Gene expression profiling in uveal melanoma: technical reliability and correlation of molecular class with pathologic characteristics

Abstract

BackgroundA 15-gene expression profile test has been clinically validated and is widely utilized in newly diagnosed uveal melanoma (UM) patients to assess metastatic potential of the tumor. As most patients are treated with eye-sparing radiotherapy, there is limited tumor tissue available for testing, and technical reliability and success of prognostic testing are critical. This study assessed the analytical performance of the 15-gene expression test for UM and the correlation of molecular class with pathologic characteristics.MethodsInter-assay, intra-assay, inter-instrument/operator, and inter-site experiments were conducted, and concordance of the 15-gene expression profile test results and associated discriminant scores for matched tumor samples were evaluated. Technical success was determined from de-identified clinical reports from January 2010 - May 2016. Pathologic characteristics of enucleated tumors were correlated with molecular class results.ResultsInter-assay concordance on 16 samples run on 3 consecutive days was 100%, and matched discriminant scores were strongly correlated (R2 = 0.9944). Inter-assay concordance of 46 samples assayed within a one year period was 100%, with an R2 value of 0.9747 for the discriminant scores. Intra-assay concordance of 12 samples run concurrently in duplicates was 100%; discriminant score correlation yielded an R2 of 0.9934. Concordance between two sites assessing the same tumors was 100% with an R2 of 0.9818 between discriminant scores. Inter-operator/instrument concordance was 96% for Class 1/2 calls and 90% for Class 1A/1B calls, and the discriminant scores had a correlation R2 of 0.9636. Technical success was 96.3% on 5516 samples tested since 2010. Increased largest basal diameter and thickness were significantly associated with Class 1B and Class 2 vs. Class 1A signatures.ConclusionsThese results show that the 15-gene expression profile test for UM has robust, reproducible performance characteristics. The technical success rate during clinical testing remains as high as first reported during validation. As molecular testing becomes more prevalent for supporting precision medicine efforts, high technical success and reliability are key characteristics when testing such limited and precious samples. The performance of the 15-gene expression profile test in this study should provide confidence to physicians who use the test’s molecular classification to inform patient management decisions.Electronic supplementary materialThe online version of this article (doi:10.1186/s13000-017-0650-3) contains supplementary material, which is available to authorized users.

Gene Expression Profiling in Uveal Melanoma: Five-Year Prospective Outcomes and Meta-Analysis

“…A prognostic 15-gene expression profile (15-GEP) test that predicts 5-year metastatic risk with Class 1A, 1B, and 2 results indicating low-, intermediate-, and highrisk groups, respectively, has been in clinical use for several years [14,15]. The test's accuracy has been documented in several retrospective and prospective studies involving more than 1,600 patients [14][15][16][17][18][19][20]; and its high technical reliability has also been reported [14,15,17,21]. It has been demonstrated that physicians use the test results in a risk-specific manner to guide metastatic surveillance recommendations including imaging, specialist referrals, laboratory testing, and clinical trial participation for adjuvant therapy [19,22,23].…”

Intraocular biopsy of uveal melanoma Risk assessment and identification of genetic prognostic markers

“…Class 1 was therefore divided into class 1a and class 1b, where 1b predicts an intermediate risk of metastatic disease (Plasseraud et al. ). Increased expression of the gene PRAME , identified by a high level of PRAME mRNA, is predictive of metastatic disease among class 1 patients.…”

“…In contrast to the above‐mentioned DNA‐based methods, gene expression profiling (GEP) uses the expression level of multiple genes to identify the profile of the tumour (Plasseraud et al. ). While all DNA‐based methods are limited by their risk of sampling error due to intratumoral heterogeneity, it is proposed that gene expression profiling is less affected by genetic heterogeneity (Onken et al.…”

Analytical Validation and Performance of a 7-gene Next-generation Sequencing Panel in Uveal Melanoma

“…Uveal melanoma (UM) is a rare but deadly intraocular cancer, with up to 50% of patients ultimately developing distant metastatic disease [1]. A 15-gene expression profiling (GEP) test commercially available as DecisionDx-UM (Castle Biosciences, Inc) is routinely used for prognostication of metastatic risk in UM patients and is considered standard of care in many ocular oncology centers across North America [2][3][4]. Testing is typically performed on fine needle aspirate biopsy (FNAB) taken from the primary tumor at the time of surgery for radiotherapy, or on formalin fixed paraffin embedded (FFPE) tissue taken from the primary tumor at the time of enucleation (eye removal).…”