Genome-wide association study of coronary artery disease in the Japanese

Abstract

A new understanding of the genetic basis of coronary artery disease (CAD) has recently emerged from genome-wide association (GWA) studies of common single-nucleotide polymorphisms (SNPs), thus far performed mostly in European-descent populations. To identify novel susceptibility gene variants for CAD and confirm those previously identified mostly in populations of European descent, a multistage GWA study was performed in the Japanese. In the discovery phase, we first genotyped 806 cases and 1337 controls with 451 382 SNP markers and subsequently assessed 34 selected SNPs with direct genotyping (541 additional cases) and in silico comparison (964 healthy controls). In the replication phase, involving 3052 cases and 6335 controls, 12 SNPs were tested; CAD association was replicated and/or verified for 4 (of 12) SNPs from 3 loci: near BRAP and ALDH2 on 12q24 (P=1.6 × 10(-34)), HLA-DQB1 on 6p21 (P=4.7 × 10(-7)), and CDKN2A/B on 9p21 (P=6.1 × 10(-16)). On 12q24, we identified the strongest association signal with the strength of association substantially pronounced for a subgroup of myocardial infarction cases (P=1.4 × 10(-40)). On 6p21, an HLA allele, DQB1(*)0604, could show one of the most prominent association signals in an ∼8-Mb interval that encompasses the LTA gene, where an association with myocardial infarction had been reported in another Japanese study. CAD association was also identified at CDKN2A/B, as previously reported in different populations of European descent and Asians. Thus, three loci confirmed in the Japanese GWA study highlight the likely presence of risk alleles with two types of genetic effects - population specific and common - on susceptibility to CAD.

Figure 1

Flowchart summarizing the multistage design of the present study. Independent SNPs (r²<0.8, in principle) were selected in the transition from stage 1a to stage 1b. The independency was secured between two parallel tracks for SNP selection in GWA scan (at stringent P-value threshold and at less stringent threshold) as well as within each track. Furthermore, on 6p21 and 12q24, we excluded SNPs that failed to show region-wide significant association with CAD after adjustment for lead SNPs: rs11752643 on 6p21 and rs3782886 on 12q24. Here, a region-wide significance level (P<4.0 × 10⁻⁵ for 6p21 and P<2.9 × 10⁻⁴ for 12q24) was set by Bonferroni correction (see Supplementary Table VI).

Figure 2

Manhattan plots for stage 1 GWA study of CAD in the Japanese. SNPs showing P<5 × 10⁻⁸ are colored in red. The color reproduction of this figure is available at the European Journal of Human Genetics journal online.

Figure 3

Plots of CAD association for the 12q24 region. In the top panel, all genotyped SNPs in the current Japanese GWA scan (dot) that passed the quality control in stage 1a, and four additionally genotyped SNPs (cross) that are in strong LD with BRAP rs11066001 are plotted with their –log₁₀(P) for CAD against chromosome positions (in Mb). In the middle panel, the –log₁₀(P) for CAD associations with statistical adjustment for rs11066001 are shown. The bottom panel shows the genomic location of RefSeq genes with intron and exon structures (NCBI Build 36).

Figure 4

Overview of SNPs and haplotypes explaining CAD association on 6p21. Genotypic association between SNPs across the 8 Mb extended major histocompatibility complex region and two HLA alleles of interest – DQB1^*0604 at HLA-DQB1 (top panels; a–c) and DRB1^*1302 at HLA-DRB1 (middle panels; d–f) – is shown for three HapMap populations: JPT (a, d), CEU (b, e), and YRI (c, f). The SNP positions across the 8 Mb region showing weak (r²<0.5; gray), moderate (0.5≤r²<0.8; blue), and strong (r²≥0.8; red) association with each HLA allele are depicted in the individual plots, above which the position of HLA-DQB1 and HLA-DRB1 is indicated by the triangle. In each plot, rs11752643 (tag SNP for DQB1^*0604 in JPT (r²=1) and CEU (r²=1)), rs2157339 (tag SNP for DRB1^*1302 in JPT (r²=0.88), CEU (r²=1), and YRI (r²=0.87)), and rs1041981 (nonsynonymous SNP in LTA) are circled in black, except that rs11752643 is not shown for YRI because of the lack of polymorphism. Data are derived from the study by de Bakker et al and HapMap (http://hapmap.ncbi.nlm.nih.gov/). Haplotype frequencies involving the three tested SNPs and CAD association in the largest district, Nagoya (g), and the phylogeny (h) are also shown. The color reproduction of this figure is available at the European Journal of Human Genetics journal online.

Figure 5

Relation of geographical variation (which may lead to population structure) with CAD association on 6p21. It is speculated that more than two independent subgroups of SNPs are present in the 6p21 region for geographical variation (a); and that one of them, including rs11752643, simultaneously accounts for CAD association and constitutes a genuine association signal (b). Pairwise LD coefficient r² among 15 SNPs that show geographical variation on 6q21 in the Japanese is demonstrated in (c).