Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

The International Cancer Genome Consortium (ICGC)’s Pan-Cancer Analysis of Whole Genomes (PCAWG) project aimed to categorize somatic and germline variations in both coding and non-coding regions in over 2,800 cancer patients. To provide this dataset to the research working groups for downstream analysis, the PCAWG Technical Working Group marshalled ~800TB of sequencing data from distributed geographical locations; developed portable software for uniform alignment, variant calling, artifact filtering and variant merging; performed the analysis in a geographically and technologically disparate collection of compute environments; and disseminated high-quality validated consensus variants to the working groups. The PCAWG dataset has been mirrored to multiple repositories and can be located using the ICGC Data Portal. The PCAWG workflows are also available as Docker images through Dockstore enabling researchers to replicate our analysis on their own data.

Wan Choi | Oliver Hofmann | Roland Eils | Lucila Ohno-Machado | Satoru Miyano | Nuno A. Fonseca | Paul Flicek | Adam P. Butler | Peter J. Campbell | Youngwook Kim | Claudiu Farcas | Marc D. Perry | Carolyn M. Hutter | Seiya Imoto | Christina K. Yung | Manuel Prinz | Brian D. O’Connor | Sergei Yakneen | Junjun Zhang | Kyle Ellrott | Kortine Kleinheinz | Naoki Miyoshi | Keiran M. Raine | Romina Royo | Gordon B. Saksena | Matthias Schlesner | Solomon I. Shorser | Miguel Vazquez | Joachim Weischenfeldt | Denis Yuen | Brandi N. Davis-Dusenbery | Vincent Ferretti | Robert L. Grossman | Olivier Harismendy | Hidewaki Nakagawa | Steven J. Newhouse | David Torrents | Lincoln D. Stein | Javier Bartolomé Rodriguez | Keith A. Boroevich | Rich Boyce | Angela N. Brooks | Alex Buchanan | Ivo Buchhalter | Niall J. Byrne | Andy Cafferkey | Zhaohong Chen | Sunghoon Cho | Peter Clapham | Francisco M. De La Vega | Jonas Demeulemeester | Michelle T. Dow | Lewis J. Dursi | Juergen Eils | Francesco Favero | Nodirjon Fayzullaev | Nuno A. Fonseca | Josep L.l. Gelpi | Gad Getz | Bob Gibson | Michael C. Heinold | Julian M. Hess | Jongwhi H. Hong | Thomas J. Hudson | Daniel Huebschmann | Barbara Hutter | Sinisa Ivkovic | Seung-Hyup Jeon | Wei Jiao | Jongsun Jung | Rolf Kabbe | Andre Kahles | Jules Kerssemakers | Hyunghwan Kim | Hyung-Lae Kim | Jihoon Kim | Jan O. Korbel | Michael Koscher | Antonios Koures | Milena Kovacevic | Chris Lawerenz | Ignaty Leshchiner | Dimitri G. Livitz | George L. Mihaiescu | Sanja Mijalkovic | Ana Mijalkovic Lazic | Hardeep K. Nahal | Mia Nastic | Jonathan Nicholson | David Ocana | Kazuhiro Ohi | Larsson Omberg | B.F. Francis Ouellette | Nagarajan Paramasivam | Todd D. Pihl | Montserrat Puiggròs | Petar Radovic | Esther Rheinbay | Mara W. Rosenberg | Charles Short | Heidi J. Sofia | Jonathan Spring | Adam J. Struck | Grace Tiao | Nebojsa Tijanic | Peter Van Loo | David Vicente | Jeremiah A. Wala | Zhining Wang | Johannes Werner | Ashley Williams | Youngchoon Woo | Adam J. Wright | Qian Xiang | Jules N. A. Kerssemakers | L. Stein | T. Hudson | G. Getz | D. Torrents | L. Ohno-Machado | R. Eils | R. Grossman | J. Korbel | V. Ferretti | F. M. De La Vega | O. Harismendy | P. Campbell | P. Flicek | S. Miyano | P. Loo | A. Butler | K. Raine | Kyle Ellrott | R. Royo | G. Saksena | B. Hutter | M. Schlesner | H. Sofia | T. Pihl | S. Imoto | L. Omberg | O. Hofmann | Rolf Kabbe | M. Perry | A. Kahles | Youngwook Kim | G. Tiao | P. Clapham | L. Dursi | C. Farcas | C. Hutter | J. Hess | Jihoon Kim | J. Weischenfeldt | F. Favero | C. Lawerenz | C. Yung | M. Vazquez | B. Davis-Dusenbery | Esther Rheinbay | H. Nakagawa | D. Livitz | I. Leshchiner | Hyung-Lae Kim | R. Boyce | I. Buchhalter | K. Kleinheinz | Mara Rosenberg | Jongsun Jung | Junjun Zhang | J. Wala | J. Demeulemeester | Juergen Eils | A. Lazić | Solomon Shorser | Michelle Dow | Alex Buchanan | Sergei Yakneen | N. Miyoshi | Andy Cafferkey | S. Newhouse | Denis Yuen | Qian Xiang | J. Gelpi | N. Paramasivam | Montserrat Puiggrós | Johannes Werner | Zhaohong Chen | Sunghoon Cho | Wan Choi | Nodirjon Fayzullaev | Sinisa Ivkovic | S. Jeon | W. Jiao | Hyunghwan Kim | M. Koscher | Antonios Koures | Milena Kovačević | S. Mijalkovic | Mia Nastic | J. Nicholson | D. Ocana | Kazuhiro Ohi | Manuel Prinz | P. Radović | Charlie Short | Jonathan Spring | Adam Struck | N. Tijanic | David Vicente | Ashley Williams | Youngchoon Woo | Adam Wright | Hardeep Nahal | Zhining Wang | B. Francis Ouellette | Bob Gibson | D. Huebschmann

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