Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations.

ABSTRACT: Driver somatic mutations are a hallmark of a tumor that can be used for diagnosis and targeted therapy. Mutations are primarily detected from tumor DNA. As dynamic molecules of gene activities, transcriptome profiling by RNA sequence (RNA-seq) is becoming increasingly popular, which not only measures gene expression but also structural variations such as mutations and fusion transcripts. Although single-nucleotide variants (SNVs) can be easily identified from RNA-seq, intermediate long insertions/deletions (indels  > 2 bases and less than sequence reads) cause significant challenges and are ignored by most RNA-seq analysis tools. This study evaluates commonly used RNA-seq analysis programs along with variant and somatic mutation callers in a series of data sets with simulated and known ind

SUBMITTER: Sun Z 

PROVIDER: S-EPMC5862335 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature