title: A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.
abstract: 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 ∼ 100 × 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.
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Tyler S
authors.identifier: http://orcid.org/0000-0002-2960-5420
authors.initials: TS
authors.lastname: Alioto
authors.affiliation: Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.|Division of Applied Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
authors.forename: Ivo
authors.identifier: http://orcid.org/0000-0003-0764-5832
authors.initials: I
authors.lastname: Buchhalter
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Sophia
authors.initials: S
authors.lastname: Derdak
authors.affiliation: Division of Applied Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
authors.forename: Barbara
authors.identifier: http://orcid.org/0000-0002-9034-0329
authors.initials: B
authors.lastname: Hutter
authors.affiliation: Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Eldridge
authors.affiliation: Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway.|Department of Informatics, University of Oslo, 0373 Oslo, Norway.
authors.forename: Eivind
authors.identifier: http://orcid.org/0000-0002-9103-1077
authors.initials: E
authors.lastname: Hovig
authors.affiliation: Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3.
authors.forename: Lawrence E
authors.initials: LE
authors.lastname: Heisler
authors.affiliation: Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3.
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Beck
authors.affiliation: Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3.
authors.forename: Jared T
authors.initials: JT
authors.lastname: Simpson
authors.affiliation: Synergie Lyon Cancer Foundation, Centre Léon Bérard, Cheney C, 28 rue Laennec, Lyon 69373, France.
authors.forename: Laurie
authors.initials: L
authors.lastname: Tonon
authors.affiliation: Synergie Lyon Cancer Foundation, Centre Léon Bérard, Cheney C, 28 rue Laennec, Lyon 69373, France.
authors.forename: Anne-Sophie
authors.initials: AS
authors.lastname: Sertier
authors.affiliation: Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.|QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.
authors.forename: Ann-Marie
authors.identifier: http://orcid.org/0000-0001-6121-4019
authors.initials: AM
authors.lastname: Patch
authors.affiliation: Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.|Department of Genetics, Stanford University, Mail Stop-5120, Stanford, California 94305-5120, USA.
authors.forename: Natalie
authors.initials: N
authors.lastname: Jäger
authors.affiliation: Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
authors.forename: Philip
authors.initials: P
authors.lastname: Ginsbach
authors.affiliation: Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
authors.forename: Ruben
authors.identifier: http://orcid.org/0000-0001-7360-4970
authors.initials: R
authors.lastname: Drews
authors.affiliation: Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
authors.forename: Nagarajan
authors.initials: N
authors.lastname: Paramasivam
authors.affiliation: Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
authors.forename: Rolf
authors.initials: R
authors.lastname: Kabbe
authors.affiliation: Genome and Proteome Core Facility, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, 69120 Germany.
authors.forename: Sasithorn
authors.initials: S
authors.lastname: Chotewutmontri
authors.affiliation: Genome and Proteome Core Facility, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, 69120 Germany.
authors.forename: Nicolle
authors.initials: N
authors.lastname: Diessl
authors.affiliation: Genome and Proteome Core Facility, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, 69120 Germany.
authors.forename: Christopher
authors.initials: C
authors.lastname: Previti
authors.affiliation: Genome and Proteome Core Facility, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, 69120 Germany.
authors.forename: Sabine
authors.initials: S
authors.lastname: Schmidt
authors.affiliation: Division of Applied Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
authors.forename: Benedikt
authors.initials: B
authors.lastname: Brors
authors.affiliation: Division of Applied Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Feuerbach
authors.affiliation: Division of Applied Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Heinold
authors.affiliation: Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg 69120, Germany.
authors.forename: Susanne
authors.initials: S
authors.lastname: Gröbner
authors.affiliation: Department of Neuropathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, Heidelberg 69120, Germany.
authors.forename: Andrey
authors.initials: A
authors.lastname: Korshunov
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Tarpey
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Adam P
authors.initials: AP
authors.lastname: Butler
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Hinton
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: David
authors.initials: D
authors.lastname: Jones
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Menzies
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Keiran
authors.identifier: http://orcid.org/0000-0002-5634-1539
authors.initials: K
authors.lastname: Raine
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Shepherd
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Lucy
authors.initials: L
authors.lastname: Stebbings
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Jon W
authors.initials: JW
authors.lastname: Teague
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Paolo
authors.identifier: http://orcid.org/0000-0001-5599-3933
authors.initials: P
authors.lastname: Ribeca
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Francesc Castro
authors.identifier: http://orcid.org/0000-0001-6111-0754
authors.initials: FC
authors.lastname: Giner
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Sergi
authors.initials: S
authors.lastname: Beltran
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Emanuele
authors.initials: E
authors.lastname: Raineri
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Marc
authors.initials: M
authors.lastname: Dabad
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Simon C
authors.identifier: http://orcid.org/0000-0002-9550-0897
authors.initials: SC
authors.lastname: Heath
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.affiliation: Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3.
authors.forename: Robert E
authors.identifier: http://orcid.org/0000-0003-2197-7083
authors.initials: RE
authors.lastname: Denroche
authors.affiliation: Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Harding
authors.affiliation: Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3.
authors.forename: Takafumi N
authors.identifier: http://orcid.org/0000-0003-1082-3871
authors.initials: TN
authors.lastname: Yamaguchi
authors.affiliation: RIKEN Center for Integrative Medical Sciences, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
authors.forename: Akihiro
authors.initials: A
authors.lastname: Fujimoto
authors.affiliation: RIKEN Center for Integrative Medical Sciences, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
authors.forename: Hidewaki
authors.initials: H
authors.lastname: Nakagawa
authors.affiliation: Universidad de Oviedo-IUOPA, C/Fernando Bongera s/n, 33006 Oviedo, Spain.
authors.forename: Víctor
authors.initials: V
authors.lastname: Quesada
authors.affiliation: Universidad de Oviedo-IUOPA, C/Fernando Bongera s/n, 33006 Oviedo, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Valdés-Mas
authors.affiliation: Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway.
authors.forename: Sigve
authors.initials: S
authors.lastname: Nakken
authors.affiliation: Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway.|The Bioinformatics Core Facility, Institute for Cancer Genetics and Informatics, Oslo University Hospital, 0310 Oslo, Norway.
authors.forename: Daniel
authors.initials: D
authors.lastname: Vodák
authors.affiliation: Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
authors.forename: Lawrence
authors.initials: L
authors.lastname: Bower
authors.affiliation: Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Lynch
authors.affiliation: Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.|Victorian Life Sciences Computation Initiative, The University of Melbourne, Melbourne, Victoria 3053, Australia.
authors.forename: Charlotte L
authors.initials: CL
authors.lastname: Anderson
authors.affiliation: Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.|QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.
authors.forename: Nicola
authors.initials: N
authors.lastname: Waddell
authors.affiliation: Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.|QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.
authors.forename: John V
authors.initials: JV
authors.lastname: Pearson
authors.affiliation: Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.|WolfsonWohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland G61 1QH, UK.
authors.forename: Sean M
authors.initials: SM
authors.lastname: Grimmond
authors.affiliation: Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239-3098, USA.
authors.forename: Myron
authors.initials: M
authors.lastname: Peto
authors.affiliation: Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239-3098, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Spellman
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Minghui
authors.initials: M
authors.lastname: He
authors.affiliation: The Genome Institute, Washington University, St Louis, Missouri 63108, USA.
authors.forename: Cyriac
authors.initials: C
authors.lastname: Kandoth
authors.affiliation: Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Semin
authors.initials: S
authors.lastname: Lee
authors.affiliation: Harvard Medical School, Boston, Massachusetts 02115, USA.|MD Anderson Cancer Center, Houston, Texas 77030, USA.
authors.forename: John
authors.initials: J
authors.lastname: Zhang
authors.affiliation: McGill University, Montreal, Quebec, Canada QC H3A 0G4.
authors.forename: Louis
authors.initials: L
authors.lastname: Létourneau
authors.affiliation: Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: Singer
authors.initials: S
authors.lastname: Ma
authors.affiliation: MD Anderson Cancer Center, Houston, Texas 77030, USA.
authors.forename: Sahil
authors.identifier: http://orcid.org/0000-0003-4579-3959
authors.initials: S
authors.lastname: Seth
authors.affiliation: IRB-BSC Joint Research Program on Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Torrents
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
authors.forename: Liu
authors.initials: L
authors.lastname: Xi
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Wheeler
authors.affiliation: Universidad de Oviedo-IUOPA, C/Fernando Bongera s/n, 33006 Oviedo, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: López-Otín
authors.affiliation: Hematopathology Unit, Department of Pathology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, 08036 Barcelona, Spain.
authors.forename: Elías
authors.initials: E
authors.lastname: Campo
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Campbell
authors.affiliation: Synergie Lyon Cancer Foundation, Centre Léon Bérard, Cheney C, 28 rue Laennec, Lyon 69373, France.|Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7.
authors.forename: Paul C
authors.identifier: http://orcid.org/0000-0003-0553-7520
authors.initials: PC
authors.lastname: Boutros
authors.affiliation: Universidad de Oviedo-IUOPA, C/Fernando Bongera s/n, 33006 Oviedo, Spain.
authors.forename: Xose S
authors.initials: XS
authors.lastname: Puente
authors.affiliation: National Cancer Institute, Office of Cancer Genomics, 31 Center Drive, 10A07, Bethesda, Maryland 20892-2580, USA.
authors.forename: Daniela S
authors.initials: DS
authors.lastname: Gerhard
authors.affiliation: Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg 69120, Germany.|Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
authors.forename: Stefan M
authors.initials: SM
authors.lastname: Pfister
authors.affiliation: Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3.|Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7.
authors.forename: John D
authors.initials: JD
authors.lastname: McPherson
authors.affiliation: Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3.|Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7.|Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8.
authors.forename: Thomas J
authors.identifier: http://orcid.org/0000-0002-1376-4849
authors.initials: TJ
authors.lastname: Hudson
authors.affiliation: Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Schlesner
authors.affiliation: Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120,Germany.|Heidelberg Center for Personalised Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Lichter
authors.affiliation: Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.|Heidelberg Center for Personalised Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany.|Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg 69120, Germany.|Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany.
authors.forename: Roland
authors.initials: R
authors.lastname: Eils
authors.affiliation: Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
authors.forename: David T W
authors.initials: DT
authors.lastname: Jones
authors.affiliation: CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.|Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Ivo G
authors.identifier: http://orcid.org/0000-0001-7219-632X
authors.initials: IG
authors.lastname: Gut
mesh_terms: D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007945:Leukemia, Lymphoid / Q000235:genetics*; D008527:Medulloblastoma / Q000235:genetics*; D009154:Mutation