A genome-wide association study identifies three loci associated with mean platelet volume

Abstract

Mean platelet volume (MPV) is increased in myocardial and cerebral infarction and is an independent and strong predictor for postevent morbidity and mortality. We conducted a genome-wide association study (GWAS), the KORA (Kooperative Gesundheitsforschung in der Region Augsburg) F3 500K study, and found MPV to be strongly associated with three common single-nucleotide polymorphisms (SNPs): rs7961894 located within intron 3 of WDR66 on chromosome 12q24.31, rs12485738 upstream of the ARHGEF3 on chromosome 3p13-p21, and rs2138852 located upstream of TAOK1 on chromosome 17q11.2. We replicated all three SNPs in another GWAS from the UK and in two population-based samples from Germany. In a combined analysis including 10,048 subjects, the SNPs had p values of 7.24 x 10(-48) for rs7961894, 3.81 x 10(-27) for rs12485738, and 7.19 x 10(-28) for rs2138852. These three quantitative trait loci together accounted for 4%-5% of the variance in MPV. In-depth sequence analysis of WDR66 in 382 samples from the extremes revealed 20 new variants and a haplotype with three coding SNPs and one SNP at the transcription start site associated with MPV (p = 6.8 x 10(-5)). In addition, expression analysis indicated a direct correlation of WDR66 transcripts and MPV. These findings may not only enhance our understanding of platelet activation and function, but may also provide a focus for several novel research avenues.

Figure 1

Summary of Genome-wide Association and Replication Results (A) Genome-wide association study for log-transformed MPV on a population-based sample of 1606 individuals from the KORA F3 500K study. The x axis represents the genomic position (in Gb) of 335,152 SNPs; the y axis shows −log10(P). The horizontal line indicates the threshold for genome-wide significance at 1.5 × 10⁻⁷. After correcting for multiple testing, we found that one SNP on chromosome 12 attained genome-wide statistical significance. (B–D) p value plots showing the association signals in the region of WDR66 on chromosome 12 (B), ARHGEF3 on chromosome 3 (C), and TAOK1 on chromosome 17 (D). −log10 p values are plotted as a function of genomic position (NCBI Build 36). Large diamonds indicate the p value for the lead SNP in KORA F3 500K (red), KORA S4 (blue), UKBS-CC1 (green), and SHIP (magenta). Proxies are indicated with diamonds for genotyped SNPs and circles for imputed SNPs of smaller size, with colors determined from their pairwise r² values from KORA F3 500K. Red diamonds indicate high LD with the lead SNP (r² > 0.8), orange diamonds indicate moderate LD with the lead SNP (0.5 < r² < 0.8), yellow indicates markers in weak LD with the lead SNP (0.2 < r² < 0.5), and white indicates no LD with the lead SNP (r² < 0.2). Recombination rate estimates (HapMap Phase II) are given in light blue, Refseq genes (NCBI) are displayed by green bars.

Figure 2

Localization of MPV-Associated SNPs within the 5′ Part of the WDR66 Gene The p values given are based on Fisher's exact test in 382 samples from the most extreme (high and low) MPV distribution in KORA S4.

Figure 3

Expression Analysis of WDR66 and Association with Log MPV WDR66 expression was analyzed via whole-blood genome-wide transcription profiling in a subgroup of 323 KORA F3 samples with Illumina Human-6 v2 Expression BeadChip (probe ID 2630343).