InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma
Creators: name: Amos, C.I.
name: Scolyer, R.A.
name: Begg, C.B.
name: Osman, I.
name: Thompson, C.
name: Brunsgaard, E.K.
name: Seshan, V.
name: Shen, R.
name: Thomas, N.E.
name: Hao, H.
name: Moschos, S.J.
name: Sadeghi, K.D.
name: Berwick, M.
name: Ngo, P.
name: Kenney, J.M.
name: Kuan, P.-F.
name: Lezcano, C.
name: Aurora, A.
name: Hernando, E.
name: Cust, A.E.
name: Wilmott, J.S.
name: Bosenberg, M.W.
name: Luo, L.
name: Rees, J.R.
name: Nagore, E.
name: Holmen, S.L.
name: Googe, P.B.
name: Orlow, I.
name: Ko, J.S.
name: Ferguson, P.M.
name: Edmiston, S.N.
name: Parrish, E.
name: Funchain, P.
name: Conway, K.
name: InterMEL Consortium
name: Busam, K.J.
name: Bogner, P.N.
name: Gorlov, I.P.
name: Burke, H.
name: Hanniford, D.
name: Mann, G.J.
name: Ernstoff, M.S.
name: Gerstenblith, M.R.
name: Gould Rothberg, B.E.
name: O'Connell, K.
name: Ollila, D.W.
name: Boyce, T.W.
name: Lee, T.K.
name: Argibay, D.
name: Shang, P.
name: Lee, J.E.
name: Jakrot, V.
name: Saenger, Y.M.
Publisher: name: Public Library of Science
Year: 2023

description: INTRODUCTION: We are conducting a multicenter study to identify classifiers predictive of disease-specific survival in patients with primary melanomas. Here we delineate the unique aspects, challenges, and best practices for optimizing a study of generally small-sized pigmented tumor samples including primary melanomas of at least 1.05mm from AJTCC TNM stage IIA-IIID patients. We also evaluated tissue-derived predictors of extracted nucleic acids' quality and success in downstream testing. This ongoing study will target 1,000 melanomas within the international InterMEL consortium. METHODS: Following a pre-established protocol, participating centers ship formalin-fixed paraffin embedded (FFPE) tissue sections to Memorial Sloan Kettering Cancer Center for the centralized handling, dermatopathology review and histology-guided coextraction of RNA and DNA. Samples are distributed for evaluation of somatic mutations using next gen sequencing (NGS) with the MSK-IMPACTTM assay, methylation-profiling (Infinium MethylationEPIC arrays), and miRNA expression (Nanostring nCounter Human v3 miRNA Expression Assay). RESULTS: Sufficient material was obtained for screening of miRNA expression in 683/685 (99%) eligible melanomas, methylation in 467 (68%), and somatic mutations in 560 (82%). In 446/685 (65%) cases, aliquots of RNA/DNA were sufficient for testing with all three platforms. Among samples evaluated by the time of this analysis, the mean NGS coverage was 249x, 59 (18.6%) samples had coverage below 100x, and 41/414 (10%) failed methylation QC due to low intensity probes or insufficient Meta-Mixed Interquartile (BMIQ)- and single sample (ss)- Noob normalizations. Six of 683 RNAs (1%) failed Nanostring QC due to the low proportion of probes above the minimum threshold. Age of the FFPE tissue blocks (p<0.001) and time elapsed from sectioning to co-extraction (p = 0.002) were associated with methylation screening failures. Melanin reduced the ability to amplify fragments of 200bp or greater (absent/lightly pigmented vs heavily pigmented, p<0.003). Conversely, heavily pigmented tumors rendered greater amounts of RNA (p<0.001), and of RNA above 200 nucleotides (p<0.001). CONCLUSION: Our experience with many archival tissues demonstrates that with careful management of tissue processing and quality control it is possible to conduct multi-omic studies in a complex multi-institutional setting for investigations involving minute quantities of FFPE tumors, as in studies of early-stage melanoma. The study describes, for the first time, the optimal strategy for obtaining archival and limited tumor tissue, the characteristics of the nucleic acids co-extracted from a unique cell lysate, and success rate in downstream applications. In addition, our findings provide an estimate of the anticipated attrition that will guide other large multicenter research and consortia.