Mapping cis- and trans-regulatory effects across multiple tissues in twins.
paper
Cited
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- Authors
- Grundberg, Elin; Small, Kerrin S; Hedman, Γ sa K; Nica, Alexandra C; Buil, Alfonso; Keildson, Sarah; Bell, Jordana T; Yang, Tsun-Po; Meduri, Eshwar; Barrett, Amy; Nisbett, James; Sekowska, Magdalena; Wilk, Alicja; Shin, So-Youn; Glass, Daniel; Travers, Mary; Min, Josine L; Ring, Sue; Ho, Karen; Thorleifsson, Gudmar; Kong, Augustine; Thorsteindottir, Unnur; Ainali, Chrysanthi; Dimas, Antigone S; Hassanali, Neelam; Ingle, Catherine; Knowles, David; Krestyaninova, Maria; Lowe, Christopher E; Di Meglio, Paola; Montgomery, Stephen B; Parts, Leopold; Potter, Simon; Surdulescu, Gabriela; Tsaprouni, Loukia; Tsoka, Sophia; Bataille, Veronique; Durbin, Richard; Nestle, Frank O; O'Rahilly, Stephen; Soranzo, Nicole; Lindgren, Cecilia M; Zondervan, Krina T; Ahmadi, Kourosh R; Schadt, Eric E; Stefansson, Kari; Smith, George Davey; McCarthy, Mark I; Deloukas, Panos; Dermitzakis, Emmanouil T; Spector, Tim D; Multiple Tissue Human Expression Resource (MuTHER) Consortium
- Year
- 2012
- Journal
- Nature genetics
- PMID
- 22941192
- DOI
- 10.1038/ng.2394
- PMCID
- PMC3784328
Sequence-based variation in gene expression is a key driver of disease risk. Common variants regulating expression in cis have been mapped in many expression quantitative trait locus (eQTL) studies, typically in single tissues from unrelated individuals. Here, we present a comprehensive analysis of gene expression across multiple tissues conducted in a large set of mono- and dizygotic twins that allows systematic dissection of genetic (cis and trans) and non-genetic effects on gene expression. Using identity-by-descent estimates, we show that at least 40% of the total heritable cis effect on expression cannot be accounted for by common cis variants, a finding that reveals the contribution of low-frequency and rare regulatory variants with respect to both transcriptional regulation and complex trait susceptibility. We show that a substantial proportion of gene expression heritability is trans to the structural gene, and we identify several replicating trans variants that act predominantly in a tissue-restricted manner and may regulate the transcription of many genes.
Genetic and non-genetic effect of gene expression across multiple tissuesEstimation of the proportion of variation in expressed transcripts in adipose (N=11394), LCL (N=10631) and skin tissue (N=11932) attributable to genetic (narrow-sense heritability, h2)(A) and familial non-genetic factors (shared common environment, CE)(B). The y-axis is showing the proportion of transcripts at h2/CE cut-off indicated on the x-axis.
The contribution of heritable cis-components to gene expression variationThe contribution of individual cis-SNPs (MAF>5%) to the genetic variance of gene expression (h2>0.1) in adipose (A), LCL (B), and skin tissue (C). The x-axis is showing the proportion of the heritability of each transcript that is explained by independent cis-SNPs.
Trans-variants regulating expression of multiple transcripts(A)P value distributions (x-axis) of genome-wide associations(N, y-axis) between two potential adipose multi-gene regulators (rs1752223 on chromosome 1, upper panel, and rs7595947 on chromosome 2, lower panel) and transcript levels in adipose (left panel), LCL (middle) and skin tissue (right panel).(B) Plots showing the median trans-Ο1 (Ο1 calculated from p-value distribution of a trans-SNP vs. all probes) at increasing levels of trans-SNP significance in adipose (left panel), LCL (middle) and skin tissue (right panel). The top trans-SNP for each probe was included and trans-SNPs were divided into non-overlapping bins based on the p value of the top trans- association. The median Ο1(y-axis) is graphed against the -log p (x-axis) of the lower limit of each bin.
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| Genetic Variants Contributing to Colistin Cytotoxicity: Identification of TGIF1 and HOXD10 Using a Population Genomics Approach. | Eadon MT et al. | β | 2017 | β |
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| Genome-Wide Association Shows thatΒ Pigmentation Genes Play a Role in SkinΒ Aging. | Law MH et al. | β | 2017 | β |
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| Higher Nevus Count Exhibits a Distinct DNA Methylation Signature in Healthy Human Skin: Implications for Melanoma. | Roos L et al. | β | 2017 | β |
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| Characterization of Expression Quantitative Trait Loci in Pedigrees from Colombia and Costa Rica Ascertained for Bipolar Disorder. | Peterson CB et al. | β | 2016 | β |
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| Mapping adipose and muscle tissue expression quantitative trait loci in African Americans to identify genes for type 2 diabetes and obesity. | Sajuthi SP et al. | β | 2016 | β |
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| Multivariate eQTL mapping uncovers functional variation on the X-chromosome associated with complex disease traits. | Brumpton BM et al. | β | 2016 | β |
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| Population-specific genome-wide mapping of expression quantitative trait loci in the colon of Han Chinese. | Guo CC et al. | β | 2016 | β |
| Quantitative Trait Loci Identify Functional Noncoding Variation in Cancer. | Heyn H | β | 2016 | β |
| Reanalysis of mGWAS results and in vitro validation show that lactate dehydrogenase interacts with branched-chain amino acid metabolism. | Heemskerk MM et al. | β | 2016 | β |
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| Transcriptome Profiling in Rat Inbred Strains and Experimental Cross Reveals Discrepant Genetic Architecture of Genome-Wide Gene Expression. | Kaisaki PJ et al. | β | 2016 | β |
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| Winner's Curse Correction and Variable Thresholding Improve Performance of Polygenic Risk Modeling Based on Genome-Wide Association Study Summary-Level Data. | Shi J et al. | β | 2016 | β |
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| Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation. | Croteau-Chonka DC et al. | β | 2015 | β |
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