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Our previous genome-wide association study (GWAS) identified two susceptibility loci for congenital heart disease (CHD) in Han Chinese. Here we identify additional loci by testing promising associations in an extended 3-stage validation consisting of 6,053 CHD cases and 7,410 controls. We find GW significant (
P
<5.0 × 10
−8
) evidence of 4 additional CHD susceptibility loci at 4q31.22 (rs1400558, upstream of
EDNRA
,
P
all
=1.63 × 10
−9
), 9p24.2 (rs7863990, close to
SMARCA2
,
P
all
=3.71 × 10
−14
), 12q24.13 (rs2433752, upstream of
TBX3
and
TBX5
,
P
all
=1.04 × 10
−10
) and 20q12 (rs490514, in
PTPRT
,
P
all
=1.20 × 10
−13
). Moreover, the data from previous European GWAS supports that rs490514 is associated with the risk of CHD (
P
=3.40 × 10
−3
). These results enhance our understanding of CHD susceptibility.
Genome-wide association studies in Chinese and Europeans have identified multiple loci associated with congenital heart disease. Here the authors use existing GWAS data to conduct an extended three-stage analysis in Han Chinese and identify four novel loci linked to disease risk in this population.