Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine.

ABSTRACT:

Background

RNA-seq is the most commonly used sequencing application. Not only does it measure gene expression but it is also an excellent media to detect important structural variants such as single nucleotide variants (SNVs), insertion/deletion (Indels) or fusion transcripts. However, detection of these variants is challenging and complex from RNA-seq. Here we describe a sensitive and accurate analytical pipeline which detects various mutations at once for translational precision medicine.

Methods

The pipeline incorporates most sensitive aligners for Indels in RNA-Seq, the best practice for data preprocessing and variant calling, and STAR-fusion is for chimeric transcripts. Variants/mutations are annotated, and key genes can be extracted for further investigation and clinic

SUBMITTER: Prodduturi N 

PROVIDER: S-EPMC6157028 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature