PLoS ONE (Jan 2023)

InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma.

  • Irene Orlow,
  • Keimya D Sadeghi,
  • Sharon N Edmiston,
  • Jessica M Kenney,
  • Cecilia Lezcano,
  • James S Wilmott,
  • Anne E Cust,
  • Richard A Scolyer,
  • Graham J Mann,
  • Tim K Lee,
  • Hazel Burke,
  • Valerie Jakrot,
  • Ping Shang,
  • Peter M Ferguson,
  • Tawny W Boyce,
  • Jennifer S Ko,
  • Peter Ngo,
  • Pauline Funchain,
  • Judy R Rees,
  • Kelli O'Connell,
  • Honglin Hao,
  • Eloise Parrish,
  • Kathleen Conway,
  • Paul B Googe,
  • David W Ollila,
  • Stergios J Moschos,
  • Eva Hernando,
  • Douglas Hanniford,
  • Diana Argibay,
  • Christopher I Amos,
  • Jeffrey E Lee,
  • Iman Osman,
  • Li Luo,
  • Pei-Fen Kuan,
  • Arshi Aurora,
  • Bonnie E Gould Rothberg,
  • Marcus W Bosenberg,
  • Meg R Gerstenblith,
  • Cheryl Thompson,
  • Paul N Bogner,
  • Ivan P Gorlov,
  • Sheri L Holmen,
  • Elise K Brunsgaard,
  • Yvonne M Saenger,
  • Ronglai Shen,
  • Venkatraman Seshan,
  • Eduardo Nagore,
  • Marc S Ernstoff,
  • Klaus J Busam,
  • Colin B Begg,
  • Nancy E Thomas,
  • Marianne Berwick,
  • InterMEL Consortium

DOI
https://doi.org/10.1371/journal.pone.0269324
Journal volume & issue
Vol. 18, no. 4
p. e0269324

Abstract

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IntroductionWe 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.MethodsFollowing 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).ResultsSufficient 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 (pConclusionOur 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.