Portal de Periódicos da CAPES

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

2020; Nature Portfolio; Volume: 11; Issue: 1 Linguagem: Inglês

10.1038/s41467-020-16785-6

2041-1723

Mary J. Goldman, Junjun Zhang, Nuno A. Fonseca, Isidro Cortés‐Ciriano, Qian Xiang, Brian Craft, Elena Piñeiro-Yáñez, Brian D. O’Connor, Wojciech Bażant, Elisabet Barrera, Alfonso Muñoz-Pomer Fuentes, Robert Petryszak, Anja Füllgrabe, Fátima Al‐Shahrour, Maria Keays, David Haussler, John N. Weinstein, Wolfgang Huber, Alfonso Valencia, Peter J. Park, Irene Papatheodorou, Jingchun Zhu, Vincent Ferretti, Miguél Vázquez,

Cancer Genomics and Diagnostics

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.