A prognostic test to predict the risk of metastasis in uveal melanoma based on a 15-gene expression profile

Abstract

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.

Fig. 1

Prognostic performance of the 15-gene assay. Kaplan–Meier survival plot of 334 uveal melanoma patients with up to 5-year follow-up

Fig. 2

Work flow for 15-gene expression profile prognostic assay. (a) A needle biopsy of the uveal melanoma is performed prior to plaque brachytherapy or immediately after enucleation (eye removal). (b) The needle biopsy aspirate is immediately expelled into an empty tube, and then the same needle is used to draw up 200 μl of extraction buffer, which is then expelled into the first tube containing the tumor sample. (c) RNA is isolated, converted to cDNA, pre-amplified, loaded onto TaqMan^® Expression Assays on microfluidics cards, and subjected to PCR using the 7900HT Real-Time PCR System. (d) C_t values are calculated and analyzed using support vector machine (SVM), which compares new test samples to a validated training set of samples. SVM assigns each new sample to class 1 or class 2