Genome-wide association meta-analysis for total serum bilirubin levels
Andrew D. Johnson
Maryam Kavousi
Albert V. Smith
Ming-Huei Chen
Abbas Dehghan
Thor Aspelund
Jing-Ping Lin
Cornelia M. van Duijn
Tamara B. Harris
L. Adrienne Cupples
Andre G. Uitterlinden
Lenore Launer
Albert Hofman
Fernando Rivadeneira
Bruno Stricker
Qiong Yang
Christopher J. O'Donnell
Vilmundur Gudnason
Jacqueline C. Witteman
Variation in serum bilirubin is associated with altered cardiovascular disease risk and drug metabolism. We aimed to identify genetic contributors to variability in serum bilirubin levels by combining results from three genome-wide association studies (Framingham heart study, n 5 3424; Rotterdam study, n 5 3847; Age, Gene, Environment and Susceptibility-Reykjavik, n 5 2193). Meta-analysis showed strong replication for a genetic influence on serum bilirubin levels of the UGT1A1 locus (P < 5 3 102324) and a 12p12.2 locus. The peak signal in the 12p12.2 region was a non-synonymous SNP in SLCO1B1 (rs4149056, P 5 6.7 3 10213), which gives rise to a valine to alanine amino acid change leading to reduced activity for a hepatic transporter with known affinity for bilirubin. There were also suggestive associations with several other loci. The top variants in UGT1A1 and SLCO1B1 explain 18.0 and 1.0% of the variation in total serum bilirubin levels, respectively. In a conditional analysis adjusted for individual genotypes for the top UGT1A1 variant, the top SLCO1B1 variant remained highly significant (P 5 7.3 3 10213), but no other variants achieved genome-wide significance. In one of the largest genetic studies of bilirubin to date (n 5 9464), we confirm the substantial genetic influence of UGT1A1 variants, consistent with past linkage and association studies, and additionally provide strong evidence of a role for allelic variation in SLCO1B1. Given the involvement of bilirubin in a number of physiological and disease processes, and the roles for UGT1A1 and SLCO1B1 in drug metabolism, these genetic findings have potential clinical importance. In analyses for association with gallbladder disease or gallstones, top bilirubin SNPs in UGT1A1 and SLCO1B1 were not associated.
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INTRODUCTION
Total serum bilirubin levels among study participants
accounts for approximately 0.6, 0.5 and 0.5% of the variation
in total serum bilirubin levels, in FHS, RS and
AGESReykjavik, respectively. There were also SNPs in partial LD
with rs4149056 and reaching genome-wide significance in
other genes in the 12p12.2 region that contains SLCO1B1,
including in LST-3TM12 (rs2417873, P 1.5 1029, r2
0.06 with rs4149056) and SLCO1A2 (rs4149000, P 2.7
1028, r2 0.56 with rs4149056) (Fig. 2).
In age sex-adjusted regression models including these
three 12p12.2 SNPs, rs4149056 (FHS P 0.11; RS P
0.03; AGES P 8.8 1025; meta-analysis P 6.3 1025)
and rs2417873 (FHS P 2.3 1026; RS P 0.02; AGES
P 0.05; meta-analysis P 1.2 1027), but not rs4149000
(FHS P 0.23; RS P 0.35; AGES P 0.03; meta-analysis
P 0.70), were independently associated with bilirubin
levels. We did not find strong evidence for gene gene
interaction between UGT1A1 (rs6742078) and SLCO1B1
(rs4149056) (FHS P 0.40; RS P 0.39; AGES P 0.48)
or for gene gender interaction for UGT1A1 (rs6742078:
FHS P 0.03; RS P 0.67; AGES P 0.99) or SLCO1B1
(rs4149056: FHS P 0.40; RS P 0.60; AGES P 0.87).
Other loci had SNPs that approached but did not exceed the
genome-wide significance threshold (SLC22A18,
rs16928809, P 1.1 1027; the KRCC1 region at 2p11.2,
rs12714207, P 5.3 1027; a histone gene cluster at
6p22.1 near HFE, rs12206204, P 7.5 1027). We provide
meta-analysis results for SNPs with P , 5.0 1025 in
Supplementary Material, Table S3. In formal tests for
homogeneity of the effect size among studies for the top associated
SNPs shown in Table 1, there was no significant evidence
for heterogeneity among the studies (data not shown).
GWA results conditional on UGT1A1 (rs6742078)
genotype
Because of the substantial proportion of variation in bilirubin
levels explained by UGT1A1, we sought to determine whether
additional loci remained significant after accounting for the
UGT1A1 effect. We added a covariate to the regression
model representing UGT1A1 genotype at one of the most
highly associated SNPs (rs6742078) and performed
conditional analysis for each cohort for all imputed SNPs
and conducted subsequent meta-analysis (Table 2). The
SLCO1B1 gene variant (rs4149056, T . C) that changes
amino acid 174 from valine to alanine showed a similar
genome-wide significant signal to that observed in
unconditional analysis. This SNP reached genome-wide significance
after adjusting for UGT1A1 genotype (FHS: P 4.5 1025,
RS: P 7.8 1029, AGES-Reykjavik: P 1.2 1024,
meta-analysis: P 7.3 10213). The most significant SNP
in the UGT1A1 region in conditional meta-analysis was
2 kb upstream of UGT1A5 and 52 kb upstream from
UGT1A1 (rs4233633, FHS: P 2.0 1023, RS: P 2.9
1025, AGES-Reykjavik: P 0.43, meta-analysis, P 5.3
1025). This indicates that our conditional anal (...truncated)