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

PLOS ONE, Apr 2023

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.

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

PLOS ONE RESEARCH ARTICLE InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Orlow I, Sadeghi KD, Edmiston SN, Kenney JM, Lezcano C, Wilmott JS, et al. (2023) InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma. PLoS ONE 18(4): e0269324. https://doi.org/10.1371/journal. pone.0269324 Editor: Sandro Pasquali, Fondazione IRCCS Istituto Nazionale dei Tumori, ITALY Received: May 12, 2022 Accepted: March 14, 2023 Published: April 3, 2023 Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Data Availability Statement: The data underlying this report can be accessed through the “InterMEL biorepository and clinical database to report methods & best practices_dataset-I,” “InterMEL biorepository, clinical database to report methods & best practices_dataset-II, clinical database to report methods & best practices_dataset-III”, available through the Harvard Dataverse Network (https://doi.org/10.7910/DVN/QG5KSR, https://doi. org/10.7910/DVN/HK7LVX, https://doi.org/10. 7910/DVN/GD8UZG). Information on the study Irene Orlow ID1*, Keimya D. Sadeghi1, Sharon N. Edmiston2,3, Jessica M. Kenney1, Cecilia Lezcano4, James S. Wilmott5,6,7,8, Anne E. Cust5,9,10, Richard A. Scolyer ID5,6,7,8, Graham J. Mann5,11,12, Tim K. Lee13, Hazel Burke5, Valerie Jakrot5, Ping Shang5, Peter M. Ferguson ID5,14, Tawny W. Boyce15, Jennifer S. Ko16, Peter Ngo17, Pauline Funchain18, Judy R. Rees19, Kelli O’Connell1, Honglin Hao2, Eloise Parrish2,3, Kathleen Conway2,3,20, Paul B. Googe2, David W. Ollila21, Stergios J. Moschos22, Eva Hernando23, Douglas Hanniford23, Diana Argibay23, Christopher I. Amos24, Jeffrey E. Lee25, Iman Osman26,27,28, Li Luo15, Pei-Fen Kuan ID29, Arshi Aurora1, Bonnie E. Gould Rothberg30, Marcus W. Bosenberg31,32,33,34, Meg R. Gerstenblith35,36, Cheryl Thompson37,38, Paul N. Bogner39,40, Ivan P. Gorlov24, Sheri L. Holmen41,42,43, Elise K. Brunsgaard42, Yvonne M. Saenger44,45, Ronglai Shen1, Venkatraman Seshan1, Eduardo Nagore46, Marc S. Ernstoff47, Klaus J. Busam4, Colin B. Begg1, Nancy E. Thomas2,3, Marianne Berwick15, on behalf of the InterMEL Consortium¶ 1 Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America, 2 Department of Dermatology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America, 3 Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America, 4 Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America, 5 Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia, 6 Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia, 7 Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia, 8 Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia, 9 The Daffodil Centre, University of Sydney, a joint venture with Cancer Council New South Wales, Australia, 10 Sydney School of Public Health, The University of Sydney, Sydney, Australia, 11 Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia, 12 John Curtin School of Medical Research, Australian National University, Canberra, Australia, 13 British Columbia Cancer Research Center, Vancouver, British Columbia, Canada, 14 Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and New South Wales Health Pathology, Sydney, New South Wales, Australia, 15 Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico, United States of America, 16 Department of Pathology, Cleveland Clinic, Cleveland, Ohio, United States of America, 17 Department of Hospital Medicine, Cleveland Clinic, Cleveland, Ohio, United States of America, 18 Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America, 19 Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America, 20 Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America, 21 Department of Surgery, Division of Surgical Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America, 22 Department of Medicine, Division of Medical Oncology, The University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, United States of America, 23 Department of Pathology, New York University Grossman School of Medicine, New York, New York, United States of America, 24 Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America, 25 Department of Surgical Oncology, University of Texas, MD Anderson Cancer Center, Houston, Texas, United States of America, 26 Department of Urology, New York University Grossman School of Medicine, New York, NY, United States of America, 27 Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States of America, 28 Department of Dermatology, New York University Grossman School of Medicine, New York, NY, United States of America, 29 Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America, 30 Smilow Cancer Hospital, YaleNew Haven Health System, New Haven, Connecticut, United States of America, 31 Department of Internal Medicine, Section of Medical Oncology, Yale School of Medicine, New Haven, Connecticut, United States of America, 32 Department of Dermatology, Yale School of Medicine, New Haven, Connecticut, United States PLOS ONE | https://doi.org/10.1371/journal.pone.0269324 April 3, 2023 1 / 25 PLOS ONE Center cannot be shared publicly at the individual level because of privacy concerns (e.g., centers contributing with few cases due to lower melanoma incidence in that region). For additional information and/or data sharing requests contact . Funding: This work was supported by the National Cancer Institute (NCI) at the National Institutes of Health (NIH), grant P01CA206980, the Cancer Center Support grants P30CA118100 (to University of New Mexico Comprehensive Cancer Center), P30CA008748 (to Memorial Sloan Kettering Cancer Center), P30 CA016087 (to the Laura and Isaac Perlmutter (...truncated)


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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, on behalf of the InterMEL Consortium. InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma, PLOS ONE, 2023, Volume 18, Issue 4, DOI: 10.1371/journal.pone.0269324