RT Journal Article
SR Electronic
T1 A comprehensive multicenter comparison of whole genome sequencing pipelines using a uniform tumor-normal sample pair
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 013177
DO 10.1101/013177
A1 Ivo Buchhalter
A1 Barbara Hutter
A1 Tyler S. Alioto
A1 Timothy A. Beck
A1 Paul C. Boutros
A1 Benedikt Brors
A1 Adam P. Butler
A1 Sasithorn Chotewutmontri
A1 Robert E. Denroche
A1 Sophia Derdak
A1 Nicolle Diessl
A1 Lars Feuerbach
A1 Akihiro Fujimoto
A1 Susanne Gröbner
A1 Marta Gut
A1 Nicholas J. Harding
A1 Michael Heinold
A1 Lawrence E. Heisler
A1 Jonathan Hinton
A1 Natalie Jäger
A1 David Jones
A1 Rolf Kabbe
A1 Andrey Korshunov
A1 John D. McPherson
A1 Andrew Menzies
A1 Hidewaki Nakagawa
A1 Christopher Previti
A1 Keiran Raine
A1 Paolo Ribeca
A1 Sabine Schmidt
A1 Rebecca Shepherd
A1 Lucy Stebbings
A1 Patrick S. Tarpey
A1 Jon W. Teague
A1 Laurie Tonon
A1 David A. Wheeler
A1 Liu Xi
A1 Takafumi N. Yamaguchi
A1 Anne-Sophie Sertier
A1 Stefan M. Pfister
A1 Peter J. Campbell
A1 Matthias Schlesner
A1 Peter Lichter
A1 Roland Eils
A1 Ivo G. Gut
A1 David T. W. Jones
A1 on behalf of the ICGC Verification and Validation Working Group
YR 2015
UL http://biorxiv.org/content/early/2015/06/12/013177.abstract
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.