Nucleic Acids Research Advance Access published online on June 15, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp507
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Methods online |
Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq
Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
*To whom correspondence should be addressed. Tel: +1 (301) 496 2098; Fax: +1 (301) 480 0961; Email: zhaok{at}nhlbi.nih.gov
Received December 10, 2008. Revised May 22, 2009. Accepted May 26, 2009.
Whole-genome resequencing is still a costly method to detect genetic mutations that lead to altered forms of proteins and may be associated with disease development. Since the majority of disease-related single nucleotide variations (SNVs) are found in protein-coding regions, we propose to identify SNVs in expressed exons of the human genome using the recently developed RNA-Seq technique. We identify 12 176 and 10 621 SNVs, respectively, in Jurkat T cells and CD4+ T cells from a healthy donor. Interestingly, our data show that one copy of the TAL-1 proto-oncogene has a point mutation in 3' UTR and only the mutant allele is expressed in Jurkat cells. We provide a comprehensive dataset for further understanding the cancer biology of Jurkat cells. Our results indicate that this is a cost-effective and efficient strategy to systematically identify SNVs in the expressed regions of the human genome.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.