The overarching goal of TCGA is to change the practice of cancer medicine and improve patient survival through cancer genomics. A key deliverable is to enable access and use of complex multi-dimensional genomic data for downstream studies. We propose to operate a GDAC-A center with the leadership, expertise and infrastructure required to develop an analysis pipeline that will generate pre-defined integrative analyses and interpretations that are tailor-designed for hypothesis-testing by basic, translational and clinical investigators. Our team consists of experts in cancer biology, genomics and bioinformatics with a track record of leadership in TCGA. The analytical tools and pipeline structure are based on our extensive TCGA experiences and designed to optimally achieve its goals. This pipeline will be built using the GenePattern bioinformatic workflow environment - a flexible and modular architecture that is caBIG and caGRID compliant, maintained in the well-established, robust and secure IT infrastructure at the Broad Institute and can be operated 24/7 as a Production Pipeline. Leveraging this well-established resource, we will pursue the following specific aims.
Aim 1. We will define caBIG compliant data format for all input and output files. To further enhance standardization, we propose two additions to the standard data structure defined in the Pilot Project (Levels 1-4). Level 0 will define specific versions of all reference databases used in the analyses and Level 5 will capture disease-level findings that incorporate prior knowledge.
Aim 2. We will design analysis modules to consolidate data from all components of TCGA and to perform integrative analyses. Results will be submitted to DCC in caBIG compliant output files accompanied by human-readable reports containing text summaries, tables and figures in a format understandable to scientists of diverse disciplines, similar to the Results Section of a publication. In addition, we are committed to continuous technical and analytical improvement of the pipeline, particularly in supporting the transition to next-generation sequencing platforms.
Aim 3. We will implement this high-throughput analysis pipeline in an industrial-level production mode with rigorous quality control, leveraging the Broad's infrastructural support and extensive experiences in running and maintaining high-throughput computational pipelines.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Resource-Related Research Projects--Cooperative Agreements (U24)
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Special Emphasis Panel (ZCA1-SRLB-U (O1))
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Lee, Jerry S
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Broad Institute, Inc.
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