Conditional eQTL analysis reveals allelic heterogeneity of gene expression

Rick Jansen, Jouke-Jan Hottenga, Michel G Nivard, A. Abdellaoui, Bram Laport, Eco J de Geus, Fred A Wright, Brenda W J H Penninx, Dorret I Boomsma

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Abstract

In recent years, multiple eQTL (expression quantitative trait loci) catalogs have become available that can help understand the functionality of complex trait-related single nucleotide polymorphisms (SNPs). In eQTL catalogs, gene expression is often strongly associated with multiple SNPs, which may reflect either one or multiple independent associations. Conditional eQTL analysis allows a distinction between dependent and independent eQTLs. We performed conditional eQTL analysis in 4,896 peripheral blood microarray gene expression samples. Our analysis showed that 35% of genes with a cis eQTL have at least two independent cis eQTLs; for several genes up to 13 independent cis eQTLs were identified. Also, 12% (671) of the independent cis eQTLs identified in conditional analyses were not significant in unconditional analyses. The number of GWAS catalog SNPs identified as eQTL in the conditional analyses increases with 24% as compared to unconditional analyses. We provide an online conditional cis eQTL mapping catalog for whole blood (https://eqtl.onderzoek.io/), which can be used to lookup eQTLs more accurately than in standard unconditional whole blood eQTL databases.

Original languageEnglish
Article numberddx043
Pages (from-to)1444-1451
Number of pages8
JournalHuman Molecular Genetics
Volume26
Issue number8
Early online date6 Feb 2017
DOIs
Publication statusPublished - 15 Apr 2017

Funding

FundersFunder number
National Institute of Mental HealthRC2MH089951

    Keywords

    • Journal Article

    Cohort Studies

    • Netherlands Twin Register (NTR)

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