Highlights from CPTAC Scientific Symposium

Dear Colleagues and Friends,

The first CPTAC Public Scientific Symposium was recently held on November 13, 2013 at the National Institutes of Health in Bethesda, MD. The symposium brought together a record number of registrants, 450 scientists, who shared and discussed novel biological discoveries, analytical methods, and translational approaches using CPTAC data.

Accomplishments presented at the meeting were in the form of new scientific discoveries and community resources. In terms of new scientific discoveries, deep proteomic characterization of TCGA colorectal tumors (95 samples annotated for microsatellite instability status, stage and anatomical location) revealed additional molecular subtypes beyond those identified by TCGA genomic data. This first set of proteogenomic raw data files (0.8 TB) was released to the research community in September 2013. In just 8 weeks, over 4.6 TB of the data has been downloaded across the world. The breast and ovarian cancer data are anticipated for release in March 2014.

Community resource accomplishments to date from the CPTAC program in just a little over 2 years, include the release of 11,419 raw files corresponding to 2.2 TB of data containing due diligence human in mouse xenografts and TCGA tumors (accessible through the NCI CPTAC data portal); the release of new monoclonal antibodies targeting cancer specific proteins and peptides (now 276 antibodies that are accessible through the NCI CPTAC antibody portal); and the announcement of 596 quantitative proteomic assays that are anticipated to become publicly available by 1Q/2014, when the new assay portal is expected to launch.

Established in 2011, CPTAC is a consortium of proteogenomic centers that utilize state-of-the-art proteomic technologies and standards (ensuring data quality and reproducibility) to identify the complex relationship between genomic (DNA, RNA) and proteomic (protein) abnormalities that are difficult to obtain from genomic analysis alone. Its mission is to develop a deeper understanding of cancer biology, identify potential targets for therapeutic intervention through proteomic analysis technologies. A unique feature of the CPTAC program is the utilization of genomically characterized tumors, such as those from the TCGA program. The feasibility phase of the CPTAC program (years 2011 to 2016) is to comprehensively analyze approximately 300 samples from 3 cancer types: colorectal, breast, and ovarian cancer (100 tumors from each cancer type), with all outputs (data, reagents, and assays) to be made publicly available as a community resource. In short, CPTAC is helping to "decode the cancer proteome" for the entire world to read.

Sincerely,

Henry Rodriguez, Ph.D., M.B.A.
Director
Office of Cancer Clinical Proteomics Research