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CPTAC Data Used to Develop Cutting Edge Tools for Illuminating the Druggable Genome

Recently, Dr. Bing Zhang and his team from the Lester and Sue Smith Breast Center at Baylor College of Medicine were awarded a two-year funding opportunity to develop Cutting Edge Informatics Tools for the NIH Common Fund program Illuminating the Druggable Genome (IDG). Recipients of this funding support the IDG Consortium and the greater scientific community by (1) developing tools to enhance the community's ability to process and visualize data, (2) prioritizing new data resources and methods to be incorporated into Pharos that will strengthen predictions about disease associations around understudied proteins, and (3) developing methods to prioritize understudied proteins for deeper study using experimental assays.

In their application, Dr. Zhang's team proposed an evolution of the existing LinkedOmics portal, a publicly available portal that includes a variety of multi-omics data from The Cancer Genome Atlas (TCGA) program and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). This proposed expansion would result in a gene-centric knowledge base built to summarize and visualize pan-cancer proteogenomics data dubbed LinkedOmicsKB. Published studies by Dr. Zhang’s team and their colleagues in the CPTAC consortium have repeatedly demonstrated the value of proteogenomics datasets as a comprehensive resource for reinforcing existing knowledge, identifying new biological insights, and generating therapeutic hypotheses. As such, the team intends to predict functional annotations for understudied genes using the data from CPTAC and, on the whole, further integrate cancer proteogenomics data into the characterization of the understudied proteins.

This proposition aligns closely with CPTAC’s mission to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteogenomics. It also represents another key example of how CPTAC data may be utilized by other trans-NIH programs and the research community at large. In response to the award, Dr. Bing Zhang commented, ‘When I saw the [request for applications] for developing Cuttinzg Edge Informatics Tools for Illuminating the Druggable Genome last year, I immediately thought about CPTAC. The large amount of CPTAC proteogenomics data, especially proteome-wide data on proteins anhangd their modifications, provides enormous opportunities for improving our understanding of understudied druggable genes, the focus of the IDG program. I hope this project will create a bridge between the two NIH programs and produce informatics tools and therapeutic knowledge that will eventually contribute to improved human health.”