Dr. Shilpa Kobren
Research Fellow in Biomedical Informatics, Harvard Medical School
Research Profile
Uncovering genes with significantly perturbed functionalities in cancer
Thursday, Dec. 5, 2 PM, RRI 101
Abstract: A major challenge in cancer genomics is to identify genes with functional roles in cancer and uncover their mechanisms of action. This is a difficult task as there is substantial mutational heterogeneity across tumors, and only a small subset of the numerous mutations in a given tumor may be functionally relevant for the disease. In my talk, I will introduce our newly developed, unified analytical framework that enables rapid integration of multiple sources of information in order to identify cancer-relevant genes by pinpointing those whose interaction or other functional sites are enriched in somatic mutations across tumors. Our method PertInInt combines knowledge about sites participating in interactions with DNA, RNA, peptides, ions or small molecules with domain, evolutionary conservation and gene-level mutation data. When applied to 10,037 tumor samples across 33 cancer types, PertInInt efficiently uncovers both known and newly predicted cancer genes. Importantly, our analytical integration of data allows PertInInt to simultaneously reveal whether interaction potential or other molecular functionalities are disrupted, thereby enabling valuable insights that may help guide personalized cancer treatments. PertInInt’s analysis demonstrates that somatic mutations are frequently enriched in binding residues and functional domains in cancer genes, and implicates interaction perturbation as a pervasive cancer driving event.
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