InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma
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 mel...
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| creator | Orlow, Irene Sadeghi, Keimya D Edmiston, Sharon N Kenney, Jessica M Lezcano, Cecilia Wilmott, James S Cust, Anne E Scolyer, Richard A Mann, Graham J Lee, Tim K Burke, Hazel Jakrot, Valerie Shang, Ping Ferguson, Peter M Boyce, Tawny W Ko, Jennifer S Ngo, Peter Funchain, Pauline Rees, Judy R O'Connell, Kelli Hao, Honglin Parrish, Eloise Conway, Kathleen Googe, Paul B Ollila, David W Moschos, Stergios J Hernando, Eva Hanniford, Douglas Argibay, Diana Amos, Christopher I Lee, Jeffrey E Osman, Iman Luo, Li Kuan, Pei-Fen Aurora, Arshi Gould Rothberg, Bonnie E Bosenberg, Marcus W Gerstenblith, Meg R Thompson, Cheryl Bogner, Paul N Gorlov, Ivan P Holmen, Sheri L Brunsgaard, Elise K Saenger, Yvonne M Shen, Ronglai Seshan, Venkatraman Nagore, Eduardo Ernstoff, Marc S Busam, Klaus J Begg, Colin B Thomas, Nancy E Berwick, Marianne |
| description | 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.
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).
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 |
| doi_str_mv | 10.1371/journal.pone.0269324 |
| format | Article |
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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).
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).
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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0269324</identifier><identifier>PMID: 37011054</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Best practice ; Biology and life sciences ; Cancer therapies ; Care and treatment ; Consortia ; Demographics ; Deoxyribonucleic acid ; DNA ; DNA - genetics ; DNA methylation ; DNA probes ; Evaluation ; FDA approval ; Formaldehyde ; Health surveillance ; Histology ; Humans ; Medical records ; Medicine and Health Sciences ; Melanin ; Melanoma ; Melanoma - genetics ; Metastasis ; Methylation ; MicroRNAs - analysis ; miRNA ; Mutation ; Nucleic Acids ; Nucleotides ; Optimization ; Paraffin ; Paraffin Embedding - methods ; Patient outcomes ; Patients ; Physical Sciences ; Probes ; Protein expression ; Quality control ; Ribonucleic acid ; RNA ; Sectioning ; Ships ; Skin cancer ; Surveillance ; Survival ; Tissue Fixation - methods ; Tissues ; Tumors</subject><ispartof>PloS one, 2023-04, Vol.18 (4), p.e0269324-e0269324</ispartof><rights>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.</rights><rights>COPYRIGHT 2023 Public Library of Science</rights><rights>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: https://creativecommons.org/publicdomain/zero/1.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>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: https://creativecommons.org/publicdomain/zero/1.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c693t-c098ab03bd821eb9c32a80b11aa8442d22a095be92b962f9f5ab09bd728f6c2d3</citedby><cites>FETCH-LOGICAL-c693t-c098ab03bd821eb9c32a80b11aa8442d22a095be92b962f9f5ab09bd728f6c2d3</cites><orcidid>0000-0001-7861-916X ; 0000-0002-8991-0013 ; 0000-0001-6234-6961 ; 0000-0002-8335-0406</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10069769/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10069769/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37011054$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Orlow, Irene</creatorcontrib><creatorcontrib>Sadeghi, Keimya D</creatorcontrib><creatorcontrib>Edmiston, Sharon N</creatorcontrib><creatorcontrib>Kenney, Jessica M</creatorcontrib><creatorcontrib>Lezcano, Cecilia</creatorcontrib><creatorcontrib>Wilmott, James S</creatorcontrib><creatorcontrib>Cust, Anne E</creatorcontrib><creatorcontrib>Scolyer, Richard A</creatorcontrib><creatorcontrib>Mann, Graham J</creatorcontrib><creatorcontrib>Lee, Tim K</creatorcontrib><creatorcontrib>Burke, Hazel</creatorcontrib><creatorcontrib>Jakrot, Valerie</creatorcontrib><creatorcontrib>Shang, Ping</creatorcontrib><creatorcontrib>Ferguson, Peter M</creatorcontrib><creatorcontrib>Boyce, Tawny W</creatorcontrib><creatorcontrib>Ko, Jennifer S</creatorcontrib><creatorcontrib>Ngo, Peter</creatorcontrib><creatorcontrib>Funchain, Pauline</creatorcontrib><creatorcontrib>Rees, Judy R</creatorcontrib><creatorcontrib>O'Connell, Kelli</creatorcontrib><creatorcontrib>Hao, Honglin</creatorcontrib><creatorcontrib>Parrish, Eloise</creatorcontrib><creatorcontrib>Conway, Kathleen</creatorcontrib><creatorcontrib>Googe, Paul B</creatorcontrib><creatorcontrib>Ollila, David W</creatorcontrib><creatorcontrib>Moschos, Stergios J</creatorcontrib><creatorcontrib>Hernando, Eva</creatorcontrib><creatorcontrib>Hanniford, Douglas</creatorcontrib><creatorcontrib>Argibay, Diana</creatorcontrib><creatorcontrib>Amos, Christopher I</creatorcontrib><creatorcontrib>Lee, Jeffrey E</creatorcontrib><creatorcontrib>Osman, Iman</creatorcontrib><creatorcontrib>Luo, Li</creatorcontrib><creatorcontrib>Kuan, Pei-Fen</creatorcontrib><creatorcontrib>Aurora, Arshi</creatorcontrib><creatorcontrib>Gould Rothberg, Bonnie E</creatorcontrib><creatorcontrib>Bosenberg, Marcus W</creatorcontrib><creatorcontrib>Gerstenblith, Meg R</creatorcontrib><creatorcontrib>Thompson, Cheryl</creatorcontrib><creatorcontrib>Bogner, Paul N</creatorcontrib><creatorcontrib>Gorlov, Ivan P</creatorcontrib><creatorcontrib>Holmen, Sheri L</creatorcontrib><creatorcontrib>Brunsgaard, Elise K</creatorcontrib><creatorcontrib>Saenger, Yvonne M</creatorcontrib><creatorcontrib>Shen, Ronglai</creatorcontrib><creatorcontrib>Seshan, Venkatraman</creatorcontrib><creatorcontrib>Nagore, Eduardo</creatorcontrib><creatorcontrib>Ernstoff, Marc S</creatorcontrib><creatorcontrib>Busam, Klaus J</creatorcontrib><creatorcontrib>Begg, Colin B</creatorcontrib><creatorcontrib>Thomas, Nancy E</creatorcontrib><creatorcontrib>Berwick, Marianne</creatorcontrib><creatorcontrib>InterMEL Consortium</creatorcontrib><creatorcontrib>on behalf of the InterMEL Consortium</creatorcontrib><title>InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>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.
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).
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).
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.</description><subject>Analysis</subject><subject>Best practice</subject><subject>Biology and life sciences</subject><subject>Cancer therapies</subject><subject>Care and treatment</subject><subject>Consortia</subject><subject>Demographics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA - genetics</subject><subject>DNA methylation</subject><subject>DNA probes</subject><subject>Evaluation</subject><subject>FDA approval</subject><subject>Formaldehyde</subject><subject>Health surveillance</subject><subject>Histology</subject><subject>Humans</subject><subject>Medical records</subject><subject>Medicine and Health Sciences</subject><subject>Melanin</subject><subject>Melanoma</subject><subject>Melanoma - genetics</subject><subject>Metastasis</subject><subject>Methylation</subject><subject>MicroRNAs - analysis</subject><subject>miRNA</subject><subject>Mutation</subject><subject>Nucleic Acids</subject><subject>Nucleotides</subject><subject>Optimization</subject><subject>Paraffin</subject><subject>Paraffin Embedding - methods</subject><subject>Patient outcomes</subject><subject>Patients</subject><subject>Physical Sciences</subject><subject>Probes</subject><subject>Protein expression</subject><subject>Quality control</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Sectioning</subject><subject>Ships</subject><subject>Skin cancer</subject><subject>Surveillance</subject><subject>Survival</subject><subject>Tissue Fixation - 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An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma</title><author>Orlow, Irene ; Sadeghi, Keimya D ; Edmiston, Sharon N ; Kenney, Jessica M ; Lezcano, Cecilia ; Wilmott, James S ; Cust, Anne E ; Scolyer, Richard A ; Mann, Graham J ; Lee, Tim K ; Burke, Hazel ; Jakrot, Valerie ; Shang, Ping ; Ferguson, Peter M ; Boyce, Tawny W ; Ko, Jennifer S ; Ngo, Peter ; Funchain, Pauline ; Rees, Judy R ; O'Connell, Kelli ; Hao, Honglin ; Parrish, Eloise ; Conway, Kathleen ; Googe, Paul B ; Ollila, David W ; Moschos, Stergios J ; Hernando, Eva ; Hanniford, Douglas ; Argibay, Diana ; Amos, Christopher I ; Lee, Jeffrey E ; Osman, Iman ; Luo, Li ; Kuan, Pei-Fen ; Aurora, Arshi ; Gould Rothberg, Bonnie E ; Bosenberg, Marcus W ; Gerstenblith, Meg R ; Thompson, Cheryl ; Bogner, Paul N ; Gorlov, Ivan P ; Holmen, Sheri L ; Brunsgaard, Elise K ; Saenger, Yvonne M ; Shen, Ronglai ; Seshan, Venkatraman ; Nagore, Eduardo ; Ernstoff, Marc S ; Busam, Klaus J ; Begg, Colin B ; Thomas, Nancy E ; Berwick, Marianne</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c693t-c098ab03bd821eb9c32a80b11aa8442d22a095be92b962f9f5ab09bd728f6c2d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Analysis</topic><topic>Best practice</topic><topic>Biology and life sciences</topic><topic>Cancer therapies</topic><topic>Care and treatment</topic><topic>Consortia</topic><topic>Demographics</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA - genetics</topic><topic>DNA methylation</topic><topic>DNA probes</topic><topic>Evaluation</topic><topic>FDA approval</topic><topic>Formaldehyde</topic><topic>Health surveillance</topic><topic>Histology</topic><topic>Humans</topic><topic>Medical records</topic><topic>Medicine and Health Sciences</topic><topic>Melanin</topic><topic>Melanoma</topic><topic>Melanoma - genetics</topic><topic>Metastasis</topic><topic>Methylation</topic><topic>MicroRNAs - analysis</topic><topic>miRNA</topic><topic>Mutation</topic><topic>Nucleic Acids</topic><topic>Nucleotides</topic><topic>Optimization</topic><topic>Paraffin</topic><topic>Paraffin Embedding - methods</topic><topic>Patient outcomes</topic><topic>Patients</topic><topic>Physical Sciences</topic><topic>Probes</topic><topic>Protein expression</topic><topic>Quality control</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>Sectioning</topic><topic>Ships</topic><topic>Skin cancer</topic><topic>Surveillance</topic><topic>Survival</topic><topic>Tissue Fixation - methods</topic><topic>Tissues</topic><topic>Tumors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Orlow, Irene</creatorcontrib><creatorcontrib>Sadeghi, Keimya D</creatorcontrib><creatorcontrib>Edmiston, Sharon N</creatorcontrib><creatorcontrib>Kenney, Jessica M</creatorcontrib><creatorcontrib>Lezcano, Cecilia</creatorcontrib><creatorcontrib>Wilmott, James S</creatorcontrib><creatorcontrib>Cust, Anne E</creatorcontrib><creatorcontrib>Scolyer, Richard A</creatorcontrib><creatorcontrib>Mann, Graham J</creatorcontrib><creatorcontrib>Lee, Tim K</creatorcontrib><creatorcontrib>Burke, Hazel</creatorcontrib><creatorcontrib>Jakrot, Valerie</creatorcontrib><creatorcontrib>Shang, Ping</creatorcontrib><creatorcontrib>Ferguson, Peter M</creatorcontrib><creatorcontrib>Boyce, Tawny W</creatorcontrib><creatorcontrib>Ko, Jennifer S</creatorcontrib><creatorcontrib>Ngo, Peter</creatorcontrib><creatorcontrib>Funchain, Pauline</creatorcontrib><creatorcontrib>Rees, Judy R</creatorcontrib><creatorcontrib>O'Connell, Kelli</creatorcontrib><creatorcontrib>Hao, Honglin</creatorcontrib><creatorcontrib>Parrish, Eloise</creatorcontrib><creatorcontrib>Conway, Kathleen</creatorcontrib><creatorcontrib>Googe, Paul B</creatorcontrib><creatorcontrib>Ollila, David W</creatorcontrib><creatorcontrib>Moschos, Stergios J</creatorcontrib><creatorcontrib>Hernando, Eva</creatorcontrib><creatorcontrib>Hanniford, Douglas</creatorcontrib><creatorcontrib>Argibay, Diana</creatorcontrib><creatorcontrib>Amos, Christopher I</creatorcontrib><creatorcontrib>Lee, Jeffrey E</creatorcontrib><creatorcontrib>Osman, Iman</creatorcontrib><creatorcontrib>Luo, Li</creatorcontrib><creatorcontrib>Kuan, Pei-Fen</creatorcontrib><creatorcontrib>Aurora, Arshi</creatorcontrib><creatorcontrib>Gould Rothberg, Bonnie E</creatorcontrib><creatorcontrib>Bosenberg, Marcus W</creatorcontrib><creatorcontrib>Gerstenblith, Meg R</creatorcontrib><creatorcontrib>Thompson, Cheryl</creatorcontrib><creatorcontrib>Bogner, Paul N</creatorcontrib><creatorcontrib>Gorlov, Ivan P</creatorcontrib><creatorcontrib>Holmen, Sheri L</creatorcontrib><creatorcontrib>Brunsgaard, Elise K</creatorcontrib><creatorcontrib>Saenger, Yvonne M</creatorcontrib><creatorcontrib>Shen, Ronglai</creatorcontrib><creatorcontrib>Seshan, Venkatraman</creatorcontrib><creatorcontrib>Nagore, Eduardo</creatorcontrib><creatorcontrib>Ernstoff, Marc S</creatorcontrib><creatorcontrib>Busam, Klaus J</creatorcontrib><creatorcontrib>Begg, Colin B</creatorcontrib><creatorcontrib>Thomas, Nancy E</creatorcontrib><creatorcontrib>Berwick, Marianne</creatorcontrib><creatorcontrib>InterMEL Consortium</creatorcontrib><creatorcontrib>on behalf of the InterMEL Consortium</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology 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Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Orlow, Irene</au><au>Sadeghi, Keimya D</au><au>Edmiston, Sharon N</au><au>Kenney, Jessica M</au><au>Lezcano, Cecilia</au><au>Wilmott, James S</au><au>Cust, Anne E</au><au>Scolyer, Richard A</au><au>Mann, Graham J</au><au>Lee, Tim K</au><au>Burke, Hazel</au><au>Jakrot, Valerie</au><au>Shang, Ping</au><au>Ferguson, Peter M</au><au>Boyce, Tawny W</au><au>Ko, Jennifer S</au><au>Ngo, Peter</au><au>Funchain, Pauline</au><au>Rees, Judy R</au><au>O'Connell, Kelli</au><au>Hao, Honglin</au><au>Parrish, Eloise</au><au>Conway, Kathleen</au><au>Googe, Paul B</au><au>Ollila, David W</au><au>Moschos, Stergios J</au><au>Hernando, Eva</au><au>Hanniford, Douglas</au><au>Argibay, Diana</au><au>Amos, Christopher I</au><au>Lee, Jeffrey E</au><au>Osman, Iman</au><au>Luo, Li</au><au>Kuan, Pei-Fen</au><au>Aurora, Arshi</au><au>Gould Rothberg, Bonnie E</au><au>Bosenberg, Marcus W</au><au>Gerstenblith, Meg R</au><au>Thompson, Cheryl</au><au>Bogner, Paul N</au><au>Gorlov, Ivan P</au><au>Holmen, Sheri L</au><au>Brunsgaard, Elise K</au><au>Saenger, Yvonne M</au><au>Shen, Ronglai</au><au>Seshan, Venkatraman</au><au>Nagore, Eduardo</au><au>Ernstoff, Marc S</au><au>Busam, Klaus J</au><au>Begg, Colin B</au><au>Thomas, Nancy E</au><au>Berwick, Marianne</au><aucorp>InterMEL Consortium</aucorp><aucorp>on behalf of the InterMEL Consortium</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2023-04-03</date><risdate>2023</risdate><volume>18</volume><issue>4</issue><spage>e0269324</spage><epage>e0269324</epage><pages>e0269324-e0269324</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>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.
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).
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).
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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>37011054</pmid><doi>10.1371/journal.pone.0269324</doi><tpages>e0269324</tpages><orcidid>https://orcid.org/0000-0001-7861-916X</orcidid><orcidid>https://orcid.org/0000-0002-8991-0013</orcidid><orcidid>https://orcid.org/0000-0001-6234-6961</orcidid><orcidid>https://orcid.org/0000-0002-8335-0406</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2023-04, Vol.18 (4), p.e0269324-e0269324 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2794627328 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Analysis Best practice Biology and life sciences Cancer therapies Care and treatment Consortia Demographics Deoxyribonucleic acid DNA DNA - genetics DNA methylation DNA probes Evaluation FDA approval Formaldehyde Health surveillance Histology Humans Medical records Medicine and Health Sciences Melanin Melanoma Melanoma - genetics Metastasis Methylation MicroRNAs - analysis miRNA Mutation Nucleic Acids Nucleotides Optimization Paraffin Paraffin Embedding - methods Patient outcomes Patients Physical Sciences Probes Protein expression Quality control Ribonucleic acid RNA Sectioning Ships Skin cancer Surveillance Survival Tissue Fixation - methods Tissues Tumors |
| title | InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma |
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