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.Database URL: http://dcc.icgc.org

Hundreds of Putative Non-Coding Cis-Regulatory Drivers in Chronic Lymphocytic Leukaemia and Skin Cancer

“…To this end, we acquired somatic mutation calls from WGS data for CLL (Puente et al, 2015) and through the International Cancer Genome Consortium data portal for skin cancer (project codes: MELA-AU and SKCA-BR) (Zhang et al, 2011). These cancers were chosen because they affect the cell types analysed in the SGX project.…”

General resources in Genetics and/or Oncology

“…The Pancancer Analysis of Whole Genomes (PCAWG) study is an international collaboration to identify common patterns of mutations in more than 2,800 cancer whole genomes from the International Cancer Genome Consortium. It contains descriptions of 36,985,985 mutations in 57,773 genes and 17,867 donors within 66 projects in 21 primary sites (Zhang J et al, 2011).…”

Integrating Open Data on Cancer in Support to Tumor Growth Analysis

“…Initiatives are already fostering openaccess research for improving patient care. There are several freely accessible web portals, yet, providing exploration support for cancer genomics due to increasing efforts in the area of Bioinformatics regarding genomic data handling [14][15][16][17][18][19][20][21][22]. For example, challenges in normalizing clinical drug data have been illustrated while using open access druggable genome datasets for target discovery in the context of cancer therapeutics [23].…”

“…The Cancer Genome Atlas -Data Portal TCGA REST, download [16] cBio Cancer Genomics Portal cBioPortal REST, download [15] NCI's Cancer Genome Anatomy Project CGAP download [43] International Cancer Genome Consortium -Data Portal ICGC REST, download [19] United States Cancer Statistics -Cancer Genomics Browser UCSC download [16] Catalogue of somatic mutations in cancer COSMIC REST, download [18] Integrative Onco Genomics INTOGEN download [20] Integrative Genomics Viewer IGV download [21] Many more general genome databases such as Ensembl ENSEMBL REST, download…”