Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

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Xiao, WenmingUS FDA, Ctr Devices & Radiol Hlth, Silver Spring, MD 20993 USA. (author)

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Article/chapterEnglish2021

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2021-09-09
Springer Nature,2021
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LIBRIS-ID:oai:DiVA.org:uu-457655
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-457655URI
https://doi.org/10.1038/s41587-021-00994-5DOI

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Language:English
Summary in:English

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Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing. Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.

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Ren, LuyaoFudan Univ, Sch Life Sci, Human Phenome Inst, State Key Lab Genet Engn, Shanghai, Peoples R China.;Fudan Univ, Shanghai Canc Ctr, Shanghai, Peoples R China. (author)
Chen, ZhongLoma Linda Univ, Sch Med, Ctr Genom, Loma Linda, CA 92350 USA. (author)
Fang, Li TaiRoche Sequencing Solut Inc, Bioinformat Res & Early Dev, Belmont, CA USA. (author)
Zhao, YongmeiFrederick Natl Lab Canc Res, Biomed Informat & Data Sci Directorate, Adv Biomed & Computat Sci, Frederick, MD USA. (author)
Lack, JustinFrederick Natl Lab Canc Res, Biomed Informat & Data Sci Directorate, Adv Biomed & Computat Sci, Frederick, MD USA. (author)
Guan, MeijianSAS Inst Inc, Cary, NC USA. (author)
Zhu, BinNCI, Div Canc Epidemiol & Genet, NIH, Rockville, MD USA. (author)
Jaeger, ErichIllumina Inc, Foster City, CA USA. (author)
Kerrigan, LizATCC, Manassas, VA USA. (author)
Blomquist, Thomas M. (author)
Hung, TiffanyGenentech Inc, San Francisco, CA 94080 USA. (author)
Sultan, MarcNovartis Inst Biomed Res, Biomarker Dev, Basel, Switzerland. (author)
Idler, KennethAbbVie, Genom Res Ctr, Computat Genom, N Chicago, IL 60064 USA. (author)
Lu, CharlesAbbVie, Genom Res Ctr, Computat Genom, N Chicago, IL 60064 USA. (author)
Scherer, AndreasUniv Helsinki, Inst Mol Med Finland, Helsinki, Finland.;European Infrastruct Translat Med, Amsterdam, Netherlands. (author)
Kusko, RebeccaImmuneering Corp, Cambridge, MA USA. (author)
Moos, MalcolmUS FDA, Ctr Biol Evaluat & Res, Silver Spring, MD USA. (author)
Xiao, ChunlinNIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bldg 10, Bethesda, MD 20892 USA. (author)
Sherry, Stephen T.NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bldg 10, Bethesda, MD 20892 USA. (author)
Abaan, Ogan D.Illumina Inc, Foster City, CA USA.;Seven Bridges Genom Inc, Cambridge, MA USA. (author)
Chen, WanqiuLoma Linda Univ, Sch Med, Ctr Genom, Loma Linda, CA 92350 USA. (author)
Chen, XinLoma Linda Univ, Sch Med, Ctr Genom, Loma Linda, CA 92350 USA. (author)
Nordlund, JessicaUppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab,European Infrastruct Translat Med, Amsterdam, Netherlands.(Swepub:uu)jesno775 (author)
Liljedahl, UlrikaEuropean Infrastruct Translat Med, Amsterdam, Netherlands.;NCI, Ctr Riferimento Oncol Aviano, IRCCS, Unit Oncogenet & Funct Oncogen, Aviano, Italy. (author)
Maestro, RobertaEuropean Infrastruct Translat Med, Amsterdam, Netherlands.;NCI, Ctr Riferimento Oncol Aviano, IRCCS, Unit Oncogenet & Funct Oncogen, Aviano, Italy. (author)
Polano, MaurizioEuropean Infrastruct Translat Med, Amsterdam, Netherlands.;NCI, Ctr Riferimento Oncol Aviano, IRCCS, Unit Oncogenet & Funct Oncogen, Aviano, Italy. (author)
Drabek, JiriEuropean Infrastruct Translat Med, Amsterdam, Netherlands.;Palacky Univ Olomouc, Fac Med & Dent, IMTM, Olomouc, Czech Republic. (author)
Vojta, PetrEuropean Infrastruct Translat Med, Amsterdam, Netherlands.;Palacky Univ Olomouc, Fac Med & Dent, IMTM, Olomouc, Czech Republic. (author)
Köks, SulevEuropean Infrastruct Translat Med, Amsterdam, Netherlands.;Perron Inst Neurol & Translat Sci, Perth, WA, Australia.;Murdoch Univ, Ctr Mol Med & Innovat Therapeut, Perth, WA, Australia. (author)
Reimann, EneEuropean Infrastruct Translat Med, Amsterdam, Netherlands.;Univ Tartu, Estonian Genome Ctr, Inst Genom, Tartu, Estonia. (author)
Madala, Bindu SwapnaKinghorn Canc Ctr, Garvan Inst Med Res, Darlinghurst, NSW, Australia. (author)
Mercer, TimothyKinghorn Canc Ctr, Garvan Inst Med Res, Darlinghurst, NSW, Australia. (author)
Miller, ChrisAbbVie, Genom Res Ctr, Computat Genom, N Chicago, IL 60064 USA. (author)
Jacob, HowardAbbVie, Genom Res Ctr, Computat Genom, N Chicago, IL 60064 USA. (author)
Truong, TiffanyIllumina Inc, Foster City, CA USA. (author)
Moshrefi, AliIllumina Inc, Foster City, CA USA. (author)
Natarajan, AparnaIllumina Inc, Foster City, CA USA. (author)
Granat, AnaIllumina Inc, Foster City, CA USA. (author)
Schroth, Gary P.Illumina Inc, Foster City, CA USA. (author)
Kalamegham, RasikaGenentech Inc, San Francisco, CA 94080 USA. (author)
Peters, EricGenentech Inc, San Francisco, CA 94080 USA. (author)
Petitjean, VirginieNovartis Inst Biomed Res, Biomarker Dev, Basel, Switzerland. (author)
Walton, AshleyFrederick Natl Lab Canc Res, Biomed Informat & Data Sci Directorate, Adv Biomed & Computat Sci, Frederick, MD USA. (author)
Shen, Tsai-WeiFrederick Natl Lab Canc Res, Biomed Informat & Data Sci Directorate, Adv Biomed & Computat Sci, Frederick, MD USA. (author)
Talsania, KeyurFrederick Natl Lab Canc Res, Biomed Informat & Data Sci Directorate, Adv Biomed & Computat Sci, Frederick, MD USA. (author)
Vera, Cristobal JuanFrederick Natl Lab Canc Res, Biomed Informat & Data Sci Directorate, Adv Biomed & Computat Sci, Frederick, MD USA. (author)
Langenbach, KurtATCC, Manassas, VA USA. (author)
de Mars, MaryellenATCC, Manassas, VA USA. (author)
Hipp, Jennifer A.Univ Toledo, Med Ctr, Dept Med, Toledo, OH USA.;Univ Toledo, Med Ctr, Dept Pathol, Toledo, OH USA. (author)
Willey, James C.Univ Toledo, Med Ctr, Dept Med, Toledo, OH USA.;Univ Toledo, Med Ctr, Dept Pathol, Toledo, OH USA. (author)
Wang, JingNatl Inst Metrol, Beijing, Peoples R China. (author)
Shetty, JyotiFrederick Natl Lab Canc Res, Canc Res Technol Program, Sequencing Facil, Frederick, MD USA. (author)
Kriga, YuliyaFrederick Natl Lab Canc Res, Canc Res Technol Program, Sequencing Facil, Frederick, MD USA. (author)
Raziuddin, AratiFrederick Natl Lab Canc Res, Canc Res Technol Program, Sequencing Facil, Frederick, MD USA. (author)
Tran, BaoFrederick Natl Lab Canc Res, Canc Res Technol Program, Sequencing Facil, Frederick, MD USA. (author)
Zheng, YuantingFudan Univ, Sch Life Sci, Human Phenome Inst, State Key Lab Genet Engn, Shanghai, Peoples R China.;Fudan Univ, Shanghai Canc Ctr, Shanghai, Peoples R China. (author)
Yu, YingFudan Univ, Sch Life Sci, Human Phenome Inst, State Key Lab Genet Engn, Shanghai, Peoples R China.;Fudan Univ, Shanghai Canc Ctr, Shanghai, Peoples R China. (author)
Cam, MargaretCtr Canc Res, Off Sci & Technol Resources, CCR Collaborat Bioinformat Resource, Bethesda, MD USA. (author)
Jailwala, ParthavCtr Canc Res, Off Sci & Technol Resources, CCR Collaborat Bioinformat Resource, Bethesda, MD USA. (author)
Nguyen, Cu (author)
Meerzaman, DaoudNCI, Computat Genom & Bioinformat Branch, Ctr Biomed Informat & Informat Technol, Rockville, MD USA. (author)
Chen, QingrongNCI, Computat Genom & Bioinformat Branch, Ctr Biomed Informat & Informat Technol, Rockville, MD USA. (author)
Yan, ChunhuaNCI, Computat Genom & Bioinformat Branch, Ctr Biomed Informat & Informat Technol, Rockville, MD USA. (author)
Ernest, BenDigicon, Mclean, VA USA. (author)
Mehra, UrvashiDigicon, Mclean, VA USA. (author)
Jensen, Roderick, VVirginia Polytech Inst & State Univ, Dept Biol Sci, Blacksburg, VA 24061 USA. (author)
Jones, WendellQ2 Solut EA Genom, Morrisville, NC USA. (author)
Li, Jian-LiangNIEHS, Integrat Bioinformat, Durham, NC USA. (author)
Papas, Brian N.NIEHS, Integrat Bioinformat, Durham, NC USA. (author)
Pirooznia, MehdiNHLBI, Bioinformat & Computat Biol Core, NIH, Bldg 10, Bethesda, MD 20892 USA. (author)
Chen, Yun-ChingNHLBI, Bioinformat & Computat Biol Core, NIH, Bldg 10, Bethesda, MD 20892 USA. (author)
Seifuddin, FayazNHLBI, Bioinformat & Computat Biol Core, NIH, Bldg 10, Bethesda, MD 20892 USA. (author)
Li, ZhipanSentieon Inc, Mountain View, CA USA. (author)
Liu, XueluNIH, Ctr Informat Technol, Bldg 10, Bethesda, MD 20892 USA. (author)
Resch, WolfgangNIH, Ctr Informat Technol, Bldg 10, Bethesda, MD 20892 USA. (author)
Wang, JingyaAstraZeneca, Gaithersburg, MD USA. (author)
Wu, LeihongUS FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA. (author)
Yavas, GokhanUS FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA. (author)
Miles, CoreyUS FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA. (author)
Ning, BaitangUS FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA. (author)
Tong, WeidaUS FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA. (author)
Mason, Christopher E.Weill Cornell Med, Dept Physiol & Biophys, New York, NY USA. (author)
Donaldson, EricUS FDA, Ctr Drug Evaluat & Res, Silver Spring, MD USA. (author)
Lababidi, SamirUS FDA, Off Chief Scientist, Off Commissioner, Silver Spring, MD USA. (author)
Staudt, Louis M.NCI, Lymphoid Malignancies Branch, Ctr Canc Res, NIH, Bethesda, MD 20892 USA. (author)
Tezak, ZivanaUS FDA, Ctr Devices & Radiol Hlth, Silver Spring, MD 20993 USA. (author)
Hong, HuixiaoUS FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA. (author)
Wang, CharlesLoma Linda Univ, Sch Med, Ctr Genom, Loma Linda, CA 92350 USA. (author)
Shi, LemingFudan Univ, Sch Life Sci, Human Phenome Inst, State Key Lab Genet Engn, Shanghai, Peoples R China.;Fudan Univ, Shanghai Canc Ctr, Shanghai, Peoples R China. (author)
US FDA, Ctr Devices & Radiol Hlth, Silver Spring, MD 20993 USA.Fudan Univ, Sch Life Sci, Human Phenome Inst, State Key Lab Genet Engn, Shanghai, Peoples R China.;Fudan Univ, Shanghai Canc Ctr, Shanghai, Peoples R China. (creator_code:org_t)

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In:Nature Biotechnology: Springer Nature39:9, s. 1141-11501087-01561546-1696

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By the author/editor: Xiao, Wenming; Ren, Luyao; Chen, Zhong; Fang, Li Tai; Zhao, Yongmei; Lack, Justin; show more...; Guan, Meijian; Zhu, Bin; Jaeger, Erich; Kerrigan, Liz; Blomquist, Thoma ...; Hung, Tiffany; Sultan, Marc; Idler, Kenneth; Lu, Charles; Scherer, Andreas; Kusko, Rebecca; Moos, Malcolm; Xiao, Chunlin; Sherry, Stephen ...; Abaan, Ogan D.; Chen, Wanqiu; Chen, Xin; Nordlund, Jessic ...; Liljedahl, Ulrik ...; Maestro, Roberta; Polano, Maurizio; Drabek, Jiri; Vojta, Petr; Köks, Sulev; Reimann, Ene; Madala, Bindu Sw ...; Mercer, Timothy; Miller, Chris; Jacob, Howard; Truong, Tiffany; Moshrefi, Ali; Natarajan, Aparn ...; Granat, Ana; Schroth, Gary P.; Kalamegham, Rasi ...; Peters, Eric; Petitjean, Virgi ...; Walton, Ashley; Shen, Tsai-Wei; Talsania, Keyur; Vera, Cristobal ...; Langenbach, Kurt; de Mars, Maryell ...; Hipp, Jennifer A ...; Willey, James C.; Wang, Jing; Shetty, Jyoti; Kriga, Yuliya; Raziuddin, Arati; Tran, Bao; Zheng, Yuanting; Yu, Ying; Cam, Margaret; Jailwala, Partha ...; Nguyen, Cu; Meerzaman, Daoud; Chen, Qingrong; Yan, Chunhua; Ernest, Ben; Mehra, Urvashi; Jensen, Roderick ...; Jones, Wendell; Li, Jian-Liang; Papas, Brian N.; Pirooznia, Mehdi; Chen, Yun-Ching; Seifuddin, Fayaz; Li, Zhipan; Liu, Xuelu; Resch, Wolfgang; Wang, Jingya; Wu, Leihong; Yavas, Gokhan; Miles, Corey; Ning, Baitang; Tong, Weida; Mason, Christoph ...; Donaldson, Eric; Lababidi, Samir; Staudt, Louis M.; Tezak, Zivana; Hong, Huixiao; Wang, Charles; Shi, Leming; show less...

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