Journal Article

DKFZ-2017-02148

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Alioto, T. S. ; Buchhalter, I. (First author)DKFZ* ; Derdak, S. ; Hutter, B.DKFZ* ; Eldridge, M. D. ; Hovig, E. ; Heisler, L. E. ; Beck, T. A. ; Simpson, J. T. ; Tonon, L. ; Sertier, A.-S. ; Patch, A.-M. ; Jäger, N.DKFZ* ; Ginsbach, P. ; Drews, R.DKFZ* ; Paramasivam, N.DKFZ* ; Kabbe, R.DKFZ* ; Chotewutmontri, S.DKFZ* ; Diessl, N.DKFZ* ; Previti, C.DKFZ* ; Schmidt, S.DKFZ* ; Brors, B.DKFZ* ; Feuerbach, L.DKFZ* ; Heinold, M.DKFZ* ; Gröbner, S.DKFZ* ; Korshunov, A.DKFZ* ; Tarpey, P. S. ; Butler, A. P. ; Hinton, J. ; Jones, D. ; Menzies, A. ; Raine, K. ; Shepherd, R. ; Stebbings, L. ; Teague, J. W. ; Ribeca, P. ; Giner, F. C. ; Beltran, S. ; Raineri, E. ; Dabad, M. ; Heath, S. C. ; Gut, M. ; Denroche, R. E. ; Harding, N. J. ; Yamaguchi, T. N. ; Fujimoto, A. ; Nakagawa, H. ; Quesada, V. ; Valdés-Mas, R. ; Nakken, S. ; Vodák, D. ; Bower, L. ; Lynch, A. G. ; Anderson, C. L. ; Waddell, N. ; Pearson, J. V. ; Grimmond, S. M. ; Peto, M. ; Spellman, P. ; He, M. ; Kandoth, C. ; Lee, S. ; Zhang, J. ; Létourneau, L. ; Ma, S. ; Seth, S. ; Torrents, D. ; Xi, L. ; Wheeler, D. A. ; López-Otín, C. ; Campo, E. ; Campbell, P. J. ; Boutros, P. C. ; Puente, X. S. ; Gerhard, D. S. ; Pfister, S.DKFZ* ; McPherson, J. D. ; Hudson, T. J. ; Schlesner, M.DKFZ* ; Lichter, P.DKFZ* ; Eils, R. (Last author)DKFZ* ; Jones, D. (Last author)DKFZ* ; Gut, I. G.

2015
Nature Publishing Group London

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Please use a persistent id in citations: doi:10.1038/ncomms10001

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.

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Contributing Institute(s):

1. Molekulare Genetik (B060)
2. Pädiatrische Neuroonkologie (B062)
3. Theoretische Bioinformatik (B080)
4. Angewandte Bioinformatik (G200)
5. Hochdurchsatz-Sequenzierung (W190)
6. KKE Neuropathologie (G380)

Research Program(s):

1. 312 - Functional and structural genomics (POF3-312) (POF3-312)

Appears in the scientific report 2015

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Database coverage:
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