Genome-wide identification of expression Quantitative Trait Loci (eQTLs) in human heart

Tamara T. Koopmann, Michiel E. Adriaens, Perry D. Moerland, Roos F. Marsman, Margriet L. Westerveld, Sean Lal, Taifang Zhang, Christine Q. Simmons, I. Baczkó, Cristobal Dos Remedios, Nanette H. Bishopric, A. Varró, Alfred L. George, Elisabeth M. Lodder, Connie R. Bezzina

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

In recent years genome-wide association studies (GWAS) have uncovered numerous chromosomal loci associated with various electrocardiographic traits and cardiac arrhythmia predisposition. A considerable fraction of these loci lie within inter-genic regions. The underlying trait-associated variants likely reside in regulatory regions and exert their effect by modulating gene expression. Hence, the key to unraveling the molecular mechanisms underlying these cardiac traits is to interrogate variants for association with differential transcript abundance by expression quantitative trait locus (eQTL) analysis. In this study we conducted an eQTL analysis of human heart. For a total of 129 left ventricular samples that were collected from non-diseased human donor hearts, genome-wide transcript abundance and genotyping was determined using microarrays. Each of the 18,402 transcripts and 897,683 SNP genotypes that remained after pre-processing and stringent quality control were tested for eQTL effects. We identified 771 eQTLs, regulating 429 unique transcripts. Overlaying these eQTLs with cardiac GWAS loci identified novel candidates for studies aimed at elucidating the functional and transcriptional impact of these loci. Thus, this work provides for the first time a comprehensive eQTL map of human heart: a powerful and unique resource that enables systems genetics approaches for the study of cardiac traits.

Original languageEnglish
Article numbere97380
JournalPLoS One
Volume9
Issue number5
DOIs
Publication statusPublished - May 20 2014

Fingerprint

Quantitative Trait Loci
quantitative trait loci
Genes
heart
Association reactions
Genome
genome
loci
Nucleic Acid Regulatory Sequences
Genome-Wide Association Study
Microarrays
Gene expression
Quality control
arrhythmia
Processing
intergenic DNA
Quality Control
genotyping
Single Nucleotide Polymorphism
quality control

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Koopmann, T. T., Adriaens, M. E., Moerland, P. D., Marsman, R. F., Westerveld, M. L., Lal, S., ... Bezzina, C. R. (2014). Genome-wide identification of expression Quantitative Trait Loci (eQTLs) in human heart. PLoS One, 9(5), [e97380]. https://doi.org/10.1371/journal.pone.0097380

Genome-wide identification of expression Quantitative Trait Loci (eQTLs) in human heart. / Koopmann, Tamara T.; Adriaens, Michiel E.; Moerland, Perry D.; Marsman, Roos F.; Westerveld, Margriet L.; Lal, Sean; Zhang, Taifang; Simmons, Christine Q.; Baczkó, I.; Dos Remedios, Cristobal; Bishopric, Nanette H.; Varró, A.; George, Alfred L.; Lodder, Elisabeth M.; Bezzina, Connie R.

In: PLoS One, Vol. 9, No. 5, e97380, 20.05.2014.

Research output: Contribution to journalArticle

Koopmann, TT, Adriaens, ME, Moerland, PD, Marsman, RF, Westerveld, ML, Lal, S, Zhang, T, Simmons, CQ, Baczkó, I, Dos Remedios, C, Bishopric, NH, Varró, A, George, AL, Lodder, EM & Bezzina, CR 2014, 'Genome-wide identification of expression Quantitative Trait Loci (eQTLs) in human heart', PLoS One, vol. 9, no. 5, e97380. https://doi.org/10.1371/journal.pone.0097380
Koopmann TT, Adriaens ME, Moerland PD, Marsman RF, Westerveld ML, Lal S et al. Genome-wide identification of expression Quantitative Trait Loci (eQTLs) in human heart. PLoS One. 2014 May 20;9(5). e97380. https://doi.org/10.1371/journal.pone.0097380
Koopmann, Tamara T. ; Adriaens, Michiel E. ; Moerland, Perry D. ; Marsman, Roos F. ; Westerveld, Margriet L. ; Lal, Sean ; Zhang, Taifang ; Simmons, Christine Q. ; Baczkó, I. ; Dos Remedios, Cristobal ; Bishopric, Nanette H. ; Varró, A. ; George, Alfred L. ; Lodder, Elisabeth M. ; Bezzina, Connie R. / Genome-wide identification of expression Quantitative Trait Loci (eQTLs) in human heart. In: PLoS One. 2014 ; Vol. 9, No. 5.
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