U24CA271075

Center for Comprehensive Proteogenomic Data Analysis - Project Summary

Proteogenomics involves the integrative multi-omic analysis of genomic, transcriptomic, proteomic, and post-translational modification data produced by next-generation sequencing and mass spectrometry-based proteomics. Several publications by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and others have highlighted the impact of proteogenomics in enabling deeper insight into the biology of cancer and identification of potential drug targets.

Integrative analysis of multi-omic data requires the deployment of complex algorithms and data processing techniques, which are generally inaccessible to scientists without a background in bioinformatics and computational biology. Our proposed Center for Comprehensive Proteogenomic Data Analysis will encapsulate a comprehensive set of analysis methods in a platform that will be:

(I) Simple to use
(II) Flexible
(III) Automated, facilitating the routine application to all CPTAC proteogenomic datasets as they become available
(IV) Able to incorporate new methods with minimal effort.

We will leverage Panoply, a cloud-based platform for automated and reproducible proteogenomic data analysis, as the foundation, with specific, carefully chosen algorithms targeted for addition to provide an expansive set of analysis capabilities that can be easily harnessed to provide a rapid and extensive baseline analysis for proteogenomic studies. This will lead to many disease-specific hypotheses that can be explored further using additional computational and wet-lab experiments.

Our collection of tools, algorithms, and interactive reports will enable unprecedented, automated, and integrative systems-biology level analyses of proteome, post-translational modification, and metabolomic data combined with genomic data for individual disease cohorts and pan-cancer analysis across cohorts. This will lead to a deeper understanding of cancer biology and enable the identification of therapeutic targets and disease/prognostic biomarkers.

The Broad Institute

TO IMPROVE SCREENING AND EARLY DETECTION STRATEGIES AND TO DEVELOP ACCURATE DIAGNOSTIC TECHNIQUES AND METHODS FOR PREDICTING THE COURSE OF DISEASE IN CANCER PATIENTS. SCREENING AND EARLY DETECTION RESEARCH INCLUDES DEVELOPMENT OF STRATEGIES TO DECREASE CANCER MORTALITY BY FINDING TUMORS EARLY WHEN THEY ARE MORE AMENABLE TO TREATMENT. DIAGNOSIS RESEARCH FOCUSES ON METHODS TO DETERMINE THE PRESENCE OF A SPECIFIC TYPE OF CANCER, TO PREDICT ITS COURSE AND RESPONSE TO THERAPY, BOTH A PARTICULAR THERAPY OR A CLASS OF AGENTS, AND TO MONITOR THE EFFECT OF THE THERAPY AND THE APPEARANCE OF DISEASE RECURRENCE. THESE METHODS INCLUDE DIAGNOSTIC IMAGING AND DIRECT ANALYSES OF SPECIMENS FROM TUMOR OR OTHER TISSUES. SUPPORT IS ALSO PROVIDED FOR ESTABLISHING AND MAINTAINING RESOURCES OF HUMAN TISSUE TO FACILITATE RESEARCH. SMALL BUSINESS INNOVATION RESEARCH (SBIR) PROGRAM: TO EXPAND AND IMPROVE THE SBIR PROGRAM, TO INCREASE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, TO INCREASE SMALL BUSINESS PARTICIPATION IN FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION. SMALL BUSINESS TECHNOLOGY TRANSFER (STTR) PROGRAM: TO STIMULATE AND FOSTER SCIENTIFIC AND TECHNOLOGICAL INNOVATION THROUGH COOPERATIVE RESEARCH AND DEVELOPMENT CARRIED OUT BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO FOSTER TECHNOLOGY TRANSFER BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO INCREASE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION.

93.394 - Cancer Detection and Diagnosis Research

National Cancer Institute (NCI) [HHS - NIH]

Cambridge, Massachusetts 021421027 United States

Single Zip Code

Proteogenomic Data Analysis Centers (PGDACs) for Clinical Proteomic Tumor Analysis Consortium (U24 Clinical Trial Not Allowed) (RFA-CA-21-024)

Amendment Since initial award the total obligations have increased 293% from $791,128 to $3,109,133.