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SASE-hunter / Signatures of Accelerated Somatic Evolution hunter

A computational method to identify regulatory elements with cancer-associated signatures of accelerated somatic evolution (SASE). SASE-hunter searches for genomic regions with a significantly higher abundance of somatic mutations in a genomic element (e.g. gene promoters) than that expected by chance and prioritizes those loci that carry the signature in multiple cancer patients. We identified a novel signature of accelerated somatic evolution marked by a significant excess of somatic mutations localized in a genomic locus, and prioritized those loci that carried the signature in multiple cancer patients.

LARVA / Large-scale Analysis of Variants in noncoding Annotations

A computational framework designed to facilitate the study of noncoding variants. LARVA addresses issues that have made it difficult to derive an accurate model of the background mutation rates of noncoding elements in cancer genomes. These issues include limited noncoding functional annotation, great mutation heterogeneity, and potential mutation correlations between neighboring sites. As a result, there is substantial overdispersion in the mutation count of noncoding elements. LARVA integrates a comprehensive set of noncoding functional elements, modeling their mutation count with a beta-binomial distribution to handle overdispersion. Moreover, LARVA uses regional genomic features such as replication timing to better estimate local mutation rates and mutational enrichments.