Bioinformatics Primers

Pathway Interaction Database provides reviews and commentary illuminating topics of particular interest.

March 2010

• The Cancer Genome Workbench: Identifying and Visualizing Complex Genetic Alterations in Tumors

  

  Original research paper Pathway Interaction Database doi:10.1038/pid.2010.1

  We present the Cancer Genome Workbench (CGWB), a web-based tool (http://cgwb.nci.nih.gov) that integrates and displays the genome-wide collection of somatic mutation, copy number alteration, gene expression and methylation data generated by a number of projects including The Cancer Genome Atlas (TCGA), the Sanger Center's COSMIC initiative, NHGRI's Tumor Sequencing Project (TSP), NCI's Therapeutically Applicable Research to Generate Effective Treatment (TARGET), Johns Hopkins University and GlaxoSmithKline Cancer Cell Line Genomic Profiling Data. Using examples from the TCGA glioblastoma multiforme (GBM) data set, we describe the utility of viewers such as the CGWB heatmap and genome browser views. We also present the use of the CGWB to evaluate the significance of regulatory processes such as methylation and microRNA expression in controlling gene expression. The integrated views of multiple data types enable a user to evaluate whether molecular data is consistent across platforms as well as to examine the correlation between different data types such as somatic DNA alterations and gene expression. Confidential data such as clinical data and individual genotypes are available to certified users who have been approved by project-specific regulatory bodies such as the TCGA Data Access Committee. We include use case scenario examples using the recently incorporated next-generation sequencing data from the TCGA ovarian serous cystadenocarcinoma data set. The rich collection of multiple-platform, high-resolution genomic data available on the CGWB will aid the discovery of the complex molecular mechanisms that underlie numerous cancers.