Abstract 5140: Individual patient cancer profiles in the cBio Cancer Genomic Portal.
Authors: Gao Jianjiong , Sumer Selcuk Onur , Dresdner Gideon , Aksoy Bülent Arman , Sander Chris , Schultz Nikolaus 
Published: August 2014

The most prominent or most interesting genomic alteration events from an individual tumor sample can now be browsed and analyzed in the cBio Cancer Genomics Portal. With the rapid accumulation of detailed and comprehensive genomic maps of thousands of tumors in The Cancer Genome Atlas and other projects it has now become feasible to nominate the functionally most significant events affecting a tumor from an individual patient.

The cBio Cancer Genomics Portal (http://cbioportal.org) allows interactive exploration of multidimensional cancer genomics data sets, currently for more than 6,000 tumor samples from 20 cancer genomics studies, including all TCGA projects. This information gateway significantly lowers the barrier between complex genomic data and their efficient use by cancer researchers for the development of biologic insights and clinical applications.

In addition to gene-by-gene alteration maps across many samples and across diverse tumor types, one can now view genomic alterations in individual tumor samples. As there are potentially hundreds or thousands of genomic alterations in any single tumor sample, it is crucially important to select, for inspection and analysis, alteration events most likely to contribute to oncogenesis or affect the response to therapy. In the cBio portal patient view, this selection is done making use of recurrence statistics, background functional knowledge and predicted functional impact, under the control of the cancer researcher.

All relevant data about a tumor are displayed on a single page, including clinical characteristics, summaries of the extent of mutations and copy-number alterations, as well as details about mutated, amplified, and deleted genes. Genomic alterations are filtered by the following criteria: recurrence of mutations or copy-number alterations across the tumor cohort (MutSig and GISTIC), mutation occurrence in COSMIC, and by cancer gene annotation (via the Sanger Cancer Gene Census and other sources). The patient view also provides information about drugs that target the altered genes and lists relevant clinical trials.

The patient view is fully interactive and enables quick and easy assessment of all relevant genomic events in individual tumor samples. All data can be viewed in the context of the other tumors in the cohort, which facilitates classification of tumor samples by genomic criteria and can supplement standard pathology. Once characterization of genomic alterations in tumor samples becomes standard practice in patient care, this tool could be used to assess prognosis and guide treatment decisions, ideally the personalized choice of targeted therapies.

Citation Format: Jianjiong Gao, Selcuk Onur Sumer, Gideon Dresdner, Bülent Arman Aksoy, Chris Sander, Nikolaus Schultz. Individual patient cancer profiles in the cBio Cancer Genomic Portal. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5140. doi:10.1158/1538-7445.AM2013-5140