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dc.contributor.authorGong, Binsheng
dc.contributor.authorLi, Dan
dc.contributor.authorKusko, Rebecca
dc.contributor.authorNovoradovskaya, Natalia
dc.contributor.authorZhang, Yifan
dc.contributor.authorWang, Shangzi
dc.contributor.authorPabon-Peña, Carlos
dc.contributor.authorZhang, Zhihong
dc.contributor.authorLai, Kevin
dc.contributor.authorCai, Wanshi
dc.contributor.authorLoCoco, Jennifer S
dc.contributor.authorLader, Eric
dc.contributor.authorRichmond, Todd A
dc.contributor.authorMittal, Vinay K
dc.contributor.authorLiu, Liang-Chun
dc.contributor.authorJohann, Donald J
dc.contributor.authorWilley, James C
dc.contributor.authorBushel, Pierre R
dc.contributor.authorYu, Ying
dc.contributor.authorXu, Chang
dc.contributor.authorChen, Guangchun
dc.contributor.authorBurgess, Daniel
dc.contributor.authorCawley, Simon
dc.contributor.authorGiorda, Kristina
dc.contributor.authorHaseley, Nathan
dc.contributor.authorQiu, Fujun
dc.contributor.authorWilkins, Katherine
dc.contributor.authorArib, Hanane
dc.contributor.authorAttwooll, Claire
dc.contributor.authorBabson, Kevin
dc.contributor.authorBao, Longlong
dc.contributor.authorBao, Wenjun
dc.contributor.authorLucas, Anne Bergstrom
dc.contributor.authorBest, Hunter
dc.contributor.authorBhandari, Ambica
dc.contributor.authorBisgin, Halil
dc.contributor.authorBlackburn, James
dc.contributor.authorBlomquist, Thomas M
dc.contributor.authorBoardman, Lisa
dc.contributor.authorBurgher, Blake
dc.contributor.authorButler, Daniel J
dc.contributor.authorChang, Chia-Jung
dc.contributor.authorChaubey, Alka
dc.contributor.authorChen, Tao
dc.contributor.authorChierici, Marco
dc.contributor.authorChin, Christopher R
dc.contributor.authorClose, Devin
dc.contributor.authorConroy, Jeffrey
dc.contributor.authorCooley Coleman, Jessica
dc.contributor.authorCraig, Daniel J
dc.contributor.authorCrawford, Erin
dc.contributor.authordel Pozo, Angela
dc.contributor.authorDeveson, Ira W
dc.contributor.authorDuncan, Daniel
dc.contributor.authorEterovic, Agda Karina
dc.contributor.authorFan, Xiaohui
dc.contributor.authorFoox, Jonathan
dc.contributor.authorFurlanello, Cesare
dc.contributor.authorGhosal, Abhisek
dc.contributor.authorGlenn, Sean
dc.contributor.authorGuan, Meijian
dc.contributor.authorHaag, Christine
dc.contributor.authorHang, Xinyi
dc.contributor.authorHappe, Scott
dc.contributor.authorHennigan, Brittany
dc.contributor.authorHipp, Jennifer
dc.contributor.authorHong, Huixiao
dc.contributor.authorHorvath, Kyle
dc.contributor.authorHu, Jianhong
dc.contributor.authorHung, Li-Yuan
dc.contributor.authorJarosz, Mirna
dc.contributor.authorKerkhof, Jennifer
dc.contributor.authorKipp, Benjamin
dc.contributor.authorKreil, David Philip
dc.contributor.authorŁabaj, Paweł
dc.contributor.authorLapunzina, Pablo
dc.contributor.authorLi, Peng
dc.contributor.authorLi, Quan-Zhen
dc.contributor.authorLi, Weihua
dc.contributor.authorLi, Zhiguang
dc.contributor.authorLiang, Yu
dc.contributor.authorLiu, Shaoqing
dc.contributor.authorLiu, Zhichao
dc.contributor.authorMa, Charles
dc.contributor.authorMarella, Narasimha
dc.contributor.authorMartín-Arenas, Rubén
dc.contributor.authorMegherbi, Dalila B
dc.contributor.authorMeng, Qingchang
dc.contributor.authorMieczkowski, Piotr A
dc.contributor.authorMorrison, Tom
dc.contributor.authorMuzny, Donna
dc.contributor.authorNing, Baitang
dc.contributor.authorParsons, Barbara L
dc.contributor.authorPaweletz, Cloud P
dc.contributor.authorPirooznia, Mehdi
dc.contributor.authorQu, Wubin
dc.contributor.authorRaymond, Amelia
dc.contributor.authorRindler, Paul
dc.contributor.authorRingler, Rebecca
dc.contributor.authorSadikovic, Bekim
dc.contributor.authorScherer, Andreas
dc.contributor.authorSchulze, Egbert
dc.contributor.authorSebra, Robert
dc.contributor.authorShaknovich, Rita
dc.contributor.authorShi, Qiang
dc.contributor.authorShi, Tieliu
dc.contributor.authorSilla-Castro, Juan Carlos 
dc.contributor.authorSmith, Melissa
dc.contributor.authorSolis-Lopez, Mario
dc.contributor.authorSong, Ping
dc.contributor.authorStetson, Daniel
dc.contributor.authorStrahl, Maya
dc.contributor.authorStuart, Alan
dc.contributor.authorSupplee, Julianna
dc.contributor.authorSzankasi, Philippe
dc.contributor.authorTan, Haowen
dc.contributor.authorTang, Lin-Ya
dc.contributor.authorTao, Yonghui
dc.contributor.authorThakkar, Shraddha
dc.contributor.authorThierry-Mieg, Danielle
dc.contributor.authorThierry-Mieg, Jean
dc.contributor.authorThodima, Venkat J
dc.contributor.authorThomas, David
dc.contributor.authorTichy, Boris
dc.contributor.authorTom, Nikola
dc.contributor.authorVallespin-Garcia, Elena
dc.contributor.authorVerma, Suman
dc.contributor.authorWalker, Kimbley
dc.contributor.authorWang, Charles
dc.contributor.authorWang, Junwen
dc.contributor.authorWang, Yexun
dc.contributor.authorWen, Zhining
dc.contributor.authorWirta, Valtteri
dc.contributor.authorWu, Leihong
dc.contributor.authorXiao, Chunlin
dc.contributor.authorXiao, Wenzhong
dc.contributor.authorXu, Shibei
dc.contributor.authorYang, Mary
dc.contributor.authorYing, Jianming
dc.contributor.authorYip, Shun H
dc.contributor.authorZhang, Guangliang
dc.contributor.authorZhang, Sa
dc.contributor.authorZhao, Meiru
dc.contributor.authorZheng, Yuanting
dc.contributor.authorZhou, Xiaoyan
dc.contributor.authorMason, Christopher E
dc.contributor.authorMercer, Timothy
dc.contributor.authorTong, Weida
dc.contributor.authorShi, Leming
dc.contributor.authorJones, Wendell
dc.contributor.authorXu, Joshua
dc.date.accessioned2021-10-04T08:59:06Z
dc.date.available2021-10-04T08:59:06Z
dc.date.issued2021-04
dc.identifier.citationGenome Biol. 2021; 22(1):109es_ES
dc.identifier.issn1474-760Xes_ES
dc.identifier.urihttp://hdl.handle.net/20.500.12105/13424
dc.description.abstractTargeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing. All panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden. This comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.es_ES
dc.description.sponsorshipAll SEQC2 participants freely donated their time, reagents, and computing resources for the completion and analysis of this project. Part of this work was carried out with the support of the Intramural Research Program of the National Institutes of Health (to Mehdi Pirooznia), National Institute of Environmental Health Sciences (to Pierre Bushel), and National Library of Medicine (to Danielle Thierry-Mieg, Jean Thierry-Mieg, and Chunlin Xiao). Leming Shi and Yuanting Zheng were supported by the National Key R&D Project of China (2018YFE0201600), the National Natural Science Foundation of China (31720103909), and Shanghai Municipal Science and Technology Major Project (2017SHZDZX01). Donald J. Johann, Jr. acknowledges the support by FDA BAA grant HHSF223201510172C. Timothy Mercer and Ira Deveson were supported by the National Health and Medical Research Council (NHMRC) of Australia grants APP1108254, APP1114016, and APP1173594 and Cancer Institute NSW Early Career Fellowship 2018/ECF013. This research has also been, in part, financially supported by the MEYS of the CR under the project CEITEC 2020 (LQ1601), by MH CR, grant No. (NV19-03-00091). Part of this work was carried out with the support of research infrastructure EATRIS-CZ, ID number LM2015064, funded by MEYS CR. Boris Tichy and Nikola Tom were supported by research infrastructure EATRIS-CZ, ID number LM2018133 funded by MEYS CR and MEYS CR project CEITEC 2020 (LQ1601).es_ES
dc.language.isoenges_ES
dc.publisherBioMed Central (BMC) es_ES
dc.type.hasVersionVoRes_ES
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.titleCross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.es_ES
dc.typejournal articlees_ES
dc.rights.licenseAtribución 4.0 Internacional*
dc.identifier.pubmedID33863344es_ES
dc.format.volume22es_ES
dc.format.number1es_ES
dc.format.page109es_ES
dc.identifier.doi10.1186/s13059-021-02315-0es_ES
dc.contributor.funderNational Institutes of Health (Estados Unidos) 
dc.contributor.funderNIH - National Institute of Environmental Health Sciences (NIEHS) (Estados Unidos) 
dc.contributor.funderUnited States National Library of Medicine 
dc.contributor.funderNational Natural Science Foundation of China 
dc.contributor.funderNational Key R&D Project of China
dc.contributor.funderShanghai Municipal Science and Technology Major Project
dc.contributor.funderNational Health and Medical Research Council (Australia) 
dc.contributor.funderNIH - National Cancer Institute (NCI) (Estados Unidos) 
dc.description.peerreviewedes_ES
dc.relation.publisherversionhttps://doi.org/10.1186/s13059-021-02315-0es_ES
dc.identifier.journalGenome biologyes_ES
dc.repisalud.orgCNICCNIC::Unidades técnicas::Bioinformáticaes_ES
dc.repisalud.institucionISCIIIes_ES
dc.rights.accessRightsopen accesses_ES


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