Abstract 6241: A large scale proteogenomic atlas for precision oncology research

Abstract Recent advances in the field of mass spectrometry proteomics have led to growth in proteomics research resulting in a massive and rapid increase in the volume of high-quality publicly available proteomics datasets. This growth creates an underutilized resource with potential for new discoveries. Effectively utilizing this vast resource of preclinical and clinical samples is a major challenge. We utilize the growing availability of proteomics and post-translational modifications (PTMs) data for drug and biomarker discovery. This innovative computational approach enables the integration of preclinical and clinical data, both public and proprietary, with a specific emphasis on extracting valuable biological insights that are only observable at the protein level or through PTMs. We developed a platform that combines multi-omic data curated from the public domain, together with internally generated high quality proteomic and phosphoproteomic data. The platform incorporates diverse clinical annotations, tumor and normal samples, drug sensitivity, patient outcomes and relevant bioinformatic knowledge bases. The platform can be leveraged to generate insights addressing diverse clinical needs. For example, we demonstrate how our platform can be utilized to estimate the clinical prevalence of a certain protein or protein signature, in order to identify novel response biomarkers with the highest likelihood of success by confirming its presence and variance in clinical datasets. In addition, these insights enable novel understanding of response and resistance mechanisms, thus establishing a framework that expedites the generation of hypotheses for subsequent investigation and experimental validation. Citation Format: Nitzan Simchi, Ofer Givton, Dina Daitchman, Eran Seger, Kirill Pevzner. A large scale proteogenomic atlas for precision oncology research abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts) ; 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84 (6Suppl): Abstract nr 6241.