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A. Ganguly, E. Chao, C. L. Shields; Mutation Profile of the Uveal Melanoma Genome. Invest. Ophthalmol. Vis. Sci. 2009;50(13):5772.
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Uveal melanoma (UM) is the most common form of adult onset primary malignant intraocular tumor with a significantly high degree of mortality and loss of vision. Monosomy 3 predicts significantly increased risk of metastasis and gains of chromosome 8,6 and 1 or loss of 16 are associated with reduced disease-free survival.
With this background, we performed a pilot experiment to obtain the mutation profile for all 950 genes (tumor sequencing project, CGAP, NCI) associated with cancer from two independent samples of UM, with and without monosomy 3. We have used DNA isolated from UM tumors with known cyto-genetic profiles and 10 years of clinical follow-up including metastatic recurrence and disease-free survival. In addition we have the whole genome copy number profiles for each UM tumor.
The coding exons for these 950 genes - 6726 in total - were captured by hybridization of fragmented genomic DNA to a custom designed, 385K microarray followed by washing and elution (Roche Nimblegen,IN). This was followed by ultra high throughput, massively parallel sequencing on the GS FLX (Roche 454) platform.
The results allow us to define unique mutation profiles that identify genes mutated in both types of UM as well as genes specifically mutated in monosomy 3 UM cases. The results translate the basic cytogenetic observations towards the identification of clinically relevant biomarkers of metastasis and potential therapeutic targets in UM.
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