GWAS on the Island of Kosrae Figure 3. Inclusion of a between-family test of association increases study power using p-value as a metric. A known effect comprising 2% of phenotypic variance explained was ‘‘spiked’’ into a dataset of 770 randomly selected SNPs with MAF$0.01. Study power was evaluated for within-only (PLINK/QFAM-Within) and within- and between-family (PLINK/QFAM-Total) tests of association. After calibrating the score distribution to the using genomic control, study power is measured as the fraction of datasets in which the ‘‘spiked’’ SNP exceeds a particular p-value threshold. doi:10.1371/journal.pgen.1000365.g003 Given the effective sample size of our cohort, we then used the Genetic Power Calculator [20] to estimate study power for effects explaining larger proportions of phenotypic variance, as our hypothesis was that such effects might exist on Kosrae (Figure 4B). Our study has ,87% power to detect effects explaining 5% phenotypic variance at a genome-wide significant threshold of p,561028, and .95% power to detect such effects at p,1026. We concluded that our genome-wide association strategy for quantitative traits on Kosrae is well-powered to identify loci with relatively strong genetic effects, should they exist and are tagged by SNPs on the genotyping array. Results from the Genome-Wide Association Analyses of 15 Quantitative Traits We applied our strategy for association analyses to the examination of 15 quantitative traits, using measurements from clinical screenings in 1994, 2001 and 2003. As anticipated from the known relatedness between sibships, scores were inflated compared to the distribution. Score inflation ranged from l = 1.10 for fasting plasma glucose to l = 2.05 for HDL-C (Figure S3). Score inflation was correlated strongly with trait heritability (r2 = 0.42). For reference, Table 3 provides a list of SNPs with p#1025 for each trait, including genome-wide significant association (p#561028) between SNPs on chromosome 11 and triglycerides. Quantile-quantile (QQ) plots and the respective genomic control correction factors (l) for select traits are shown in Figure 5; plots for all 15 quantitative traits are presented in Figure S3. The results from our genome wide scans indicate an excess of association signal over that expected by chance for LDL-C, triglycerides and thyroid stimulating hormone. We observed strong association between SNPs in previously established loci and HDL-C, LDL-C, triglyceride levels, TSH and CRP, supporting the validity of our analytic approach. For HDL- C, we observe association with rs4783962 and rs1800775 near CETP (p = 1.6861024 and 1.7161024, respectively), with the same allele and direction of effect as reported in Caucasian populations [21,22]. The best-associated SNP for LDL-C is rs4420638 in the APOE/C1/C4/C2 gene cluster on chromosome 19 (p = 1.8961027), a known locus influencing plasma levels of LDL-C and total cholesterol [23]. We also observed association between LDL-C levels and multiple SNPs in and around the gene encoding HMG-CoA reductase (HMGCR), the target for choles- terol-lowering statin drugs [24,25]. Studies in Caucasian cohorts recently established this locus as a true association, with genome- wide significant p-values ,1610220 [21]. For TSH, three SNPs (rs4704397, rs6885099, and rs2046045) previously identified in Caucasian cohorts are also associated in Kosraens, with p-values ranging from 361024 to 1.861024 [26]. For CRP, SNPs at the CRP and HNF1A gene loci show association and the same direction of effect on Kosrae (p = 2.061025 and 361024, respectively) as previously observed in a Caucasian cohort, in which the associated SNPs were either directly genotyped or are in perfect correlation (r2 = 1 in both HapMap CEU and ASN) [27]. The strongest association for CRP on Kosrae is with rs4420638 near the APOE gene (p = 1.661026; Table 3), another previously known locus [27,28]. This SNP is less well-correlated with the most highly-associated SNP reported in the literature (rs2075650; r2 = 0.37 and 0.49 in HapMap CEU and ASN, respectively) [27]. Seven SNPs near APOC3/A5 have genome-wide significant association (p,561028) with triglyceride levels (p = 1.261029 to 8.661029), including specific variants not previously implicated in Caucasian cohorts. In Kosrae, the best-associated SNP for triglyceride levels (rs7396835, p = 1.261029) is ,23 kb down- stream of the variant recognized in Caucasians (rs2266788). Correlation between these two SNPs has not been evaluated in Kosraens, since rs2266788 is neither directly genotyped nor well- covered by other SNPs in our 500 k dataset. However, rs2266788 is uncorrelated in HapMap Asian or Caucasian samples (r2#0.32 and r2#0.14, respectively) with any of the seven SNPs associated with triglycerides in Kosraens. As the causal variant for this locus has not been identified, it remains to be determined whether these PLoS Genetics | www.plosgenetics.org 6 February 2009 | Volume 5 | Issue 2 | e1000365