uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Enström, Camilla
Publications (1 of 1) Show all publications
Almlöf, J. C., Lundmark, P., Lundmark, A., Ge, B., Maouche, S., Göring, H. H., . . . Syvänen, A.-C. (2012). Powerful Identification of Cis-regulatory SNPs in Human Primary Monocytes Using Allele-Specific Gene Expression. PLoS ONE, 7(12), e52260
Open this publication in new window or tab >>Powerful Identification of Cis-regulatory SNPs in Human Primary Monocytes Using Allele-Specific Gene Expression
Show others...
2012 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 12, p. e52260-Article in journal (Refereed) Published
Abstract [en]

A large number of genome-wide association studies have been performed during the past five years to identify associations between SNPs and human complex diseases and traits. The assignment of a functional role for the identified disease-associated SNP is not straight-forward. Genome-wide expression quantitative trait locus (eQTL) analysis is frequently used as the initial step to define a function while allele-specific gene expression (ASE) analysis has not yet gained a wide-spread use in disease mapping studies. We compared the power to identify cis-acting regulatory SNPs (cis-rSNPs) by genome-wide allele-specific gene expression (ASE) analysis with that of traditional expression quantitative trait locus (eQTL) mapping. Our study included 395 healthy blood donors for whom global gene expression profiles in circulating monocytes were determined by Illumina BeadArrays. ASE was assessed in a subset of these monocytes from 188 donors by quantitative genotyping of mRNA using a genome-wide panel of SNP markers. The performance of the two methods for detecting cis-rSNPs was evaluated by comparing associations between SNP genotypes and gene expression levels in sample sets of varying size. We found that up to 8-fold more samples are required for eQTL mapping to reach the same statistical power as that obtained by ASE analysis for the same rSNPs. The performance of ASE is insensitive to SNPs with low minor allele frequencies and detects a larger number of significantly associated rSNPs using the same sample size as eQTL mapping. An unequivocal conclusion from our comparison is that ASE analysis is more sensitive for detecting cis-rSNPs than standard eQTL mapping. Our study shows the potential of ASE mapping in tissue samples and primary cells which are difficult to obtain in large numbers.

Keywords
messenger RNA, allele specific gene expression analysis, article, blood donor, DNA flanking region, gene expression, gene frequency, gene mapping, genetic analysis, genetic association, genotype, genotyping expression analysis, human, human cell, intermethod comparison, monocyte, quantitative trait locus mapping, sample size, single nucleotide polymorphism
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-195164 (URN)10.1371/journal.pone.0052260 (DOI)000313618800062 ()
Available from: 2013-02-22 Created: 2013-02-21 Last updated: 2017-12-06Bibliographically approved
Organisations

Search in DiVA

Show all publications