Type

Journal Article

Authors

Derek W Morris
Aiden P Corvin
Michael Gill
Richard Anney
Matthew Hill
Elaine M Kenny
Paul Cormican
Emma M Quinn

Subjects

Microbiology

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

Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data. (2012)

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.
Collections Ireland -> Trinity College Dublin -> PubMed

Full list of authors on original publication

Derek W Morris, Aiden P Corvin, Michael Gill, Richard Anney, Matthew Hill, Elaine M Kenny, Paul Cormican, Emma M Quinn

Experts in our system

1
Derek Morris
Trinity College Dublin
Total Publications: 150
 
2
Aiden Corvin
Trinity College Dublin
Total Publications: 190
 
3
Michael Gill
Trinity College Dublin
Total Publications: 260
 
4
Richard Anney
Trinity College Dublin
Total Publications: 38
 
5
Matthew Hill
Trinity College Dublin
Total Publications: 10
 
6
Elaine Kenny
Trinity College Dublin
Total Publications: 28
 
7
Paul Cormican
Trinity College Dublin
Total Publications: 39
 
8
Emma M Quinn
Trinity College Dublin
Total Publications: 11