InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma.
<h4<Introduction</h4<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 tu...
Ausführliche Beschreibung
Autor*in: |
Irene Orlow [verfasserIn] Keimya D Sadeghi [verfasserIn] Sharon N Edmiston [verfasserIn] Jessica M Kenney [verfasserIn] Cecilia Lezcano [verfasserIn] James S Wilmott [verfasserIn] Anne E Cust [verfasserIn] Richard A Scolyer [verfasserIn] Graham J Mann [verfasserIn] Tim K Lee [verfasserIn] Hazel Burke [verfasserIn] Valerie Jakrot [verfasserIn] Ping Shang [verfasserIn] Peter M Ferguson [verfasserIn] Tawny W Boyce [verfasserIn] Jennifer S Ko [verfasserIn] Peter Ngo [verfasserIn] Pauline Funchain [verfasserIn] Judy R Rees [verfasserIn] Kelli O'Connell [verfasserIn] Honglin Hao [verfasserIn] Eloise Parrish [verfasserIn] Kathleen Conway [verfasserIn] Paul B Googe [verfasserIn] David W Ollila [verfasserIn] Stergios J Moschos [verfasserIn] Eva Hernando [verfasserIn] Douglas Hanniford [verfasserIn] Diana Argibay [verfasserIn] Christopher I Amos [verfasserIn] Jeffrey E Lee [verfasserIn] Iman Osman [verfasserIn] Li Luo [verfasserIn] Pei-Fen Kuan [verfasserIn] Arshi Aurora [verfasserIn] Bonnie E Gould Rothberg [verfasserIn] Marcus W Bosenberg [verfasserIn] Meg R Gerstenblith [verfasserIn] Cheryl Thompson [verfasserIn] Paul N Bogner [verfasserIn] Ivan P Gorlov [verfasserIn] Sheri L Holmen [verfasserIn] Elise K Brunsgaard [verfasserIn] Yvonne M Saenger [verfasserIn] Ronglai Shen [verfasserIn] Venkatraman Seshan [verfasserIn] Eduardo Nagore [verfasserIn] Marc S Ernstoff [verfasserIn] Klaus J Busam [verfasserIn] Colin B Begg [verfasserIn] Nancy E Thomas [verfasserIn] Marianne Berwick [verfasserIn] InterMEL Consortium [verfasserIn] |
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E-Artikel |
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Sprache: |
Englisch |
Erschienen: |
2023 |
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Übergeordnetes Werk: |
In: PLoS ONE - Public Library of Science (PLoS), 2007, 18(2023), 4, p e0269324 |
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Übergeordnetes Werk: |
volume:18 ; year:2023 ; number:4, p e0269324 |
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DOI / URN: |
10.1371/journal.pone.0269324 |
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Katalog-ID: |
DOAJ089056396 |
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245 | 1 | 0 | |a InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma. |
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520 | |a <h4<Introduction</h4<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.<h4<Methods</h4<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).<h4<Results</h4<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).<h4<Conclusion</h4<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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700 | 0 | |a Sharon N Edmiston |e verfasserin |4 aut | |
700 | 0 | |a Jessica M Kenney |e verfasserin |4 aut | |
700 | 0 | |a Cecilia Lezcano |e verfasserin |4 aut | |
700 | 0 | |a James S Wilmott |e verfasserin |4 aut | |
700 | 0 | |a Anne E Cust |e verfasserin |4 aut | |
700 | 0 | |a Richard A Scolyer |e verfasserin |4 aut | |
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700 | 0 | |a Tim K Lee |e verfasserin |4 aut | |
700 | 0 | |a Hazel Burke |e verfasserin |4 aut | |
700 | 0 | |a Valerie Jakrot |e verfasserin |4 aut | |
700 | 0 | |a Ping Shang |e verfasserin |4 aut | |
700 | 0 | |a Peter M Ferguson |e verfasserin |4 aut | |
700 | 0 | |a Tawny W Boyce |e verfasserin |4 aut | |
700 | 0 | |a Jennifer S Ko |e verfasserin |4 aut | |
700 | 0 | |a Peter Ngo |e verfasserin |4 aut | |
700 | 0 | |a Pauline Funchain |e verfasserin |4 aut | |
700 | 0 | |a Judy R Rees |e verfasserin |4 aut | |
700 | 0 | |a Kelli O'Connell |e verfasserin |4 aut | |
700 | 0 | |a Honglin Hao |e verfasserin |4 aut | |
700 | 0 | |a Eloise Parrish |e verfasserin |4 aut | |
700 | 0 | |a Kathleen Conway |e verfasserin |4 aut | |
700 | 0 | |a Paul B Googe |e verfasserin |4 aut | |
700 | 0 | |a David W Ollila |e verfasserin |4 aut | |
700 | 0 | |a Stergios J Moschos |e verfasserin |4 aut | |
700 | 0 | |a Eva Hernando |e verfasserin |4 aut | |
700 | 0 | |a Douglas Hanniford |e verfasserin |4 aut | |
700 | 0 | |a Diana Argibay |e verfasserin |4 aut | |
700 | 0 | |a Christopher I Amos |e verfasserin |4 aut | |
700 | 0 | |a Jeffrey E Lee |e verfasserin |4 aut | |
700 | 0 | |a Iman Osman |e verfasserin |4 aut | |
700 | 0 | |a Li Luo |e verfasserin |4 aut | |
700 | 0 | |a Pei-Fen Kuan |e verfasserin |4 aut | |
700 | 0 | |a Arshi Aurora |e verfasserin |4 aut | |
700 | 0 | |a Bonnie E Gould Rothberg |e verfasserin |4 aut | |
700 | 0 | |a Marcus W Bosenberg |e verfasserin |4 aut | |
700 | 0 | |a Meg R Gerstenblith |e verfasserin |4 aut | |
700 | 0 | |a Cheryl Thompson |e verfasserin |4 aut | |
700 | 0 | |a Paul N Bogner |e verfasserin |4 aut | |
700 | 0 | |a Ivan P Gorlov |e verfasserin |4 aut | |
700 | 0 | |a Sheri L Holmen |e verfasserin |4 aut | |
700 | 0 | |a Elise K Brunsgaard |e verfasserin |4 aut | |
700 | 0 | |a Yvonne M Saenger |e verfasserin |4 aut | |
700 | 0 | |a Ronglai Shen |e verfasserin |4 aut | |
700 | 0 | |a Venkatraman Seshan |e verfasserin |4 aut | |
700 | 0 | |a Eduardo Nagore |e verfasserin |4 aut | |
700 | 0 | |a Marc S Ernstoff |e verfasserin |4 aut | |
700 | 0 | |a Klaus J Busam |e verfasserin |4 aut | |
700 | 0 | |a Colin B Begg |e verfasserin |4 aut | |
700 | 0 | |a Nancy E Thomas |e verfasserin |4 aut | |
700 | 0 | |a Marianne Berwick |e verfasserin |4 aut | |
700 | 0 | |a InterMEL Consortium |e verfasserin |4 aut | |
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10.1371/journal.pone.0269324 doi (DE-627)DOAJ089056396 (DE-599)DOAJ2122630446b94345873b74cdda1850a8 DE-627 ger DE-627 rakwb eng Irene Orlow verfasserin aut InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma. 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <h4<Introduction</h4<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.<h4<Methods</h4<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).<h4<Results</h4<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).<h4<Conclusion</h4<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. Medicine R Science Q Keimya D Sadeghi verfasserin aut Sharon N Edmiston verfasserin aut Jessica M Kenney verfasserin aut Cecilia Lezcano verfasserin aut James S Wilmott verfasserin aut Anne E Cust verfasserin aut Richard A Scolyer verfasserin aut Graham J Mann verfasserin aut Tim K Lee verfasserin aut Hazel Burke verfasserin aut Valerie Jakrot verfasserin aut Ping Shang verfasserin aut Peter M Ferguson verfasserin aut Tawny W Boyce verfasserin aut Jennifer S Ko verfasserin aut Peter Ngo verfasserin aut Pauline Funchain verfasserin aut Judy R Rees verfasserin aut Kelli O'Connell verfasserin aut Honglin Hao verfasserin aut Eloise Parrish verfasserin aut Kathleen Conway verfasserin aut Paul B Googe verfasserin aut David W Ollila verfasserin aut Stergios J Moschos verfasserin aut Eva Hernando verfasserin aut Douglas Hanniford verfasserin aut Diana Argibay verfasserin aut Christopher I Amos verfasserin aut Jeffrey E Lee verfasserin aut Iman Osman verfasserin aut Li Luo verfasserin aut Pei-Fen Kuan verfasserin aut Arshi Aurora verfasserin aut Bonnie E Gould Rothberg verfasserin aut Marcus W Bosenberg verfasserin aut Meg R Gerstenblith verfasserin aut Cheryl Thompson verfasserin aut Paul N Bogner verfasserin aut Ivan P Gorlov verfasserin aut Sheri L Holmen verfasserin aut Elise K Brunsgaard verfasserin aut Yvonne M Saenger verfasserin aut Ronglai Shen verfasserin aut Venkatraman Seshan verfasserin aut Eduardo Nagore verfasserin aut Marc S Ernstoff verfasserin aut Klaus J Busam verfasserin aut Colin B Begg verfasserin aut Nancy E Thomas verfasserin aut Marianne Berwick verfasserin aut InterMEL Consortium verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 18(2023), 4, p e0269324 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:18 year:2023 number:4, p e0269324 https://doi.org/10.1371/journal.pone.0269324 kostenfrei https://doaj.org/article/2122630446b94345873b74cdda1850a8 kostenfrei https://doi.org/10.1371/journal.pone.0269324 kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 18 2023 4, p e0269324 |
spelling |
10.1371/journal.pone.0269324 doi (DE-627)DOAJ089056396 (DE-599)DOAJ2122630446b94345873b74cdda1850a8 DE-627 ger DE-627 rakwb eng Irene Orlow verfasserin aut InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma. 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <h4<Introduction</h4<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.<h4<Methods</h4<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).<h4<Results</h4<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).<h4<Conclusion</h4<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. Medicine R Science Q Keimya D Sadeghi verfasserin aut Sharon N Edmiston verfasserin aut Jessica M Kenney verfasserin aut Cecilia Lezcano verfasserin aut James S Wilmott verfasserin aut Anne E Cust verfasserin aut Richard A Scolyer verfasserin aut Graham J Mann verfasserin aut Tim K Lee verfasserin aut Hazel Burke verfasserin aut Valerie Jakrot verfasserin aut Ping Shang verfasserin aut Peter M Ferguson verfasserin aut Tawny W Boyce verfasserin aut Jennifer S Ko verfasserin aut Peter Ngo verfasserin aut Pauline Funchain verfasserin aut Judy R Rees verfasserin aut Kelli O'Connell verfasserin aut Honglin Hao verfasserin aut Eloise Parrish verfasserin aut Kathleen Conway verfasserin aut Paul B Googe verfasserin aut David W Ollila verfasserin aut Stergios J Moschos verfasserin aut Eva Hernando verfasserin aut Douglas Hanniford verfasserin aut Diana Argibay verfasserin aut Christopher I Amos verfasserin aut Jeffrey E Lee verfasserin aut Iman Osman verfasserin aut Li Luo verfasserin aut Pei-Fen Kuan verfasserin aut Arshi Aurora verfasserin aut Bonnie E Gould Rothberg verfasserin aut Marcus W Bosenberg verfasserin aut Meg R Gerstenblith verfasserin aut Cheryl Thompson verfasserin aut Paul N Bogner verfasserin aut Ivan P Gorlov verfasserin aut Sheri L Holmen verfasserin aut Elise K Brunsgaard verfasserin aut Yvonne M Saenger verfasserin aut Ronglai Shen verfasserin aut Venkatraman Seshan verfasserin aut Eduardo Nagore verfasserin aut Marc S Ernstoff verfasserin aut Klaus J Busam verfasserin aut Colin B Begg verfasserin aut Nancy E Thomas verfasserin aut Marianne Berwick verfasserin aut InterMEL Consortium verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 18(2023), 4, p e0269324 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:18 year:2023 number:4, p e0269324 https://doi.org/10.1371/journal.pone.0269324 kostenfrei https://doaj.org/article/2122630446b94345873b74cdda1850a8 kostenfrei https://doi.org/10.1371/journal.pone.0269324 kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 18 2023 4, p e0269324 |
allfields_unstemmed |
10.1371/journal.pone.0269324 doi (DE-627)DOAJ089056396 (DE-599)DOAJ2122630446b94345873b74cdda1850a8 DE-627 ger DE-627 rakwb eng Irene Orlow verfasserin aut InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma. 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <h4<Introduction</h4<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.<h4<Methods</h4<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).<h4<Results</h4<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).<h4<Conclusion</h4<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. Medicine R Science Q Keimya D Sadeghi verfasserin aut Sharon N Edmiston verfasserin aut Jessica M Kenney verfasserin aut Cecilia Lezcano verfasserin aut James S Wilmott verfasserin aut Anne E Cust verfasserin aut Richard A Scolyer verfasserin aut Graham J Mann verfasserin aut Tim K Lee verfasserin aut Hazel Burke verfasserin aut Valerie Jakrot verfasserin aut Ping Shang verfasserin aut Peter M Ferguson verfasserin aut Tawny W Boyce verfasserin aut Jennifer S Ko verfasserin aut Peter Ngo verfasserin aut Pauline Funchain verfasserin aut Judy R Rees verfasserin aut Kelli O'Connell verfasserin aut Honglin Hao verfasserin aut Eloise Parrish verfasserin aut Kathleen Conway verfasserin aut Paul B Googe verfasserin aut David W Ollila verfasserin aut Stergios J Moschos verfasserin aut Eva Hernando verfasserin aut Douglas Hanniford verfasserin aut Diana Argibay verfasserin aut Christopher I Amos verfasserin aut Jeffrey E Lee verfasserin aut Iman Osman verfasserin aut Li Luo verfasserin aut Pei-Fen Kuan verfasserin aut Arshi Aurora verfasserin aut Bonnie E Gould Rothberg verfasserin aut Marcus W Bosenberg verfasserin aut Meg R Gerstenblith verfasserin aut Cheryl Thompson verfasserin aut Paul N Bogner verfasserin aut Ivan P Gorlov verfasserin aut Sheri L Holmen verfasserin aut Elise K Brunsgaard verfasserin aut Yvonne M Saenger verfasserin aut Ronglai Shen verfasserin aut Venkatraman Seshan verfasserin aut Eduardo Nagore verfasserin aut Marc S Ernstoff verfasserin aut Klaus J Busam verfasserin aut Colin B Begg verfasserin aut Nancy E Thomas verfasserin aut Marianne Berwick verfasserin aut InterMEL Consortium verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 18(2023), 4, p e0269324 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:18 year:2023 number:4, p e0269324 https://doi.org/10.1371/journal.pone.0269324 kostenfrei https://doaj.org/article/2122630446b94345873b74cdda1850a8 kostenfrei https://doi.org/10.1371/journal.pone.0269324 kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 18 2023 4, p e0269324 |
allfieldsGer |
10.1371/journal.pone.0269324 doi (DE-627)DOAJ089056396 (DE-599)DOAJ2122630446b94345873b74cdda1850a8 DE-627 ger DE-627 rakwb eng Irene Orlow verfasserin aut InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma. 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <h4<Introduction</h4<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.<h4<Methods</h4<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).<h4<Results</h4<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).<h4<Conclusion</h4<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. Medicine R Science Q Keimya D Sadeghi verfasserin aut Sharon N Edmiston verfasserin aut Jessica M Kenney verfasserin aut Cecilia Lezcano verfasserin aut James S Wilmott verfasserin aut Anne E Cust verfasserin aut Richard A Scolyer verfasserin aut Graham J Mann verfasserin aut Tim K Lee verfasserin aut Hazel Burke verfasserin aut Valerie Jakrot verfasserin aut Ping Shang verfasserin aut Peter M Ferguson verfasserin aut Tawny W Boyce verfasserin aut Jennifer S Ko verfasserin aut Peter Ngo verfasserin aut Pauline Funchain verfasserin aut Judy R Rees verfasserin aut Kelli O'Connell verfasserin aut Honglin Hao verfasserin aut Eloise Parrish verfasserin aut Kathleen Conway verfasserin aut Paul B Googe verfasserin aut David W Ollila verfasserin aut Stergios J Moschos verfasserin aut Eva Hernando verfasserin aut Douglas Hanniford verfasserin aut Diana Argibay verfasserin aut Christopher I Amos verfasserin aut Jeffrey E Lee verfasserin aut Iman Osman verfasserin aut Li Luo verfasserin aut Pei-Fen Kuan verfasserin aut Arshi Aurora verfasserin aut Bonnie E Gould Rothberg verfasserin aut Marcus W Bosenberg verfasserin aut Meg R Gerstenblith verfasserin aut Cheryl Thompson verfasserin aut Paul N Bogner verfasserin aut Ivan P Gorlov verfasserin aut Sheri L Holmen verfasserin aut Elise K Brunsgaard verfasserin aut Yvonne M Saenger verfasserin aut Ronglai Shen verfasserin aut Venkatraman Seshan verfasserin aut Eduardo Nagore verfasserin aut Marc S Ernstoff verfasserin aut Klaus J Busam verfasserin aut Colin B Begg verfasserin aut Nancy E Thomas verfasserin aut Marianne Berwick verfasserin aut InterMEL Consortium verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 18(2023), 4, p e0269324 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:18 year:2023 number:4, p e0269324 https://doi.org/10.1371/journal.pone.0269324 kostenfrei https://doaj.org/article/2122630446b94345873b74cdda1850a8 kostenfrei https://doi.org/10.1371/journal.pone.0269324 kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 18 2023 4, p e0269324 |
allfieldsSound |
10.1371/journal.pone.0269324 doi (DE-627)DOAJ089056396 (DE-599)DOAJ2122630446b94345873b74cdda1850a8 DE-627 ger DE-627 rakwb eng Irene Orlow verfasserin aut InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma. 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <h4<Introduction</h4<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.<h4<Methods</h4<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).<h4<Results</h4<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).<h4<Conclusion</h4<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. Medicine R Science Q Keimya D Sadeghi verfasserin aut Sharon N Edmiston verfasserin aut Jessica M Kenney verfasserin aut Cecilia Lezcano verfasserin aut James S Wilmott verfasserin aut Anne E Cust verfasserin aut Richard A Scolyer verfasserin aut Graham J Mann verfasserin aut Tim K Lee verfasserin aut Hazel Burke verfasserin aut Valerie Jakrot verfasserin aut Ping Shang verfasserin aut Peter M Ferguson verfasserin aut Tawny W Boyce verfasserin aut Jennifer S Ko verfasserin aut Peter Ngo verfasserin aut Pauline Funchain verfasserin aut Judy R Rees verfasserin aut Kelli O'Connell verfasserin aut Honglin Hao verfasserin aut Eloise Parrish verfasserin aut Kathleen Conway verfasserin aut Paul B Googe verfasserin aut David W Ollila verfasserin aut Stergios J Moschos verfasserin aut Eva Hernando verfasserin aut Douglas Hanniford verfasserin aut Diana Argibay verfasserin aut Christopher I Amos verfasserin aut Jeffrey E Lee verfasserin aut Iman Osman verfasserin aut Li Luo verfasserin aut Pei-Fen Kuan verfasserin aut Arshi Aurora verfasserin aut Bonnie E Gould Rothberg verfasserin aut Marcus W Bosenberg verfasserin aut Meg R Gerstenblith verfasserin aut Cheryl Thompson verfasserin aut Paul N Bogner verfasserin aut Ivan P Gorlov verfasserin aut Sheri L Holmen verfasserin aut Elise K Brunsgaard verfasserin aut Yvonne M Saenger verfasserin aut Ronglai Shen verfasserin aut Venkatraman Seshan verfasserin aut Eduardo Nagore verfasserin aut Marc S Ernstoff verfasserin aut Klaus J Busam verfasserin aut Colin B Begg verfasserin aut Nancy E Thomas verfasserin aut Marianne Berwick verfasserin aut InterMEL Consortium verfasserin aut In PLoS ONE Public Library of Science (PLoS), 2007 18(2023), 4, p e0269324 (DE-627)523574592 (DE-600)2267670-3 19326203 nnns volume:18 year:2023 number:4, p e0269324 https://doi.org/10.1371/journal.pone.0269324 kostenfrei https://doaj.org/article/2122630446b94345873b74cdda1850a8 kostenfrei https://doi.org/10.1371/journal.pone.0269324 kostenfrei https://doaj.org/toc/1932-6203 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_34 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_235 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 18 2023 4, p e0269324 |
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PLoS ONE |
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Irene Orlow @@aut@@ Keimya D Sadeghi @@aut@@ Sharon N Edmiston @@aut@@ Jessica M Kenney @@aut@@ Cecilia Lezcano @@aut@@ James S Wilmott @@aut@@ Anne E Cust @@aut@@ Richard A Scolyer @@aut@@ Graham J Mann @@aut@@ Tim K Lee @@aut@@ Hazel Burke @@aut@@ Valerie Jakrot @@aut@@ Ping Shang @@aut@@ Peter M Ferguson @@aut@@ Tawny W Boyce @@aut@@ Jennifer S Ko @@aut@@ Peter Ngo @@aut@@ Pauline Funchain @@aut@@ Judy R Rees @@aut@@ Kelli O'Connell @@aut@@ Honglin Hao @@aut@@ Eloise Parrish @@aut@@ Kathleen Conway @@aut@@ Paul B Googe @@aut@@ David W Ollila @@aut@@ Stergios J Moschos @@aut@@ Eva Hernando @@aut@@ Douglas Hanniford @@aut@@ Diana Argibay @@aut@@ Christopher I Amos @@aut@@ Jeffrey E Lee @@aut@@ Iman Osman @@aut@@ Li Luo @@aut@@ Pei-Fen Kuan @@aut@@ Arshi Aurora @@aut@@ Bonnie E Gould Rothberg @@aut@@ Marcus W Bosenberg @@aut@@ Meg R Gerstenblith @@aut@@ Cheryl Thompson @@aut@@ Paul N Bogner @@aut@@ Ivan P Gorlov @@aut@@ Sheri L Holmen @@aut@@ Elise K Brunsgaard @@aut@@ Yvonne M Saenger @@aut@@ Ronglai Shen @@aut@@ Venkatraman Seshan @@aut@@ Eduardo Nagore @@aut@@ Marc S Ernstoff @@aut@@ Klaus J Busam @@aut@@ Colin B Begg @@aut@@ Nancy E Thomas @@aut@@ Marianne Berwick @@aut@@ InterMEL Consortium @@aut@@ |
publishDateDaySort_date |
2023-01-01T00:00:00Z |
hierarchy_top_id |
523574592 |
id |
DOAJ089056396 |
language_de |
englisch |
fullrecord |
<?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01000naa a22002652 4500</leader><controlfield tag="001">DOAJ089056396</controlfield><controlfield tag="003">DE-627</controlfield><controlfield tag="005">20230505005459.0</controlfield><controlfield tag="007">cr uuu---uuuuu</controlfield><controlfield tag="008">230505s2023 xx |||||o 00| ||eng c</controlfield><datafield tag="024" ind1="7" ind2=" "><subfield code="a">10.1371/journal.pone.0269324</subfield><subfield code="2">doi</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-627)DOAJ089056396</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)DOAJ2122630446b94345873b74cdda1850a8</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-627</subfield><subfield code="b">ger</subfield><subfield code="c">DE-627</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1=" " ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="100" ind1="0" ind2=" "><subfield code="a">Irene Orlow</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma.</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2023</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a"><h4<Introduction</h4<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.<h4<Methods</h4<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).<h4<Results</h4<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).<h4<Conclusion</h4<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. 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InterMEL: An international biorepository and clinical database to uncover predictors of survival in early-stage melanoma. |
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<h4<Introduction</h4<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.<h4<Methods</h4<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).<h4<Results</h4<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).<h4<Conclusion</h4<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. |
abstractGer |
<h4<Introduction</h4<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.<h4<Methods</h4<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).<h4<Results</h4<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).<h4<Conclusion</h4<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_unstemmed |
<h4<Introduction</h4<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.<h4<Methods</h4<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).<h4<Results</h4<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).<h4<Conclusion</h4<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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7.400463 |