A comprehensive multicenter comparison of whole genome sequencing pipelines using a uniform tumor-normal sample pair
| Autor: | Benedikt Brors, Hidewaki Nakagawa, Peter J. Campbell, Susanne Gröbner, Natalie Jäger, Jones Dtw, Fujimoto A, Sasithorn Chotewutmontri, Patrick S. Tarpey, Keiran Raine, Matthias Schlesner, Liu Xi, Sophia Derdak, Stefan M. Pfister, Paolo Ribeca, David A. Wheeler, Takafumi N. Yamaguchi, John Douglas Mcpherson, Adam Butler, Jonathon Hinton, Sertier A, Christopher Previti, Peter Lichter, Michael Heinold, Andrey Korshunov, Jon W. Teague, Lawrence E. Heisler, Rolf Kabbe, Robert E. Denroche, Lucy Stebbings, Timothy Beck, Barbara Hutter, Ivo Buchhalter, Andy Menzies, Gut M, Roland Eils, Gut I, Paul C. Boutros, Nicolle Diessl, Lars Feuerbach, Rebecca Shepherd, Sabine Schmidt, Tyler Alioto, Laurie Tonon, Nicholas J. Harding, David T. Jones |
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| Rok vydání: | 2014 |
| Předmět: |
Whole genome sequencing
Genetics 0303 health sciences Library preparation Sample (statistics) Genomics Benchmarking Computational biology Biology Deep sequencing 03 medical and health sciences 0302 clinical medicine Coverage ratio 030220 oncology & carcinogenesis Clinical care 030304 developmental biology |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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