Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs

Xiaoling Zhang, Hinco J. Gierman, Daniel Levy, Andrew Plump, Radu Dobrin, Harald H H Goring, Joanne E. Curran, Matthew P. Johnson, John Blangero, Stuart K. Kim, Christopher J. O'Donnell, Valur Emilsson, Andrew D. Johnson

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

Background: Gene expression genetic studies in human tissues and cells identify cis- and trans-acting expression quantitative trait loci (eQTLs). These eQTLs provide insights into regulatory mechanisms underlying disease risk. However, few studies systematically characterized eQTL results across cell and tissues types. We synthesized eQTL results from >50 datasets, including new primary data from human brain, peripheral plaque and kidney samples, in order to discover features of human eQTLs.Results: We find a substantial number of robust cis-eQTLs and far fewer trans-eQTLs consistent across tissues. Analysis of 45 full human GWAS scans indicates eQTLs are enriched overall, and above nSNPs, among positive statistical signals in genetic mapping studies, and account for a significant fraction of the strongest human trait effects. Expression QTLs are enriched for gene centricity, higher population allele frequencies, in housekeeping genes, and for coincidence with regulatory features, though there is little evidence of 5' or 3' positional bias. Several regulatory categories are not enriched including microRNAs and their predicted binding sites and long, intergenic non-coding RNAs. Among the most tissue-ubiquitous cis-eQTLs, there is enrichment for genes involved in xenobiotic metabolism and mitochondrial function, suggesting these eQTLs may have adaptive origins. Several strong eQTLs (CDK5RAP2, NBPFs) coincide with regions of reported human lineage selection. The intersection of new kidney and plaque eQTLs with related GWAS suggest possible gene prioritization. For example, butyrophilins are now linked to arterial pathogenesis via multiple genetic and expression studies. Expression QTL and GWAS results are made available as a community resource through the NHLBI GRASP database [http://apps.nhlbi.nih.gov/grasp/].Conclusions: Expression QTLs inform the interpretation of human trait variability, and may account for a greater fraction of phenotypic variability than protein-coding variants. The synthesis of available tissue eQTL data highlights many strong cis-eQTLs that may have important biologic roles and could serve as positive controls in future studies. Our results indicate some strong tissue-ubiquitous eQTLs may have adaptive origins in humans. Efforts to expand the genetic, splicing and tissue coverage of known eQTLs will provide further insights into human gene regulation.

Original languageEnglish (US)
Article number532
JournalBMC Genomics
Volume15
Issue number1
DOIs
StatePublished - Jun 27 2014
Externally publishedYes

Fingerprint

Quantitative Trait Loci
Cell Line
Genome-Wide Association Study
Datasets
Genes
Long Noncoding RNA
National Heart, Lung, and Blood Institute (U.S.)
Kidney
Essential Genes
Hand Strength
Xenobiotics
MicroRNAs
Gene Frequency

Keywords

  • Cis
  • EQTL
  • Gene expression
  • Genome-wide
  • Genomics
  • GWAS
  • RNA
  • Tissue
  • Trans
  • Transcriptome

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Zhang, X., Gierman, H. J., Levy, D., Plump, A., Dobrin, R., Goring, H. H. H., ... Johnson, A. D. (2014). Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. BMC Genomics, 15(1), [532]. https://doi.org/10.1186/1471-2164-15-532

Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. / Zhang, Xiaoling; Gierman, Hinco J.; Levy, Daniel; Plump, Andrew; Dobrin, Radu; Goring, Harald H H; Curran, Joanne E.; Johnson, Matthew P.; Blangero, John; Kim, Stuart K.; O'Donnell, Christopher J.; Emilsson, Valur; Johnson, Andrew D.

In: BMC Genomics, Vol. 15, No. 1, 532, 27.06.2014.

Research output: Contribution to journalArticle

Zhang, X, Gierman, HJ, Levy, D, Plump, A, Dobrin, R, Goring, HHH, Curran, JE, Johnson, MP, Blangero, J, Kim, SK, O'Donnell, CJ, Emilsson, V & Johnson, AD 2014, 'Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs', BMC Genomics, vol. 15, no. 1, 532. https://doi.org/10.1186/1471-2164-15-532
Zhang X, Gierman HJ, Levy D, Plump A, Dobrin R, Goring HHH et al. Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. BMC Genomics. 2014 Jun 27;15(1). 532. https://doi.org/10.1186/1471-2164-15-532
Zhang, Xiaoling ; Gierman, Hinco J. ; Levy, Daniel ; Plump, Andrew ; Dobrin, Radu ; Goring, Harald H H ; Curran, Joanne E. ; Johnson, Matthew P. ; Blangero, John ; Kim, Stuart K. ; O'Donnell, Christopher J. ; Emilsson, Valur ; Johnson, Andrew D. / Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. In: BMC Genomics. 2014 ; Vol. 15, No. 1.
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AU - Gierman, Hinco J.

AU - Levy, Daniel

AU - Plump, Andrew

AU - Dobrin, Radu

AU - Goring, Harald H H

AU - Curran, Joanne E.

AU - Johnson, Matthew P.

AU - Blangero, John

AU - Kim, Stuart K.

AU - O'Donnell, Christopher J.

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N2 - Background: Gene expression genetic studies in human tissues and cells identify cis- and trans-acting expression quantitative trait loci (eQTLs). These eQTLs provide insights into regulatory mechanisms underlying disease risk. However, few studies systematically characterized eQTL results across cell and tissues types. We synthesized eQTL results from >50 datasets, including new primary data from human brain, peripheral plaque and kidney samples, in order to discover features of human eQTLs.Results: We find a substantial number of robust cis-eQTLs and far fewer trans-eQTLs consistent across tissues. Analysis of 45 full human GWAS scans indicates eQTLs are enriched overall, and above nSNPs, among positive statistical signals in genetic mapping studies, and account for a significant fraction of the strongest human trait effects. Expression QTLs are enriched for gene centricity, higher population allele frequencies, in housekeeping genes, and for coincidence with regulatory features, though there is little evidence of 5' or 3' positional bias. Several regulatory categories are not enriched including microRNAs and their predicted binding sites and long, intergenic non-coding RNAs. Among the most tissue-ubiquitous cis-eQTLs, there is enrichment for genes involved in xenobiotic metabolism and mitochondrial function, suggesting these eQTLs may have adaptive origins. Several strong eQTLs (CDK5RAP2, NBPFs) coincide with regions of reported human lineage selection. The intersection of new kidney and plaque eQTLs with related GWAS suggest possible gene prioritization. For example, butyrophilins are now linked to arterial pathogenesis via multiple genetic and expression studies. Expression QTL and GWAS results are made available as a community resource through the NHLBI GRASP database [http://apps.nhlbi.nih.gov/grasp/].Conclusions: Expression QTLs inform the interpretation of human trait variability, and may account for a greater fraction of phenotypic variability than protein-coding variants. The synthesis of available tissue eQTL data highlights many strong cis-eQTLs that may have important biologic roles and could serve as positive controls in future studies. Our results indicate some strong tissue-ubiquitous eQTLs may have adaptive origins in humans. Efforts to expand the genetic, splicing and tissue coverage of known eQTLs will provide further insights into human gene regulation.

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KW - RNA

KW - Tissue

KW - Trans

KW - Transcriptome

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