A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

被引：207

作者：

Alioto, Tyler S. ^{[1
,2
]}

Buchhalter, Ivo ^{[3
,4
]}

Derdak, Sophia ^{[1
,2
]}

Hutter, Barbara ^{[4
]}

Eldridge, Matthew D. ^{[5
]}

Hovig, Eivind ^{[6
,7
]}

Heisler, Lawrence E. ^{[8
]}

Beck, Timothy A. ^{[8
]}

Simpson, Jared T. ^{[8
]}

Tonon, Laurie ^{[9
]}

Sertier, Anne-Sophie ^{[9
]}

Patch, Ann-Marie ^{[10
,11
]}

Jaeger, Natalie ^{[3
,12
]}

Ginsbach, Philip ^{[3
]}

Drews, Ruben ^{[3
]}

Paramasivam, Nagarajan ^{[3
]}

Kabbe, Rolf ^{[3
]}

Chotewutmontri, Sasithorn ^{[13
]}

Diessl, Nicolle ^{[13
]}

Previti, Christopher ^{[13
]}

Schmidt, Sabine ^{[4
]}

Brors, Benedikt ^{[4
]}

Feuerbach, Lars ^{[4
]}

Heinold, Michael ^{[14
]}

Groebner, Susanne ^{[15
]}

Korshunov, Andrey ^{[16
]}

Tarpey, Patrick S. ^{[16
]}

Butler, Adam P. ^{[16
]}

Hinton, Jonathan ^{[16
]}

Jones, David ^{[16
]}

Menzies, Andrew ^{[16
]}

Raine, Keiran ^{[16
]}

Shepherd, Rebecca ^{[16
]}

Stebbings, Lucy ^{[16
]}

Teague, Jon W. ^{[16
]}

Ribeca, Paolo ^{[1
,2
]}

Giner, Francesc Castro ^{[1
,2
]}

Beltran, Sergi ^{[1
,2
]}

Raineri, Emanuele ^{[1
,2
]}

Dabad, Marc ^{[1
,2
]}

Heath, Simon C. ^{[1
,2
]}

Gut, Marta ^{[1
,2
]}

Denroche, Robert E. ^{[8
]}

Harding, Nicholas J. ^{[8
]}

Yamaguchi, Takafumi N. ^{[8
]}

Fujimoto, Akihiro ^{[17
]}

Nakagawa, Hidewaki ^{[17
]}

Quesada, Ctor ^{[18
]}

Valdes-Mas, Rafael ^{[18
]}

Nakken, Sigve ^{[6
]}

机构：

[1] BIST, Ctr Genom Regulat, CNAG CRG, Barcelona 08028, Spain

[2] Univ Pompeu Fabra, Barcelona 08002, Spain

[3] German Canc Res Ctr, Div Theoret Bioinformat, D-69120 Heidelberg, Germany

[4] German Canc Res Ctr, Div Appl Bioinformat, D-69120 Heidelberg, Germany

[5] Univ Cambridge, Li Ka Shing Ctr, Canc Res, UK Cambridge Inst, Cambridge CB2 0RE, England

[6] Oslo Univ Hosp, Inst Canc Res, Dept Tumor Biol, N-0424 Oslo, Norway

[7] Univ Oslo, Dept Informat, N-0373 Oslo, Norway

[8] Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada

[9] Ctr Leon Berard, Synergie Lyon Canc Fdn, F-69373 Lyon, France

[10] Univ Queensland, Inst Mol Biosci, Queensland Ctr Med Gen, Brisbane, Qld 4072, Australia

[11] QIMR Berghofer Med Res Inst, Brisbane, Qld 4006, Australia

[12] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[13] German Canc Res Ctr, Genome & Proteome Core Facil, D-69120 Heidelberg, Germany

[14] Univ Heidelberg Hosp, Dept Pediat Hematol & Oncol, D-69120 Heidelberg, Germany

[15] Univ Heidelberg Hosp, Dept Neuropathol, D-69120 Heidelberg, Germany

[16] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[17] RIKEN, Ctr Integrat Med Sci, Minato Ku, Tokyo 1088639, Japan

[18] Univ Oviedo IUOPA, Oviedo 33006, Spain

[19] Oslo Univ Hosp, Inst Canc Genet & Informat, Bioinformat Core Facil, N-0310 Oslo, Norway

[20] Univ Melbourne, Victorian Life Sci Computat Initiat, Melbourne, Vic 3053, Australia

[21] Univ Glasgow, Inst Canc Sci, WolfsonWohl Canc Res Ctr, Glasgow G61 1QH, Lanark, Scotland

[22] Oregon Hlth & Sci Univ, Knight Canc Inst, Portland, OR 97239 USA

[23] BGI Shenzhen, Shenzhen 518083, Peoples R China

[24] Washington Univ, Genome Inst, St Louis, MO 63108 USA

[25] Harvard Univ, Sch Med, Boston, MA 02115 USA

[26] MD Anderson Canc Ctr, Houston, TX 77030 USA

[27] McGill Univ, Montreal, PQ H3A 0G4, Canada

[28] Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA

[29] Barcelona Supercomputing Ctr, IRB BSC Joint Res Program Computat Biol, Barcelona 08034, Spain

[30] Baylor Coll Med, Human Genome Sequencing Ctr, Houston, TX 77030 USA

[31] Univ Barcelona, Hosp Clin, Dept Pathol, Inst Invest Biomed August Pi & Sunyer,Hematopatho, Barcelona 08036, Spain

[32] Univ Toronto, Dept Med Biophys, Toronto, ON M5G 1L7, Canada

[33] NCI, Off Canc Gen, Bethesda, MD 20892 USA

[34] German Canc Res Ctr, Div Pediat Neurooncol, D-69120 Heidelberg, Germany

[35] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A8, Canada

[36] German Canc Res Ctr, Div Mol Genet, D-69120 Heidelberg, Germany

[37] German Canc Res Ctr, Heidelberg Ctr Personalised Oncol DKFZ HIPO, Heidelberg, Germany

[38] Heidelberg Univ, Inst Pharm & Mol Biotechnol, D-69120 Heidelberg, Germany

[39] Heidelberg Univ, Bioquant Ctr, D-69120 Heidelberg, Germany

[40] German Canc Res Ctr, Div Pediat Neurooncol, D-69120 Heidelberg, Germany

来源：

NATURE COMMUNICATIONS | 2015年 / 6卷

基金：

芬兰科学院; 加拿大创新基金会; 英国生物技术与生命科学研究理事会;

关键词：

VARIANT ANALYSIS; POINT MUTATIONS; EXOME; ACCURATE; SIGNATURES; FRAMEWORK; ALIGNMENT;

D O I：

10.1038/ncomms10001

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to similar to 100 x shows benefits, as long as the tumour: control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.

引用

页数：13

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