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A user’s guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)

Mary 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, Miguel Vazquez, on behalf of the PCAWG Portals and Visualization Working Group, the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network
doi: https://doi.org/10.1101/163907
Mary Goldman
1UC Santa Cruz Genomics Institute, Santa Cruz, 95064, USA
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Junjun Zhang
2Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
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Nuno A. Fonseca
3European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, CB10 1SD, UK
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Isidro Cortés-Ciriano
4Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
5Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Qian Xiang
2Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
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Brian Craft
1UC Santa Cruz Genomics Institute, Santa Cruz, 95064, USA
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Elena Piñeiro-Yáñez
6Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
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Brian D O’Connor
1UC Santa Cruz Genomics Institute, Santa Cruz, 95064, USA
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Wojciech Bazant
3European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, CB10 1SD, UK
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Elisabet Barrera
3European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, CB10 1SD, UK
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Alfonso Muñoz-Pomer
3European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, CB10 1SD, UK
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Robert Petryszak
3European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, CB10 1SD, UK
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Anja Füllgrabe
3European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, CB10 1SD, UK
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Fatima Al-Shahrour
6Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
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Maria Keays
3European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, CB10 1SD, UK
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David Haussler
1UC Santa Cruz Genomics Institute, Santa Cruz, 95064, USA
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John N. Weinstein
7UT MD Anderson Cancer Center, Houston, 77030, USA
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Wolfgang Huber
8European Molecular Biology Laboratory, Heidelberg, 69117, Germany
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Alfonso Valencia
9Barcelona Supercomputing Center (BSC), Barcelona, 08034, Spain
10ICREA, Barcelona, 08010, Spain
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Peter J. Park
4Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Irene Papatheodorou
3European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, CB10 1SD, UK
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Jingchun Zhu
1UC Santa Cruz Genomics Institute, Santa Cruz, 95064, USA
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  • For correspondence: jzhu@soe.ucsc.edu
Vincent Ferretti
11CHU Sainte-Justine Research Center, Montreal, Quebec, H3T 1C5, Canada
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Miguel Vazquez
9Barcelona Supercomputing Center (BSC), Barcelona, 08034, Spain
12Norwegian University of Science and Technology, Trondheim, Norway
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Abstract

The Pan-Cancer Analysis of Whole Genomes (PCAWG) project has generated, to our knowledge, the largest whole-genome cancer sequencing resource to date. Here we provide a user’s guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper: The ICGC Data Portal, UCSC Xena, Expression Atlas, PCAWG-Scout, and Chromothripsis Explorer. We detail use cases and analyses for each tool, show how they incorporate outside resources from the larger genomics ecosystem, as well as demonstrate how the tools can be used together to more deeply understand tumor biology. Together, these tools enable researchers to dynamically query complex genomics data and integrate external information, enabling and enhancing PCAWG data interpretation. More information on these tools and their capabilities is available from The PCAWG Data Portals and Visualizations Page (http://docs.icgc.org/pcawg).

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Posted February 04, 2020.
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A user’s guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)
Mary 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, Miguel Vazquez, on behalf of the PCAWG Portals and Visualization Working Group, the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network
bioRxiv 163907; doi: https://doi.org/10.1101/163907
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A user’s guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)
Mary 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, Miguel Vazquez, on behalf of the PCAWG Portals and Visualization Working Group, the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network
bioRxiv 163907; doi: https://doi.org/10.1101/163907

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