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Nat Commun. 2015 Dec 9;6:10001. doi: 10.1038/ncomms10001.

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

Author information

1
CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
2
Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
3
Division of Theoretical Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
4
Division of Applied Bioinformatics, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
5
Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
6
Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway.
7
Department of Informatics, University of Oslo, 0373 Oslo, Norway.
8
Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3.
9
Synergie Lyon Cancer Foundation, Centre Léon Bérard, Cheney C, 28 rue Laennec, Lyon 69373, France.
10
Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.
11
QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.
12
Department of Genetics, Stanford University, Mail Stop-5120, Stanford, California 94305-5120, USA.
13
Genome and Proteome Core Facility, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, 69120 Germany.
14
Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg 69120, Germany.
15
Department of Neuropathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, Heidelberg 69120, Germany.
16
Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
17
RIKEN Center for Integrative Medical Sciences, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
18
Universidad de Oviedo-IUOPA, C/Fernando Bongera s/n, 33006 Oviedo, Spain.
19
The Bioinformatics Core Facility, Institute for Cancer Genetics and Informatics, Oslo University Hospital, 0310 Oslo, Norway.
20
Victorian Life Sciences Computation Initiative, The University of Melbourne, Melbourne, Victoria 3053, Australia.
21
WolfsonWohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland G61 1QH, UK.
22
Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239-3098, USA.
23
BGI-Shenzhen, Shenzhen 518083, China.
24
The Genome Institute, Washington University, St Louis, Missouri 63108, USA.
25
Harvard Medical School, Boston, Massachusetts 02115, USA.
26
MD Anderson Cancer Center, Houston, Texas 77030, USA.
27
McGill University, Montreal, Quebec, Canada QC H3A 0G4.
28
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA.
29
IRB-BSC Joint Research Program on Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain.
30
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
31
Hematopathology Unit, Department of Pathology, Hospital Clinic, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, 08036 Barcelona, Spain.
32
Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7.
33
National Cancer Institute, Office of Cancer Genomics, 31 Center Drive, 10A07, Bethesda, Maryland 20892-2580, USA.
34
Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany.
35
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8.
36
Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120,Germany.
37
Heidelberg Center for Personalised Oncology (DKFZ-HIPO), German Cancer Research Center (DKFZ), Heidelberg, Germany.
38
Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg 69120, Germany.
39
Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany.

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.

PMID:
26647970
PMCID:
PMC4682041
DOI:
10.1038/ncomms10001
[Indexed for MEDLINE]
Free PMC Article

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