Type

Journal Article

Authors

Michael Gill
Aiden Peter Corvin
Richard James Leon Anney
Derek Morris

Subjects

Microbiology

Topics
next generation sequencing snps samtools cell line sensitivity and specificity application development data quality cell lines rna seq

Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data. (2013)

Abstract Next-generation RNA sequencing (RNA-seq) maps and analyzes transcriptomes and generates data on sequence variation in expressed genes. There are few reported studies on analysis strategies to maximize the yield of quality RNA-seq SNP data. We evaluated the performance of different SNP-calling methods following alignment to both genome and transcriptome by applying them to RNA-seq data from a HapMap lymphoblastoid cell line sample and comparing results with sequence variation data from 1000 Genomes. We determined that the best method to achieve high specificity and sensitivity, and greatest number of SNP calls, is to remove duplicate sequence reads after alignment to the genome and to call SNPs using SAMtools. The accuracy of SNP calls is dependent on sequence coverage available. In terms of specificity, 89% of RNA-seq SNPs calls were true variants where coverage is >10X. In terms of sensitivity, at >10X coverage 92% of all expected SNPs in expressed exons could be detected. Overall, the results indicate that RNA-seq SNP data are a very useful by-product of sequence-based transcriptome analysis. If RNA-seq is applied to disease tissue samples and assuming that genes carrying mutations relevant to disease biology are being expressed, a very high proportion of these mutations can be detected
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Full list of authors on original publication

Michael Gill, Aiden Peter Corvin, Richard James Leon Anney, Derek Morris

Experts in our system

1
Michael Gill
Trinity College Dublin
Total Publications: 260
 
2
Aiden Corvin
Trinity College Dublin
Total Publications: 190
 
3
Richard Anney
Trinity College Dublin
Total Publications: 38
 
4
Derek Morris
Trinity College Dublin
Total Publications: 150