RT Journal
A1 Huang, Guo-Jen
A1 Shifman, Sagiv
A1 Valdar, William
A1 Johannesson, Martina
A1 Yalcin, Binnaz
A1 Taylor, Martin S.
A1 Taylor, Jennifer M.
A1 Mott, Richard
A1 Flint, Jonathan
T1 High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues
JF Genome Research 
JO Genome Research 
YR 2009 
FD June 01 
VO 19 
IS 6 
SP 1133 
OP 1140 
DO 10.1101/gr.088120.108 
UL http://genome.cshlp.org/content/19/6/1133.abstract 
AB A proportion of the genetic variants underlying complex phenotypes do so through their effects on gene expression, so an important challenge in complex trait analysis is to discover the genetic basis for the variation in transcript abundance. So far, the potential of mapping both quantitative trait loci (QTLs) and expression quantitative trait loci (eQTLs) in rodents has been limited by the low mapping resolution inherent in crosses between inbred strains. We provide a megabase resolution map of thousands of eQTLs in hippocampus, lung, and liver samples from heterogeneous stock (HS) mice in which 843 QTLs have also been mapped at megabase resolution. We exploit dense mouse SNP data to show that artifacts due to allele-specific hybridization occur in ∼30% of the cis-acting eQTLs and, by comparison with exon expression data, we show that alternative splicing of the 3′ end of the genes accounts for <1% of cis-acting eQTLs. Approximately one third of cis-acting eQTLs and one half of trans-acting eQTLs are tissue specific. We have created an important systems biology resource for the genetic analysis of complex traits in a key model organism.