International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data

Abstract

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. To make this data available, the ICGC has created the ICGC Data Portal. Powered by the BioMart software, the Data Portal allows each ICGC member institution to manage and maintain its own databases locally, while seamlessly presenting all the data in a single access point for users. The Data Portal currently contains data from 24 cancer projects, including ICGC, The Cancer Genome Atlas (TCGA), Johns Hopkins University, and the Tumor Sequencing Project. It consists of 3478 genomes and 13 cancer types and subtypes. Available open access data types include simple somatic mutations, copy number alterations, structural rearrangements, gene expression, microRNAs, DNA methylation and exon junctions. Additionally, simple germline variations are available as controlled access data. The Data Portal uses a web-based graphical user interface (GUI) to offer researchers multiple ways to quickly and easily search and analyze the available data. The web interface can assist in constructing complicated queries across multiple data sets. Several application programming interfaces are also available for programmatic access. Here we describe the organization, functionality, and capabilities of the ICGC Data Portal.

Figure 1.

International Cancer Genome Consortium (ICGC) projects (March 2011).

Figure 2.

An overview of the ICGC Data Portal architecture.

Figure 3.

Screenshot of the ICGC Data Portal home page. Three main entry points are available: (A) Identifier search, (B) Analysis and (C) Database search.

Figure 4.

Gene Report for KRAS includes: (A) Gene annotation data from Ensembl, Pathway annotation from (B) KEGG and (C) Reactome, (D) Summary of mutation frequencies in each cancer project, (E) Mutation data from COSMIC, Expression data from (F) Pancreatic Expression Database and (G) Breast Cancer Campaign Tissue Bank (BCCTB). Different sections of this page come from federated BioMart sources.

Figure 5.

Results from affected pathways analysis for breast cancer (JHU, US). (A) Affected pathways are shown in a chart, with bars representing the number of affected genes in each pathway. (B) By clicking on the bar, users are able to view and download the genes that were mutated in each pathway.

Figure 6.

A screenshot of the Quickquery interface.

Figure 7.

A screenshot of the Flexiblequery interface.

Figure 8.

A screenshot of the Advancedquery interface.