PT  - JOURNAL ARTICLE
AU  - Ivo Buchhalter
AU  - Barbara Hutter
AU  - Tyler S. Alioto
AU  - Timothy A. Beck
AU  - Paul C. Boutros
AU  - Benedikt Brors
AU  - Adam P. Butler
AU  - Sasithorn Chotewutmontri
AU  - Robert E. Denroche
AU  - Sophia Derdak
AU  - Nicolle Diessl
AU  - Lars Feuerbach
AU  - Akihiro Fujimoto
AU  - Susanne Gröbner
AU  - Marta Gut
AU  - Nicholas J. Harding
AU  - Michael Heinold
AU  - Lawrence E. Heisler
AU  - Jonathan Hinton
AU  - Natalie Jäger
AU  - David Jones
AU  - Rolf Kabbe
AU  - Andrey Korshunov
AU  - John D. McPherson
AU  - Andrew Menzies
AU  - Hidewaki Nakagawa
AU  - Christopher Previti
AU  - Keiran Raine
AU  - Paolo Ribeca
AU  - Sabine Schmidt
AU  - Rebecca Shepherd
AU  - Lucy Stebbings
AU  - Patrick S. Tarpey
AU  - Jon W. Teague
AU  - Laurie Tonon
AU  - David A. Wheeler
AU  - Liu Xi
AU  - Takafumi N. Yamaguchi
AU  - Anne-Sophie Sertier
AU  - Stefan M. Pfister
AU  - Peter J. Campbell
AU  - Matthias Schlesner
AU  - Peter Lichter
AU  - Roland Eils
AU  - Ivo G. Gut
AU  - David T. W. Jones
AU  - on behalf of the ICGC Verification and Validation Working Group
TI  - A comprehensive multicenter comparison of whole genome sequencing pipelines using a uniform tumor-normal sample pair
AID  - 10.1101/013177
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 013177
4099  - http://biorxiv.org/content/early/2015/06/12/013177.short
4100  - http://biorxiv.org/content/early/2015/06/12/013177.full
AB  - As next-generation sequencing becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Through the International Cancer Genome Consortium (ICGC), we compared sequencing pipelines at five independent centers (CNAG, DKFZ, OICR, RIKEN and WTSI) using a single tumor-blood DNA pair. Analyses by each center and with one standardized algorithm revealed significant discrepancies. Although most pipelines performed well for coding mutations, library preparation methods and sequencing coverage metrics clearly influenced downstream results. PCR-free methods showed reduced GC-bias and more even coverage. Increasing sequencing depth to ∼100x (two- to three-fold higher than current standards) showed a benefit, as long as the tumor:control coverage ratio remained balanced. To become part of routine clinical care, high-throughput sequencing must be globally compatible and comparable. This benchmarking exercise has highlighted several fundamental parameters to consider in this regard, which will allow for better optimization and planning of both basic and translational studies.