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

Author

Listed:
  • 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
    University of Cambridge
    European Molecular Biology Laboratory, European Bioinformatics Institute)

  • 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)
    ICREA)

  • 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
    Norwegian University of Science and Technology)

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.

Suggested Citation

  • 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, 2020. "A user guide for the online exploration and visualization of PCAWG data," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16785-6
    DOI: 10.1038/s41467-020-16785-6
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