SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types.

ABSTRACT: Recent genome-wide CRISPR-Cas9 loss-of-function screens have identified genetic dependencies across many cancer cell lines. Associations between these dependencies and genomic alterations in the same cell lines reveal phenomena such as oncogene addiction and synthetic lethality. However, comprehensive identification of such associations is complicated by complex interactions between genes across genetically heterogeneous cancer types. We introduce and apply the algorithm SuperDendrix to CRISPR-Cas9 loss-of-function screens from 769 cancer cell lines, to identify differential dependencies across cell lines and to find associations between differential dependencies and combinations of genomic alterations and cell-type-specific markers. These associations respect the position and type of inte

SUBMITTER: Park TY 

PROVIDER: S-EPMC8979493 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature