A user guide for the online exploration and visualization of PCAWG data

Mary J. Goldman (), Junjun Zhang, Nuno A. Fonseca, Isidro Cortés-Ciriano, Qian Xiang, Brian Craft, Elena Piñeiro-Yáñez, Brian D. O’Connor, Wojciech Bazant, Elisabet Barrera, Alfonso Muñoz-Pomer, Robert Petryszak, Anja Füllgrabe, Fatima Al-Shahrour, Maria Keays, David Haussler, John N. Weinstein, Wolfgang Huber, Alfonso Valencia, Peter J. Park, Irene Papatheodorou, Jingchun Zhu, Vincent Ferretti and Miguel Vazquez
Additional contact information
Mary J. Goldman: UC Santa Cruz Genomics Institute
Junjun Zhang: Ontario Institute for Cancer Research
Nuno A. Fonseca: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI
Isidro Cortés-Ciriano: Harvard Medical School
Qian Xiang: Ontario Institute for Cancer Research
Brian Craft: UC Santa Cruz Genomics Institute
Elena Piñeiro-Yáñez: Spanish National Cancer Research Centre (CNIO)
Brian D. O’Connor: Broad Institute
Wojciech Bazant: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI
Elisabet Barrera: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI
Alfonso Muñoz-Pomer: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI
Robert Petryszak: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI
Anja Füllgrabe: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI
Fatima Al-Shahrour: Spanish National Cancer Research Centre (CNIO)
Maria Keays: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI
David Haussler: UC Santa Cruz Genomics Institute
John N. Weinstein: UT MD Anderson Cancer Center
Wolfgang Huber: European Molecular Biology Laboratory
Alfonso Valencia: Barcelona Supercomputing Center (BSC)
Peter J. Park: Harvard Medical School
Irene Papatheodorou: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI
Jingchun Zhu: UC Santa Cruz Genomics Institute
Vincent Ferretti: CHU Sainte-Justine Research Center
Miguel Vazquez: European Molecular Biology Laboratory

Nature Communications, 2020, vol. 11, issue 1, 1-9

Abstract: Abstract The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we provide a user’s guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper. These tools are ICGC Data Portal, UCSC Xena, Chromothripsis Explorer, Expression Atlas, and PCAWG-Scout. We detail use cases and analyses for each tool, show how they incorporate outside resources from the larger genomics ecosystem, and demonstrate how the tools can be used together to understand the biology of cancers more deeply. Together, the tools enable researchers to query the complex genomic PCAWG data dynamically and integrate external information, enabling and enhancing interpretation.

Date: 2020
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DOI: 10.1038/s41467-020-16785-6

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