TY - JOUR T1 - A comprehensive multicenter comparison of whole genome sequencing pipelines using a uniform tumor-normal sample pair JF - bioRxiv DO - 10.1101/013177 SP - 013177 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 Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/06/12/013177.abstract N2 - 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. ER -