogle Scholar
  40. 40.
    Onken MD, Worley LA, Tuscan MD, Harbour JW (2010) An accurate, clinically feasible multi-gene expression assay for predicting metastasis in uveal melanoma. J Mol Diagn 12:461–468CrossRefPubMedGoogle Scholar
  41. 41.
    Onken M, Worley L, Char D, Augsburger J, Correa Z, Nudleman E, Aaberg TM Jr, Altaweel M, Bardenstein D, Finger P, Gallie B, Harocopos G, Hovland P, McGowan H, Milman T, Mruthyunjaya P, Simpson E, Smith M, Wilson D, Wirostko W, Harbour J (2012) Collaborative Ocular Oncology Group Report No. 1: prospective validation of a multi-gene prognostic assay in uveal melanoma. Ophthalmology 119(8):1596–1603. doi: 10.1016/j.ophtha.2012.02.017 CrossRefPubMedGoogle Scholar
  42. 42.
    Onken MD, Ehlers JP, Worley LA, Makita J, Yokota Y, Harbour JW (2006) Functional gene expression analysis uncovers phenotypic switch in aggressive uveal melanomas. Cancer Res 66:4602–4609CrossRefPubMedGoogle Scholar
  43. 43.
    Chang SH, Worley LA, Onken MD, Harbour JW (2008) Prognostic biomarkers in uveal melanoma: evidence for a stem cell-like phenotype associated with metastasis. Melanoma Res 18:191–200CrossRefPubMedGoogle Scholar
  44. 44.
    Harbour JW, Onken MD, Roberson ED, Duan S, Cao L, Worley LA, Council ML, Matatall KA, Helms C, Bowcock AM (2010) Frequent mutation of BAP1 in metastasizing uveal melanomas. Science 330:1410–1413CrossRefPubMedGoogle Scholar
  45. 45.
    Scheuermann JC, de Ayala Alonso AG, Oktaba K, Ly-Hartig N, McGinty RK, Fraterman S, Wilm M, Muir TW, Muller J (2010) Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Nature 465:243–247CrossRefPubMedGoogle Scholar
  46. 46.
    Abdel-Rahman MH, Pilarski R, Cebulla CM, Massengill JB, Christopher BN, Boru G, Hovland P, Davidorf FH (2011) Germline BAP1 mutation predisposes to uveal melanoma, lung adenocarcinoma, meningioma, and other cancers. J Med Genet 48:856–859CrossRefPubMedGoogle Scholar
  47. 47.
    Bott M, Brevet M, Taylor BS, Shimizu S, Ito T, Wang L, Creaney J, Lake RA, Zakowski MF, Reva B, Sander C, Delsite R, Powell S, Zhou Q, Shen R, Olshen A, Rusch V, Ladanyi M (2011) The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nat Genet 43:668–672CrossRefPubMedGoogle Scholar
  48. 48.
    Testa JR, Cheung M, Pei J, Below JE, Tan Y, Sementino E, Cox NJ, Dogan AU, Pass HI, Trusa S, Hesdorffer M, Nasu M, Powers A, Rivera Z, Comertpay S, Tanji M, Gaudino G, Yang H, Carbone M (2011) Germline BAP1 mutations predispose to malignant mesothelioma. Nat Genet 43:1022–1025CrossRefPubMedGoogle Scholar
  49. 49.
    Wiesner T, Obenauf AC, Murali R, Fried I, Griewank KG, Ulz P, Windpassinger C, Wackernagel W, Loy S, Wolf I, Viale A, Lash AE, Pirun M, Socci ND, Rutten A, Palmedo G, Abramson D, Offit K, Ott A, Becker JC, Cerroni L, Kutzner H, Bastian BC, Speicher MR (2011) Germline mutations in BAP1 predispose to melanocytic tumors. Nat Genet 43:1018–1021CrossRefPubMedGoogle Scholar
  50. 50.
    Njauw CN, Kim I, Piris A, Gabree M, Taylor M, Lane AM, Deangelis MM, Gragoudas E, Duncan LM, Tsao H (2012) Germline BAP1 inactivation is preferentially associated with metastatic ocular melanoma and cutaneous-ocular melanoma families. PLoS One 7(4):e35295. doi: 10.1371/journal.pone.0035295 CrossRefPubMedGoogle Scholar
  51. 51.
    Pena-Llopis S, Vega-Rubin-de-Celis S, Liao A, Leng N, Pavia-Jimenez A, Wang S, Yamasaki T, Zhrebker L, Sivanand S, Spence P, Kinch L, Hambuch T, Jain S, Lotan Y, Margulis V, Sagalowsky AI, Summerour PB, Kabbani W, Wong SW, Grishin N, Laurent M, Xie XJ, Haudenschild CD, Ross MT, Bentley DR, Kapur P, Brugarolas J (2012) BAP1 loss defines a new class of renal cell carcinoma. Nat Genet 44(7):751–759. doi: 10.1038/ng.2323 CrossRefPubMedGoogle Scholar
  52. 52.
    Wiesner T, Murali R, Fried I, Cerroni L, Busam K, Kutzner H, Bastian BC (2012) A distinct subset of atypical spitz tumors is characterized by BRAF mutation and loss of BAP1 expression. Am J Surg Pathol 36(6):818–830CrossRefPubMedGoogle Scholar
  53. 53.
    Yoshikawa Y, Sato A, Tsujimura T, Emi M, Morinaga T, Fukuoka K, Yamada S, Murakami A, Kondo N, Matsumoto S, Okumura Y, Tanaka F, Hasegawa S, Nakano T, Hashimoto-Tamaoki T (2012) Frequent inactivation of the BAP1 gene in epithelioid-type malignant mesothelioma. Cancer Sci 103:868–874CrossRefPubMedGoogle Scholar
  54. 54.
    Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D (2000) Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A 97:262–267CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  • J. William Harbour
    • 1
  1. 1.Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer CenterUniversity of Miami Miller School of MedicineMiamiUSA

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