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oai:repisalud.isciii.es:20.500.12105/134242024-10-31T11:45:51Zcom_20.500.12105_19604com_20.500.12105_2051col_20.500.12105_19607
Repisalud author Gong, Binsheng author Li, Dan author Kusko, Rebecca author Novoradovskaya, Natalia author Zhang, Yifan author Wang, Shangzi author Pabon-Peña, Carlos author Zhang, Zhihong author Lai, Kevin author Cai, Wanshi author LoCoco, Jennifer S author Lader, Eric author Richmond, Todd A author Mittal, Vinay K author Liu, Liang-Chun author Johann, Donald J author Willey, James C author Bushel, Pierre R author Yu, Ying author Xu, Chang author Chen, Guangchun author Burgess, Daniel author Cawley, Simon author Giorda, Kristina author Haseley, Nathan author Qiu, Fujun author Wilkins, Katherine author Arib, Hanane author Attwooll, Claire author Babson, Kevin author Bao, Longlong author Bao, Wenjun author Lucas, Anne Bergstrom author Best, Hunter author Bhandari, Ambica author Bisgin, Halil author Blackburn, James author Blomquist, Thomas M author Boardman, Lisa author Burgher, Blake author Butler, Daniel J author Chang, Chia-Jung author Chaubey, Alka author Chen, Tao author Chierici, Marco author Chin, Christopher R author Close, Devin author Conroy, Jeffrey author Cooley Coleman, Jessica author Craig, Daniel J author Crawford, Erin author del Pozo, Angela author Deveson, Ira W author Duncan, Daniel author Eterovic, Agda Karina author Fan, Xiaohui author Foox, Jonathan author Furlanello, Cesare author Ghosal, Abhisek author Glenn, Sean author Guan, Meijian author Haag, Christine author Hang, Xinyi author Happe, Scott author Hennigan, Brittany author Hipp, Jennifer author Hong, Huixiao author Horvath, Kyle author Hu, Jianhong author Hung, Li-Yuan author Jarosz, Mirna author Kerkhof, Jennifer author Kipp, Benjamin author Kreil, David Philip author Łabaj, Paweł author Lapunzina, Pablo author Li, Peng author Li, Quan-Zhen author Li, Weihua author Li, Zhiguang author Liang, Yu author Liu, Shaoqing author Liu, Zhichao author Ma, Charles author Marella, Narasimha author Martín-Arenas, Rubén author Megherbi, Dalila B author Meng, Qingchang author Mieczkowski, Piotr A author Morrison, Tom author Muzny, Donna author Ning, Baitang author Parsons, Barbara L author Paweletz, Cloud P author Pirooznia, Mehdi author Qu, Wubin author Raymond, Amelia author Rindler, Paul author Ringler, Rebecca author Sadikovic, Bekim author Scherer, Andreas author Schulze, Egbert author Sebra, Robert author Shaknovich, Rita author Shi, Qiang author Shi, Tieliu author Silla-Castro, Juan Carlos author Smith, Melissa author Solis-Lopez, Mario author Song, Ping author Stetson, Daniel author Strahl, Maya author Stuart, Alan author Supplee, Julianna author Szankasi, Philippe author Tan, Haowen author Tang, Lin-Ya author Tao, Yonghui author Thakkar, Shraddha author Thierry-Mieg, Danielle author Thierry-Mieg, Jean author Thodima, Venkat J author Thomas, David author Tichy, Boris author Tom, Nikola author Vallespin-Garcia, Elena author Verma, Suman author Walker, Kimbley author Wang, Charles author Wang, Junwen author Wang, Yexun author Wen, Zhining author Wirta, Valtteri author Wu, Leihong author Xiao, Chunlin author Xiao, Wenzhong author Xu, Shibei author Yang, Mary author Ying, Jianming author Yip, Shun H author Zhang, Guangliang author Zhang, Sa author Zhao, Meiru author Zheng, Yuanting author Zhou, Xiaoyan author Mason, Christopher E author Mercer, Timothy author Tong, Weida author Shi, Leming author Jones, Wendell author Xu, Joshua funder National Institutes of Health (Estados Unidos) funder NIH - National Institute of Environmental Health Sciences (NIEHS) (Estados Unidos) funder United States National Library of Medicine funder National Natural Science Foundation of China funder National Key R&D Project of China funder Shanghai Municipal Science and Technology Major Project funder National Health and Medical Research Council (Australia) funder NIH - National Cancer Institute (NCI) (Estados Unidos) 2021-10-04T08:59:06Z 2021-10-04T08:59:06Z 2021-04 Genome Biol. 2021; 22(1):109 1474-760X http://hdl.handle.net/20.500.12105/13424 33863344 10.1186/s13059-021-02315-0 Genome biology Targeted 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. eng Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. journal article 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 URL https://repisalud.isciii.es/bitstreams/b9b13ecd-a9ae-4aa1-8a04-d50b62ecd301/download File MD5 45d0a1015f5f0c857b577c60034e4d74 1937591 application/pdf Cross-oncopanelstudyreveals_2021.pdf URL https://repisalud.isciii.es/bitstreams/4db89c6e-0022-4fce-96f2-cd4b2ac7cf21/download File MD5 dd9468d7d821be2faf89515e8ad69b51 2544559 application/pdf Cross-oncopanelstudyreveals_2021_supp1.pdf URL https://repisalud.isciii.es/bitstreams/d4bb6011-f67e-4adf-a315-7f776032e75b/download File MD5 a7299a433e610edf99e746f421db4978 882560 application/pdf Cross-oncopanelstudyreveals_2021_supp2.pdf URL https://repisalud.isciii.es/bitstreams/c3a62149-4e46-423f-806b-9741d9fb2a30/download File MD5 a116612f53b51e41eb2bd08af3caec1c 1394541 application/pdf Cross-oncopanelstudyreveals_2021_supp3.pdf URL https://repisalud.isciii.es/bitstreams/6772efe8-8cff-4c5d-9cc4-23d4e5e3ab9b/download File MD5 0bb0f5eeb70c714b3254d650694e9eeb 28826 application/vnd.openxmlformats-officedocument.wordprocessingml.document Cross-oncopanelstudyreveals_2021_supp4.docx URL https://repisalud.isciii.es/bitstreams/d3a803a1-acad-4911-af8d-1c63ddce1695/download File MD5 b16a218bcc8c0b44b3eb75c1de1a67d7 93032 text/plain Cross-oncopanelstudyreveals_2021.pdf.txt URL https://repisalud.isciii.es/bitstreams/39b9e6e4-cb84-48e8-b030-6e6fd2cc11d0/download File MD5 897b0a7690a99c0978098f412eb8a4b6 9924 text/plain Cross-oncopanelstudyreveals_2021_supp1.pdf.txt URL https://repisalud.isciii.es/bitstreams/12388d75-cbee-4c25-868a-34b8b82a6db8/download File MD5 fd9df3b5f4806c052fb8420ddb6076cf 43275 text/plain Cross-oncopanelstudyreveals_2021_supp2.pdf.txt URL https://repisalud.isciii.es/bitstreams/bffb5b7d-925a-46f5-a361-42b5dedfa0fe/download File MD5 2aa616e4443bfc4178f78b6dc0a2ab85 7097 text/plain Cross-oncopanelstudyreveals_2021_supp3.pdf.txt URL https://repisalud.isciii.es/bitstreams/cd6fca71-1d44-48aa-98d6-25cc6f6f1793/download File MD5 5d2a7cbeba6c03dcc55a9ba125f2a854 35374 text/plain Cross-oncopanelstudyreveals_2021_supp4.docx.txt