Title: | A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. |
Author: | Alioto, Tyler S. Buchhalter, Ivo Derdak, Sophia Hutter, Barbara Eldridge, Matthew D. Hovig, Eivind Heisler, Lawrence E. Beck, Timothy A. Simpson, Jared T. Tonon, Laurie Sertier, Anne-Sophie Patch, Ann-Marie Jäger, Natalie Ginsbach, Philip Drews, Ruben Paramasivam, Nagarajan Kabbe, Rolf Chotewutmontri, Sasithorn Diessl, Nicolle Previti, Christopher Schmidt, Sabine Brors, Benedikt Feuerbach, Lars Heinold, Michael Gröbner, Susanne Korshunov, Andrey Tarpey, Patrick Butler, Adam P. Hinton, Jonathan Jones, David T.W. Menzies, Andrew Raine, Keiran Shepherd, Rebecca Stebbings, Lucy Teague, John W. Ribeca, Paolo Castro Giner, Francesc Beltran i Agulló, Sergi Raineri, Emanuele Dabad, Marc Heath, Simon C. Gut, Marta Denroche, Robert E. Harding, Nicholas J. Yamaguchi, Takafumi N. Nakagawa, Hidewaki Quesada, Victor Valdés Mas, Rafael Nakken, Sigve Vodák, Daniel Bower, Lawrence Lynch, Andrew G. Anderson, Charlotte L. Waddell, Nicola Pearson, John V. Grimmond, Sean M. Peto, Myron Spellman, Paul He, Minghui Kandoth, Cyriac Lee, Semin Zhang, John Létourneau, Louis Ma, Singer Seth, Sahil Torrents Arenales, David Xi, Liu Wheeler, David A. López-Otin, Carlos Campo Güerri, Elias Campbell, Peter J. Boutros, Paul C. Puente, Xose S. Gerhard, Daniela S. Pfister, Stefan M. McPherson, John D. Hudson, Thomas J. Schlesner, Matthias Lichter, Peter Eils, Roland Jones, David T.W. Gut, Ivo G. |
Keywords: | Genètica humana Mutació (Biologia) Càncer Genètica mèdica Human genetics Mutation (Biology) Cancer Medical genetics |
Issue Date: | 9-Dec-2015 |
Publisher: | Nature Publishing Group |
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. |
Note: | Reproducció del document publicat a: https://doi.org/10.1038/ncomms10001 |
It is part of: | Nature Communications, 2015, vol. 6, p. 10001 |
URI: | http://hdl.handle.net/2445/120214 |
Related resource: | https://doi.org/10.1038/ncomms10001 |
ISSN: | 2041-1723 |
Appears in Collections: | Articles publicats en revistes (Fonaments Clínics) Articles publicats en revistes (IDIBAPS: Institut d'investigacions Biomèdiques August Pi i Sunyer)
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