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; Miguel Vazquez

doi:10.1038/s41467-020-16785-6

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. ParkIrene Papatheodorou, Jingchun Zhu, Vincent Ferretti, Miguel Vazquez

Bioinformatics & Computational Biology

Research output: Contribution to journal › Article › peer-review

23 Scopus citations

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.

Original language	English (US)
Article number	3400
Journal	Nature communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-16785-6
State	Published - Dec 1 2020

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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Goldman, M. J., Zhang, J., Fonseca, N. A., Cortés-Ciriano, I., Xiang, Q., Craft, B., Piñeiro-Yáñez, E., O’Connor, B. D., Bazant, W., Barrera, E., Muñoz-Pomer, A., Petryszak, R., Füllgrabe, A., Al-Shahrour, F., Keays, M., Haussler, D., Weinstein, J. N., Huber, W., Valencia, A., ... Vazquez, M. (2020). A user guide for the online exploration and visualization of PCAWG data. Nature communications, 11(1), Article 3400. https://doi.org/10.1038/s41467-020-16785-6

Goldman, MJ, Zhang, J, Fonseca, NA, Cortés-Ciriano, I, Xiang, Q, Craft, B, Piñeiro-Yáñez, E, O’Connor, BD, Bazant, W, Barrera, E, Muñoz-Pomer, A, Petryszak, R, Füllgrabe, A, Al-Shahrour, F, Keays, M, Haussler, D, Weinstein, JN, Huber, W, Valencia, A, Park, PJ, Papatheodorou, I, Zhu, J, Ferretti, V & Vazquez, M 2020, 'A user guide for the online exploration and visualization of PCAWG data', Nature communications, vol. 11, no. 1, 3400. https://doi.org/10.1038/s41467-020-16785-6

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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{\textquoteright}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.",

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AU - Huber, Wolfgang

AU - Valencia, Alfonso

AU - Park, Peter J.

AU - Papatheodorou, Irene

AU - Zhu, Jingchun

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AU - Vazquez, Miguel

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

Abstract

ASJC Scopus subject areas

MD Anderson CCSG core facilities

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