Identifying multi-hit carcinogenic gene combinations: Scaling up a weighted set cover algorithm using compressed binary matrix representation on a GPU.

ABSTRACT: Despite decades of research, effective treatments for most cancers remain elusive. One reason is that different instances of cancer result from different combinations of multiple genetic mutations (hits). Therefore, treatments that may be effective in some cases are not effective in others. We previously developed an algorithm for identifying combinations of carcinogenic genes with mutations (multi-hit combinations), which could suggest a likely cause for individual instances of cancer. Most cancers are estimated to require three or more hits. However, the computational complexity of the algorithm scales exponentially with the number of hits, making it impractical for identifying combinations of more than two hits. To identify combinations of greater than two hits, we used a compressed bin

SUBMITTER: Al Hajri Q 

PROVIDER: S-EPMC7005272 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature