Quantification of mutant-allele expression at isoform level in cancer from RNA-seq data.

ABSTRACT: Even though the role of DNA mutations in cancer is well recognized, current quantification of the RNA expression, performed either at gene or isoform level, typically ignores the mutation status. Standard methods for estimating allele-specific expression (ASE) consider gene-level expression, but the functional impact of a mutation is best assessed at isoform level. Hence our goal is to quantify the mutant-allele expression at isoform level. We have developed and implemented a method, named MAX, for quantifying mutant-allele expression given a list of mutations. For a gene of interest, a mutant reference is constructed by incorporating all possible mutant versions of the wild-type isoforms in the transcriptome annotation. The mutant reference is then used for the RNA-seq reads mapping, whic

SUBMITTER: Deng W 

PROVIDER: S-EPMC9278039 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature