TY - JOUR
T1 - Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA
AU - Fehrmann, Rudolf S.N.
AU - Jansen, Ritsert C.
AU - Veldink, Jan H.
AU - Westra, Harm-Jan
AU - Arends, Danny
AU - Bonder, Marc Jan
AU - Fu, Jingyuan
AU - Deelen, Patrick
AU - Groen, Harry J.M.
AU - Smolonska, Asia
AU - Weersma, Rinse K.
AU - Hofstra, Robert M.W.
AU - Buurman, Wim A.
AU - Rensen, Sander
AU - Wolfs, Marcel G.M.
AU - Platteel, Mathieu
AU - Zhernakova, Alexandra
AU - Elbers, Clara C.
AU - Festen, Eleanora M.
AU - Trynka, Gosia
AU - Hofker, Marten H.
AU - Saris, Christiaan G.J.
AU - Ophoff, Roel A.
AU - van den Berg, Leonard H.
AU - van Heel, David A.
AU - Wijmenga, Cisca
AU - te Meerman, Gerard J.
AU - Franke, Lude
PY - 2011/8/4
Y1 - 2011/8/4
N2 - For many complex traits, genetic variants have been found associated. However, it is still mostly unclear through which downstream mechanism these variants cause these phenotypes. Knowledge of these intermediate steps is crucial to understand pathogenesis, while also providing leads for potential pharmacological intervention. Here we relied upon natural human genetic variation to identify effects of these variants on trans-gene expression (expression quantitative trait locus mapping, eQTL) in whole peripheral blood from 1,469 unrelated individuals. We looked at 1,167 published trait- or disease-associated SNPs and observed trans-eQTL effects on 113 different genes, of which we replicated 46 in monocytes of 1,490 different individuals and 18 in a smaller dataset that comprised subcutaneous adipose, visceral adipose, liver tissue, and muscle tissue. HLA single-nucleotide polymorphisms (SNPs) were 10-fold enriched for trans-eQTLs: 48% of the trans-acting SNPs map within the HLA, including ulcerative colitis susceptibility variants that affect plausible candidate genes AOAH and TRBV18 in trans. We identified 18 pairs of unlinked SNPs associated with the same phenotype and affecting expression of the same trans-gene (21 times more than expected, P
AB - For many complex traits, genetic variants have been found associated. However, it is still mostly unclear through which downstream mechanism these variants cause these phenotypes. Knowledge of these intermediate steps is crucial to understand pathogenesis, while also providing leads for potential pharmacological intervention. Here we relied upon natural human genetic variation to identify effects of these variants on trans-gene expression (expression quantitative trait locus mapping, eQTL) in whole peripheral blood from 1,469 unrelated individuals. We looked at 1,167 published trait- or disease-associated SNPs and observed trans-eQTL effects on 113 different genes, of which we replicated 46 in monocytes of 1,490 different individuals and 18 in a smaller dataset that comprised subcutaneous adipose, visceral adipose, liver tissue, and muscle tissue. HLA single-nucleotide polymorphisms (SNPs) were 10-fold enriched for trans-eQTLs: 48% of the trans-acting SNPs map within the HLA, including ulcerative colitis susceptibility variants that affect plausible candidate genes AOAH and TRBV18 in trans. We identified 18 pairs of unlinked SNPs associated with the same phenotype and affecting expression of the same trans-gene (21 times more than expected, P
U2 - 10.1371/journal.pgen.1002197
DO - 10.1371/journal.pgen.1002197
M3 - Article
SN - 1553-7390
VL - 7
JO - PLoS Genetics
JF - PLoS Genetics
IS - 8
ER -
