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ISVASE: identification of sequence variant associated with splicing event using RNA-seq data.

Hasan Awad Aljohi¹, Wanfei Liu^1,2,3, Qiang Lin^1,2

¹Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh, 11442, Saudi Arabia.

BMC Bioinformatics

|June 30, 2017

Summary

We developed ISVASE, a novel tool to identify sequence variants associated with splicing events using RNA-seq data. This method improves upon existing tools by offering higher precision and detecting both known and novel splicing events, aiding in disease mutation research.

Keywords:

Association DNA mutation RNA editing RNA-seq Sequence variant Splicing event

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Area of Science:

Genomics and Molecular Biology
Bioinformatics and Computational Biology

Background:

Accurate mRNA maturation relies on precise spliceosome-mediated exon recognition and splicing.
A significant proportion of disease-related mutations (33-50%) impact RNA splicing.
Existing tools like PVAAS assume normal annotated splicing sites, which is not always accurate.

Purpose of the Study:

To develop an improved computational tool, ISVASE, for identifying sequence variants associated with splicing events (SVASE) directly from RNA-seq data.
To overcome limitations of previous methods by not assuming normal annotated splicing sites.

Main Methods:

Developed ISVASE, a tool utilizing RNA-seq data for SVASE identification.
Incorporated multi-pass stringent rule-dependent and statistical filters.
Employed split-reads for independent variant identification at each splicing junction, supporting known and novel splicing events.

Main Results:

ISVASE demonstrated advantages over PVAAS, including higher precision, consistency, and shorter running times.
The tool can detect novel splicing events and exon-exon junction shifts.
A case study using a realistic RNA-seq dataset validated the method's functionality and effectiveness.

Conclusions:

ISVASE is a valuable tool for researchers investigating sequence variants (DNA mutations, RNA editing) linked to splicing events.
The software package is freely available for academic use.
ISVASE outputs facilitate downstream analyses, including splicing regulatory element and functional variant studies.