Integrative annotation scores of variants for impact on RNA binding protein activities.

ABSTRACT:

Motivation

The ENCODE project generated a large collection of eCLIP-seq RNA binding protein (RBP) profiling data with accompanying RNA-seq transcriptomes of shRNA knockdown of RBPs. These data could have utility in understanding the functional impact of genetic variants, however their potential has not been fully exploited. We implement INCA (Integrative annotation scores of variants for impact on RBP activities) as a multi-step genetic variant scoring approach that leverages the ENCODE RBP data together with ClinVar and integrates multiple computational approaches to aggregate evidence.

Results

INCA evaluates variant impacts on RBP activities by leveraging genotypic differences in cell lines used for eCLIP-seq. We show that INCA provides critical specificity, beyond generic

SUBMITTER: Duan J 

PROVIDER: S-EPMC11042904 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature