Immunochip analyses identify a novel risk locus for primary biliary cirrhosis at 13q14, multiple independent associations at four established risk loci and epistasis between 1p31 and 7q32 risk variants

Abstract

To further characterize the genetic basis of primary biliary cirrhosis (PBC), we genotyped 2426 PBC patients and 5731 unaffected controls from three independent cohorts using a single nucleotide polymorphism (SNP) array (Immunochip) enriched for autoimmune disease risk loci. Meta-analysis of the genotype data sets identified a novel disease-associated locus near the TNFSF11 gene at 13q14, provided evidence for association at six additional immune-related loci not previously implicated in PBC and confirmed associations at 19 of 22 established risk loci. Results of conditional analyses also provided evidence for multiple independent association signals at four risk loci, with haplotype analyses suggesting independent SNP effects at the 2q32 and 16p13 loci, but complex haplotype driven effects at the 3q25 and 6p21 loci. By imputing classical HLA alleles from this data set, four class II alleles independently contributing to the association signal from this region were identified. Imputation of genotypes at the non-HLA loci also provided additional associations, but none with stronger effects than the genotyped variants. An epistatic interaction between the IL12RB2 risk locus at 1p31and the IRF5 risk locus at 7q32 was also identified and suggests a complementary effect of these loci in predisposing to disease. These data expand the repertoire of genes with potential roles in PBC pathogenesis that need to be explored by follow-up biological studies.

Figure 1.

Manhattan plot illustrating the results of a meta-analysis of Immunochip association studies of three independent cohorts of PBC patients and unaffected controls.

Figure 2.

Quantile–quantile plot of observed versus expected P-values for the meta-analysis. Black circles specify the results of the complete Immunochip, gray circles specify the results after all known loci (as identified by previous GWAS) are removed. The genomic control (λ_GC = 1.29) was estimated after removal of the known loci. The gray shaded region of the expectation line represents the 95% confidence interval for the expected range of P-values.

Figure 3.

Association results from meta-analysis of three independent cohorts for the AKAP11/TNFSF11 region on chromosome 13q14.11. Genotyped SNPs are illustrated as circles and imputed SNPs as squares. The peak SNP, rs3862738, is shown in purple and pairwise correlation (r²) with this SNP is indicated by a color gradient ranging from red (high LD) to dark blue (low LD).

Figure 4.

Association results from meta-analysis of three independent cohorts illustrating independent association signals identified by conditional analyses at 2q32, 16p13 and 3q25. The peak SNPs are indicated by large dark blue circles and correlated SNPs (r² ≥ 0.5) as medium-sized light blue circles. The peak SNP remaining after the first round of conditioning (SNP2) is indicated by large red circle and correlated SNPs as medium-sized pink circles. For 3q25, the peak and correlated SNPs representing the third signal remaining after the second round of conditioning are indicated by dark and light gold circles.

Figure 5.

Risk allele frequencies of interacting SNPs at 1p31 (IL12RB2) and 7q32 (IRF5/TNPO3) stratified by the genotype at the alternate locus. (A) The rs10488631 risk allele ‘C’ at 7q32 is highly associated with PBC only in patients with the non-risk rs72678531 genotype ‘TT’ at 1p31. Conversely (B), the rs72678531 risk allele ‘C’ at 1p31 is highly associated with PBC only in patients with rs10488631 ‘TT’ genotypes. These findings suggest the possibility of a complementary effect between the risk alleles at these two loci. Results from logistic regression analyses in three independent cohorts under a log-additive model; combined by meta-analysis.