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Diagnostic Distinction of Malignant Melanoma and Benign Nevi by a Gene Expression Signature and Correlation to Clinical Outcomes

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Diagnostic Distinction of Malignant Melanoma and Benign Nevi by a Gene Expression Signature and Correlation to Clinical Outcomes Published OnlineFirst April 4, 2017; DOI: 10.1158/1055-9965.EPI-16-0958 Research Article Cancer Epidemiology, Biomarkers Diagnostic Distinction of Malignant Melanoma and & Prevention Benign Nevi by a Gene Expression Signature and Correlation to Clinical Outcomes Jennifer S. Ko1, Balwir Matharoo-Ball2, Steven D. Billings1, Brian J.Thomson2, Jean Y.Tang3, Kavita Y. Sarin3, Emily Cai3, Jinah Kim3, Colleen Rock4, Hillary Z. Kimbrell4, Darl D. Flake II4, M. Bryan Warf4, Jonathan Nelson4, Thaylon Davis4, Catherine Miller4, Kristen Rushton4, Anne-Renee Hartman4, Richard J. Wenstrup4, and Loren E. Clarke4 Abstract Background: Histopathologic examination alone can be inad- were excluded. Benign lesions were defined as cutaneous mela- equate for diagnosis of certain melanocytic neoplasms. Recently, a nocytic lesions with no adverse long-term events reported. 23-gene expression signature was clinically validated as an ancil- Results: Of 239 submitted samples, 182 met inclusion criteria lary diagnostic test to differentiate benign nevi from melanoma. and produced a valid gene expression result. This included 99 The current study assessed the performance of this test in an primary cutaneous melanomas with proven distant metastases independent cohort of melanocytic lesions against clinically and 83 melanocytic nevi. Median time to melanoma metastasis proven outcomes. was 18 months. Median follow-up time for nevi was 74.9 months. Methods: Archival tissue from primary cutaneous melanomas The gene expression score differentiated melanoma from nevi and melanocytic nevi was obtained from four independent insti- with a sensitivity of 93.8% and a specificity of 96.2%. tutions and tested with the gene signature. Cases were selected Conclusions: The results of gene expression testing closely according to pre-defined clinical outcome measures. Malignant correlate with long-term clinical outcomes of patients with mel- lesions were defined as stage I–III primary cutaneous melanomas anocytic neoplasms. that produced distant metastases (metastatic to sites other than Impact: Collectively, this provides strong evidence that the proximal sentinel lymph node(s)) following diagnosis of the gene signature adds valuable adjunctive information to aid in primary lesion. Melanomas that were metastatic at the time of the accurate diagnosis of melanoma. Cancer Epidemiol Biomarkers Prev; diagnosis, all re-excisions, and lesions with <10% tumor volume 26(7); 1107–13. Ó2017 AACR. Introduction light microscopy; however, numerous studies have demonstrated that pathologists arrive at different diagnoses in 15% to 38% of Melanoma is now the seventh most common cancer among cases when evaluating the same specimens (1, 4–6). Studies have adults, and approximately 2 million melanocytic lesions are also shown that the consensus diagnosis of multiple experienced biopsied annually in the United States for clinical suspicion of dermatopathologists may not align with ultimate clinical out- melanoma (1). Although the majority of these lesions are benign, comes (7, 8). melanoma will account for an estimated 10,130 deaths in 2016 To improve diagnostic accuracy, ancillary techniques have (2). However, many melanomas are curable if detected early, with been sought to provide adjunctive diagnostic information for a 10-year survival rate of 95% for stage IA melanoma compared pathologists confronting histopathologically ambiguous mel- to only 10% to 15% for stage IV (3). This marked difference in anocytic lesions. These methods include array comparative biologic potential and clinical outcome underscores the value of genomic hybridization (aCGH) and fluorescence in-situ early and accurate diagnosis. hybridization(FISH),bothofwhichrelyonthedetectionof Many melanocytic lesions can be accurately classified as benign chromosomal copy number aberrations within neoplastic mel- or malignant by a skilled histopathologist using conventional anocytes (9–11). Recently, a gene expression signature has been developed to evaluate 23 genes that are differentially expressed 1The Cleveland Clinic, Cleveland, Ohio. 2University of Nottingham, Nottingham, in malignant melanoma and benign melanocytic nevi using United Kingdom. 3Stanford University, Stanford, California. 4Myriad Genetic Laboratories, Inc., Salt Lake City, Utah. quantitative reverse transcription polymerase chain reaction (qRT-PCR) (12, 13). Note: Supplementary data for this article are available at Cancer Epidemiology, Biomarkers & Prevention Online (http://cebp.aacrjournals.org/). Previous validations of the gene signature have demonstrated that this test is capable of differentiating melanoma from benign J.S. Ko and B. Matharoo-Ball contributed equally to this article. nevi with greater than 90% accuracy compared with consensus Corresponding Author: Loren E. Clarke, Myriad Genetic Laboratories, Inc., 320 diagnosis of multiple expert dermatopathologists (12, 13). These Wakara Way, Salt Lake City, UT 84108. Phone: 801-883-3470; Fax: 801-584- studies are in line with standard practice to validate new diag- 3099; E-mail: [email protected] nostic methods against the current diagnostic standard or clinical doi: 10.1158/1055-9965.EPI-16-0958 outcomes (14). Collecting long-term clinical follow-up for mel- Ó2017 American Association for Cancer Research. anocytic lesions can be a challenge, given the duration of follow- www.aacrjournals.org 1107 Downloaded from cebp.aacrjournals.org on September 28, 2021. © 2017 American Association for Cancer Research. Published OnlineFirst April 4, 2017; DOI: 10.1158/1055-9965.EPI-16-0958 Ko et al. up required for benign cases and the high rate of excision anoma. Re-excision specimens, metastatic melanomas, and of suspected melanoma. In addition, the requirement for meta- lesions that did not contain at least 10% tumor volume were static disease to prove malignancy may limit the types of lesions also excluded in accordance with the technical specifications of available for analysis. For example, some lesions that fulfill the assay (13). morphologic criteria for melanoma may lack metastatic capability De-identified clinical data for each sample were obtained (15). For this reason, aCGH, FISH, and the 23-gene signature have from the submitting institution and included patient age, all been previously validated against the current diagnostic stan- gender, anatomic site of the primary lesion, Breslow depth, dard of histopathology. Although the known limitations of his- ulceration status, sentinel lymph node biopsy status, anatomic topathology may impact the reported diagnostic accuracy in such location of metastases, time to metastasis, and length of follow- studies, the extent of this impact is unknown. In addition, var- up. Eleven melanomas were received without ulceration status iability in the diagnostic accuracy of histopathology across dif- indicated. The presence or absence of ulceration was deter- ferent melanocytic subtypes suggests that the magnitude of this mined by review of hematoxylin and eosin (H&E) stained effect is likely dependent on the composition and size of the sections of the lesions by a dermatopathologist (L.E. Clarke) validation cohort. at the testing institution. Histopathologic subtypes (e.g., super- To date, evaluation of adjunctive melanoma diagnostic meth- ficial spreading melanoma, nodular melanoma, etc.) were ods against clinical outcomes has been limited to relatively small determined for all cases by a panel of three dermatopatholo- samples sizes (9, 16–24), and previously published validations of gists (J.S. Ko, S.D. Billings, and L.E. Clarke) who were blinded the 23-gene signature have been based on histopathologic diag- to the diagnosis of the submitting pathologist(s) and the gene nosis. However, validation against a large, clinical cohort is expression score. necessary to accurately assess the performance of a diagnostic test for clinical use. Therefore, the current study aimed to evaluate Gene expression testing the diagnostic accuracy of the 23-gene signature utilizing a large Gene expression analysis (Myriad Genetic Laboratories, cohort of melanocytic lesions with clinical outcomes. This was Inc.) was carried out on archival formalin-fixed paraffin- done by determining the sensitivity of the gene signature in embedded (FFPE) tissue sections from each lesion according primary cutaneous melanomas with proven distant metastases to previously described methods (12, 13, 25). Briefly, a fi and the speci city in melanocytic nevi with long-term event-free pathologist identified representative areas of the lesion using follow-up. a single H&E-stained section. Lesions with <10% tumor vol- ume were excluded from testing based on previous evidence Materials and Methods that these lesions can produce false-negative results due to dilution by nonlesional cells (13). The representative area of Sample cohort the lesion identified for testing was macrodissected from The study was conducted with Institutional Review Board unstained tissue sections and pooled into a single tube for oversight and was approved with a waiver for individual patient RNA extraction. The qRT-PCR assay measured the differential informed consent (Quorum Review IRB). Archived melanocytic expression of 23 genes (14 tumor marker genes and 9 house- neoplasms not previously assessed by the gene expression keeper genes, Table 1). signature that met inclusion criteria were independently The gene signature included three categories of tumor marker fi identi ed and submitted for testing by the Cleveland Clinic genes that are differentially
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