The Ilya Shmulevich Group at ISB has been participating in The Cancer Genome Atlas (TCGA) project as a Genome Data Analysis Center. The first paper resulting from the main phase of the TCGA project – "Comprehensive molecular characterization of human colon and rectal cancer" – was published in the July 19, 2012, issue of Nature and also featured on the front page of the New York Times. ISB teamed up with the MD Anderson Cancer Center to contribute analysis and we were co-authors of the paper in Nature. Here's a YouTube video, featuring ISB senior research scientist Vesteinn Thorsson, that explains our work.
One of ISB's unique contributions to the project was a web tool that allows researchers – and the public – to explore the molecular signatures that were found to be associated with aggressive colorectal cancer. This web tool, the CRC Aggressiveness Explorer, is part of the Regulome Explorer, which was designed and developed at the ISB to facilitate the integrative exploration of associations in clinical and molecular data from the TCGA. The Regulome Explorer technology also was featured in the June 28 keynote presentation at the Google I/O developers conference.
Here's a more detailed description the ISB's contribution to the TCGA publication on colorectal cancer:
Collaborating with Timothy A. Chan, MD, PhD, of the Memorial Sloan-Kettering Cancer Center (mskcc.org) we identified a set of six clinical measurements that are indicative of aggressive colorectal cancer. This includes whether the tumor has found its way into the bloodstream or into neighboring lymph nodes, whether the tumor has metastasized, and what stage the tumor has reached. We scored each of the thousands of molecular features available to us in the TCGA data set to indicate the degree of association with tumor aggressiveness. The score results from combining results from individual statistical association tests (p-values) between molecular variable and the six clinical variables using a weighted form of Fisher's method. This yielded ranked lists of genes whose expression may be indicative of aggressive or less aggressive tumors. It also yielded corresponding lists for other kinds of colorectal tumor data generated by the TCGA: DNA mutations, DNA copy number variation, methylation of gene promoters, and the expression of microRNAs. To examine the molecular features associated with tumor aggressiveness in the context of the cancer genome, we used the CRC Aggressiveness Explorer, developed at the ISB.