ArticlePLoS genetics2008
Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression.
Article in PLoS genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers, 1 of them a synthesis that pooled it.
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Who cites it
140 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Identification of a common variant in the TFR2 gene implicated in the physiological regulation of serum iron levels.Human molecular genetics · 2011Pooled it
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- Ornaments for efficient allele-specific expression estimation with bias correction.American journal of human genetics · 2024Article
- Contribution of miR-124 rs531564 polymorphism to the occurrence of congenital Zika syndrome.Epigenetics · 2023Article
- IRIDA Phenotype inGenes · 2022Article
- Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus.Scientific reports · 2021Article
- Correlation Between SNPs at the 3'UTR of the FGF2 Gene and Their Interaction with Environmental Factors in Han Chinese Diabetic Peripheral Neuropathy Patients.Journal of molecular neuroscience : MN · 2021Article
- Induced pluripotent stem cell reprogramming-associated methylation at the GABRA2 promoter and chr4p12 GABAAmerican journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2020Article
- Synonymous GATA2 mutations result in selective loss of mutated RNA and are common in patients with GATA2 deficiency.Leukemia · 2020Article
- Transcriptional differentiation of UV-B protectant genes in maize landraces spanning an elevational gradient in Chiapas, Mexico.Evolutionary applications · 2020Article
- A SNP upstream of the cyclic GMP-AMP synthase (cGAS) gene protects from relapse and extra-pulmonary TB and relates to BCG vaccination status in an Indian cohort.Genes and immunity · 2020Article
- Statin Use Associates With Risk of Type 2 Diabetes via Epigenetic Patterns atFrontiers in genetics · 2020Article
- Allele-Specific Expression of CD4Genes · 2019Article
- Quantification of allelic differential expression using a simple Fluorescence primer PCR-RFLP-based method.Scientific reports · 2019Article
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- Genetic Variation in Genes Underlying Diverse Dementias May Explain a Small Proportion of Cases in the Alzheimer's Disease Sequencing Project.Dementia and geriatric cognitive disorders · 2018Article
- Wilson disease: At the crossroads between genetics and epigenetics-A review of the evidence.Liver research (Beijing, China) · 2017Article
- Intrinsic MYH7 expression regulation contributes to tissue level allelic imbalance in hypertrophic cardiomyopathy.Journal of muscle research and cell motility · 2017Article
80 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recent development of whole genome association studies has lead to the robust identification of several loci involved in different common human diseases. Interestingly, some of the strongest signals of association observed in these studies arise from non-coding regions located in very large introns or far away from any annotated genes, raising the possibility that these regions are involved in the etiology of the disease through some unidentified regulatory mechanisms. These findings highlight the importance of better understanding the mechanisms leading to inter-individual differences in gene expression in humans. Most of the existing approaches developed to identify common regulatory polymorphisms are based on linkage/association mapping of gene expression to genotypes. However, these methods have some limitations, notably their cost and the requirement of extensive genotyping information from all the individuals studied which limits their applications to a specific cohort or tissue. Here we describe a robust and high-throughput method to directly measure differences in allelic expression for a large number of genes using the Illumina Allele-Specific Expression BeadArray platform and quantitative sequencing of RT-PCR products. We show that this approach allows reliable identification of differences in the relative expression of the two alleles larger than 1.5-fold (i.e., deviations of the allelic ratio larger than 60:40) and offers several advantages over the mapping of total gene expression, particularly for studying humans or outbred populations. Our analysis of more than 80 individuals for 2,968 SNPs located in 1,380 genes confirms that differential allelic expression is a widespread phenomenon affecting the expression of 20% of human genes and shows that our method successfully captures expression differences resulting from both genetic and epigenetic cis-acting mechanisms.
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