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.
Highlights
The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data
The Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium aggregated whole-genome sequencing (WGS) data from 2658 cancers across 38 tumor types generated by the International Cancer Genome Consortium (ICGC) and The
The data generated by the PCAWG consortium provide a valuable resource for understanding complex cancer biology
Summary
The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. The Xena Browser excels at integrating the diverse datasets generated by the PCAWG Consortium using the Xena Visual Spreadsheet, which enables users to view multiple types of data side by side (Fig. 1b).
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