ArticleHuman molecular genetics2010
Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing.
Article in Human molecular genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers.
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Who cites it
119 citing papers in PubMed.
- A functional synonymous coding variant in the IL1RN gene is associated with survival in septic shock.American journal of respiratory and critical care medicine · 2014Trial
- Bayesian estimation of allele-specific expression in the presence of phasing uncertainty.Bioinformatics (Oxford, England) · 2025Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- Analysis of subcellular RNA fractions demonstrates significant genetic regulation of gene expression in human brain post-transcriptionally.Scientific reports · 2023Article
- Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity.Nature communications · 2022Article
- Anterior Circulation Acute Ischemic Stroke in the Plateau of China: Risk Factors and Clinical Characteristics.Frontiers in neurology · 2022Article
- RNA-SSNV: A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data.Frontiers in genetics · 2022Article
- Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas.G3 (Bethesda, Md.) · 2021Article
- Integration of Transformative Platforms for the Discovery of Causative Genes in Cardiovascular Diseases.Cardiovascular drugs and therapy · 2021Review
- Fixation of allelic gene expression landscapes and expression bias pattern shape the transcriptome of the clonal Amazon molly.Genome research · 2021Article
- Allele-specific expression of Parkinson's disease susceptibility genes in human brain.Scientific reports · 2021Article
- Homeolog expression quantification methods for allopolyploids.Briefings in bioinformatics · 2020Review
- Allele-Specific Expression of CD4Genes · 2019Article
- Quantification of allelic differential expression using a simple Fluorescence primer PCR-RFLP-based method.Scientific reports · 2019Article
- Single-nucleotide variants in human RNA: RNA editing and beyond.Briefings in functional genomics · 2019Review
- Pervasive Inter-Individual Variation in Allele-Specific Expression in Monozygotic Twins.Frontiers in genetics · 2019Article
- Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle.BMC genomics · 2018Article
- Targeting CD6 for the treatment of experimental autoimmune uveitis.Journal of autoimmunity · 2018Article
- ASElux: an ultra-fast and accurate allelic reads counter.Bioinformatics (Oxford, England) · 2018Article
- A Genome-Wide Study of Allele-Specific Expression in Colorectal Cancer.Frontiers in genetics · 2018Article
59 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors.
Funding
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.
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