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

BMC Bioinformatics

Software

Hasan Awad Aljohi¹  Jun Yu²  Songnian Hu²  Qiang Lin²  Wanfei Liu³ 

[1] Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, 11442, Riyadh, Saudi Arabia;Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, 11442, Riyadh, Saudi Arabia;CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, 100101, Beijing, China;Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, 11442, Riyadh, Saudi Arabia;CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, 100101, Beijing, China;Current address: Grail Scientific Co. Ltd., Room 26–1, Build A, Meilong Jiayuan, NO. 80 South Nanjing Street, Heping District, 110000, Shenyang, Liaoning, China;

关键词: Sequence variant;    Splicing event;    Association;    RNA-seq;    DNA mutation;    RNA editing;   

DOI  :  10.1186/s12859-017-1732-7

 received in 2016-12-21, accepted in 2017-06-15,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundExon recognition and splicing precisely and efficiently by spliceosome is the key to generate mature mRNAs. About one third or a half of disease-related mutations affect RNA splicing. Software PVAAS has been developed to identify variants associated with aberrant splicing by directly using RNA-seq data. However, it bases on the assumption that annotated splicing site is normal splicing, which is not true in fact.ResultsWe develop the ISVASE, a tool for specifically identifying sequence variants associated with splicing events (SVASE) by using RNA-seq data. Comparing with PVAAS, our tool has several advantages, such as multi-pass stringent rule-dependent filters and statistical filters, only using split-reads, independent sequence variant identification in each part of splicing (junction), sequence variant detection for both of known and novel splicing event, additional exon-exon junction shift event detection if known splicing events provided, splicing signal evaluation, known DNA mutation and/or RNA editing data supported, higher precision and consistency, and short running time. Using a realistic RNA-seq dataset, we performed a case study to illustrate the functionality and effectiveness of our method. Moreover, the output of SVASEs can be used for downstream analysis such as splicing regulatory element study and sequence variant functional analysis.ConclusionsISVASE is useful for researchers interested in sequence variants (DNA mutation and/or RNA editing) associated with splicing events. The package is freely available at https://sourceforge.net/projects/isvase/.

【 授权许可】

CC BY   
© The Author(s). 2017