Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing

Graham A Heap, Jennie HM Yang, Kate Downes, Barry C Healy, Karen A Hunt, Nicholas Bockett, Lude Franke, Patrick C Dubois, Charles A Mein, Richard J Dobson, Thomas J. Albert, Matthew J. Rodesch, David G. Clayton, John A. Todd, David A. van Heel, Vincent Plagnol

Research output: Contribution to journalArticlepeer-review

149 Citations (Scopus)

Abstract

Many disease-associated variants identified by genome-wide association (GWA) studies are expected to regulate gene expression. Allele-specific expression (ASE) quantifies transcription from both haplotypes using individuals heterozygous at tested SNPs. We performed deep human transcriptome-wide resequencing (RNA-seq) for ASE analysis and expression quantitative trait locus discovery. We resequenced double poly(A)-selected RNA from primary CD4(+) T cells (n = 4 individuals, both activated and untreated conditions) and developed tools for paired-end RNA-seq alignment and ASE analysis. We generated an average of 20 million uniquely mapping 45 base reads per sample. We obtained sufficient read depth to test 1371 unique transcripts for ASE. Multiple biases inflate the false discovery rate which we estimate to be approximately 50% for random SNPs. However, after controlling for these biases and considering the subset of SNPs that pass HapMap QC, 4.6% of heterozygous SNP-sample pairs show evidence of imbalance (P <0.001). We validated four findings by both bacterial cloning and Sanger sequencing assays. We also found convincing evidence for allelic imbalance at multiple reporter exonic SNPs in CD6 for two samples heterozygous at the multiple sclerosis-associated variant rs17824933, linking GWA findings with variation in gene expression. Finally, we show in CD4(+) T cells from a further individual that high-throughput sequencing of genomic DNA and RNA-seq following enrichment for targeted gene sequences by sequence capture methods offers an unbiased means to increase the read depth for transcripts of interest, and therefore a method to investigate the regulatory role of many disease-associated genetic variants.
Original languageEnglish
Pages (from-to)122-134
Number of pages13
JournalHuman Molecular Genetics
Volume19
Issue number1
DOIs
Publication statusPublished - 1 Jan 2010

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