@article {Buchhalter013177, author = {Ivo Buchhalter and Barbara Hutter and Tyler S. Alioto and Timothy A. Beck and Paul C. Boutros and Benedikt Brors and Adam P. Butler and Sasithorn Chotewutmontri and Robert E. Denroche and Sophia Derdak and Nicolle Diessl and Lars Feuerbach and Akihiro Fujimoto and Susanne Gr{\"o}bner and Marta Gut and Nicholas J. Harding and Michael Heinold and Lawrence E. Heisler and Jonathan Hinton and Natalie J{\"a}ger and David Jones and Rolf Kabbe and Andrey Korshunov and John D. McPherson and Andrew Menzies and Hidewaki Nakagawa and Christopher Previti and Keiran Raine and Paolo Ribeca and Sabine Schmidt and Rebecca Shepherd and Lucy Stebbings and Patrick S. Tarpey and Jon W. Teague and Laurie Tonon and David A. Wheeler and Liu Xi and Takafumi N. Yamaguchi and Anne-Sophie Sertier and Stefan M. Pfister and Peter J. Campbell and Matthias Schlesner and Peter Lichter and Roland Eils and Ivo G. Gut and David T. W. Jones and on behalf of the ICGC Verification and Validation Working Group}, title = {A comprehensive multicenter comparison of whole genome sequencing pipelines using a uniform tumor-normal sample pair}, elocation-id = {013177}, year = {2014}, doi = {10.1101/013177}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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 GCbias and more even coverage. Increasing sequencing depth to ~100x (about three times 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.}, URL = {https://www.biorxiv.org/content/early/2014/12/24/013177}, eprint = {https://www.biorxiv.org/content/early/2014/12/24/013177.full.pdf}, journal = {bioRxiv} }