Variant Discovery and Fine Mapping of Genetic Loci Associated with Blood Pressure Traits in Hispanics and African Americans

Despite the substantial burden of hypertension in US minority populations, few genetic studies of blood pressure have been conducted in Hispanics and African Americans, and it is unclear whether many of the established loci identified in European-descent populations contribute to blood pressure variation in non-European descent populations. Using the Metabochip array, we sought to characterize the genetic architecture of previously identified blood pressure loci, and identify novel cardiometabolic variants related to systolic and diastolic blood pressure in a multi-ethnic US population including Hispanics (n = 19,706) and African Americans (n = 18,744). Several known blood pressure loci replicated in African Americans and Hispanics. Fourteen variants in three loci (KCNK3, FGF5, ATXN2-SH2B3) were significantly associated with blood pressure in Hispanics. The most significant diastolic blood pressure variant identified in our analysis, rs2586886/KCNK3 (P = 5.2 x 10−9), also replicated in independent Hispanic and European-descent samples. African American and trans-ethnic meta-analysis data identified novel variants in the FGF5, ULK4 and HOXA-EVX1 loci, which have not been previously associated with blood pressure traits. Our identification and independent replication of variants in KCNK3, a gene implicated in primary hyperaldosteronism, as well as a variant in HOTTIP (HOXA-EVX1) suggest that further work to clarify the roles of these genes may be warranted. Overall, our findings suggest that loci identified in European descent populations also contribute to blood pressure variation in diverse populations including Hispanics and African Americans—populations that are understudied for hypertension genetic risk factors.

Supporting Information: Discovery and fine mapping of genetic loci associated with blood pressure traits in Hispanics and African Americans

B) loci for diastolic BP in Hispanics
In panel A, the plotted SNP (purple diamond) is a missense variant in high LD with other significant variants in the region. Other SNPs in Table A are also shown. Regional plot of the MTHFR/CLCN6 region in African American samples using LD based on the 1000G European ancestry sample (EUR). The most significant SNP at this locus, rs56153133 (CLCN6, purple star), is in high LD with the GWAS SNP rs17367504 (MTHFR) in 1000G EUR. However, this SNP was not significantly associated with diastolic BP in PAGE African Americans, suggesting that it may not be the causal variant (if it is assumed that the causal variant is common to multiple ancestral groups).

Figure D. Fine-mapping regional plots of 15q26.1 SBP Locus in African Americans
SNPs in both Locus Zoom plots reflect AA p-values. LD between the previously reported GWAS SNP, rs2521501/FES (purple star) and other SNPs is shown based on European (panel A) and African (plot B) ancestries. Rs2521501/FES is in high LD in 1000G EUR (r 2 >0.6) with several SNPs shown in red and orange (panel A), which may make it difficult to know which SNP is driving the signal in EUR. LD across the region is reduced in AA and rs2521501/FES is in modest LD with only a few SNPs in AA (r 2 >0.4) and none are even nominally significant in AA (panel B). In AA, the best markers in this region are the FURIN intronic SNPs, rs6224 and rs17514846, and rs116516152 (7.7kb 5' of FURIN); none are strongly correlated with the GWAS SNP in AA, which could suggest that rs2521501/FES (purple star) is less likely to be the functional SNP.

Figure E. Trans-ethnic results: fine-mapping regional plots of the SBP HOTTIP Locus
Plot of the HOTTIP region using p-values from the trans-ethnic analysis (fixed effects model) and LD based on the 1000G EUR sample. The most significant SNP at this locus, rs2023843 (HOTTIP/intron, purple star), is in high LD with other HOTTIP SNPs and in modest LD with a few neighbouring SNPs in EVX1 and the HOXA genes. The GWAS SNPs previously reported in African ancestry samples (rs17428471, rs17471520, and rs11564022) located downstream from EVX1 were not available on the Metabochip, and are not shown. However, LD between rs2023843 and a) rs17428471 or b) rs17471520 is low in both 1000G EUR and AFR, r 2 <0.03.
LD between rs2023843 and rs11564022 is higher in 1000G AFR, r 2 =0.27; it is unclear whether these two SNPs reflect the same signal.

Figure F. Trans-ethnic results: fine mapping regional plots of the SBP FGF5 Locus
Regional plot of the FGF5 region using p-values from the trans-ethnic analysis (fixed effects model) and LD based on the 1000G EUR sample. The most significant trans-ethnic SNP at this locus, rs13125101 (purple diamond), is in high LD with the prior GWAS SNPs rs16998073 and rs11099098 (shown in grey text), and with rs1458038, the top SNP in PAGE Hispanics. It is also in high LD with a novel intronic FGF5 SNP, rs36034102 and a few neighbouring SNPs in the 5`region of FGF5.

PAGE and FBPP Studies
The PAGE consortium includes Hispanic participants from the Hispanic Community Health ARIC is a multi-center cohort of predominantly white and African Americans [5]. ARIC A detailed study protocol is available on the ARIC study website (https://urldefense.proofpoint.com/v2/url?u=https-3A__www2.cscc.unc.edu_aric_&d=CwIFAg&c=Zoipt4Nmcnjorr_6TBHi1A&r=iBSSe3ANUkj PpNQzMcRsTV24Jb8Fi6V1PRcIs4e6qNs&m=fAzniVCF6TuI11xOGNiuKdgD6XsjUMwaVK UfH7TmNuE&s=TAUBClZcTHR2hEvcr9yMo6mtYrMqXbCG_Vlu4oFDSDo&e). BP was measured using a standardized Hawksley random-zero mercury column sphygmomanometer with participants in a sitting position after a resting period of 5 minutes. The size of the cuff was chosen according to the arm circumference. Three sequential recordings for systolic and diastolic blood pressure were obtained; the mean of the last two measurements was used in this analysis.
BP lowering medication use was recorded from the medication history.
WHI is a prospective study investigating post-menopausal women's health [6,7]. and Oakland, CA [8]. Baseline measurements were repeated, and additional measurements performed, at Years 2, 5, 7, 10, 15, and 20. The current analysis included data measured at Year 0 (1985-1986) and only African Americans. Seated BP was measured on the right arm following five minutes rest using a random-zero sphygmomanometer. SBP and DBP were recorded as Phase I and Phase V Korotkoff sounds. Three measurements were taken at 1 minute intervals with the average of the second and third measurements taken for the BP values.

FBPP.
The Family Blood Pressure Program (FBPP), composed of four independent networks without overlap in participants (HyperGEN, GENOA, GenNet, and SAPPHIRe), was established to investigate the genetic determinants of high blood pressure (BP) in multiple ethnic groups [9,10]. Families were ascertained based on higher than normal BP or diagnosed hypertension.