期刊
AMERICAN JOURNAL OF HUMAN GENETICS
卷 93, 期 4, 页码 641-651出版社
CELL PRESS
DOI: 10.1016/j.ajhg.2013.08.008
关键词
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资金
- German Academic Exchange Service
- Stanford Genome Training Program
- National Institutes of Health (NIH)
- Stanford Graduate Fellowship
- Stanford University Department of Genetics
- NIH
- Ellison Medical Foundation
Identifying genomic variation is a crucial step for unraveling the relationship between genotype and phenotype and can yield important insights into human diseases. Prevailing methods rely on cost-intensive whole-genome sequencing (WGS) or whole-exome sequencing (WES) approaches while the identification of genomic variants from often existing RNA sequencing (RNA-seq) data remains a challenge because of the intrinsic complexity in the transcriptome. Here, we present a highly accurate approach termed SNPiR to identify SNPs in RNA-seq data. We applied SNPiR to RNA-seq data of samples for which WGS and WES data are also available and achieved high specificity and sensitivity. Of the SNPs called from the RNA-seq data, >98% were also identified by WGS or WES. Over 70% of all expressed coding variants were identified from RNA-seq, and comparable numbers of exonic variants were identified in RNA-seq and WES. Despite our method's limitation in detecting variants in expressed regions only, our results demonstrate that SNPiR outperforms current state-of-the-art approaches for variant detection from RNA-seq data and offers a cost-effective and reliable alternative for SNP discovery.
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