Ancestry-specific associations identified in genome-wide combined-phenotype study of red blood cell traits emphasize benefits of diversity in genomics

Abstract

Background: Quantitative red blood cell (RBC) traits are highly polygenic clinically relevant traits, with approximately 500 reported GWAS loci. The majority of RBC trait GWAS have been performed in European- or East Asian-ancestry populations, despite evidence that rare or ancestry-specific variation contributes substantially to RBC trait heritability. Recently developed combined-phenotype methods which leverage genetic trait correlation to improve statistical power have not yet been applied to these traits. Here we leveraged correlation of seven quantitative RBC traits in performing a combined-phenotype analysis in a multi-ethnic study population.

Results: We used the adaptive sum of powered scores (aSPU) test to assess combined-phenotype associations between ~ 21 million SNPs and seven RBC traits in a multi-ethnic population (maximum n = 67,885 participants; 24% African American, 30% Hispanic/Latino, and 43% European American; 76% female). Thirty-nine loci in our multi-ethnic population contained at least one significant association signal (p < 5E-9), with lead SNPs at nine loci significantly associated with three or more RBC traits. A majority of the lead SNPs were common (MAF > 5%) across all ancestral populations. Nineteen additional independent association signals were identified at seven known loci (HFE, KIT, HBS1L/MYB, CITED2/FILNC1, ABO, HBA1/2, and PLIN4/5). For example, the HBA1/2 locus contained 14 conditionally independent association signals, 11 of which were previously unreported and are specific to African and Amerindian ancestries. One variant in this region was common in all ancestries, but exhibited a narrower LD block in African Americans than European Americans or Hispanics/Latinos. GTEx eQTL analysis of all independent lead SNPs yielded 31 significant associations in relevant tissues, over half of which were not at the gene immediately proximal to the lead SNP.

Conclusion: This work identified seven loci containing multiple independent association signals for RBC traits using a combined-phenotype approach, which may improve discovery in genetically correlated traits. Highly complex genetic architecture at the HBA1/2 locus was only revealed by the inclusion of African Americans and Hispanics/Latinos, underscoring the continued importance of expanding large GWAS to include ancestrally diverse populations.

Keywords: Blood cell traits; Combined-phenotype analysis; Diversity; GWAS; Multi-ethnic; Pleiotropy.

Fig. 1

Identification and characterization of 58 independent lead variants in 39 loci in a multi-ethnic study population. a Lead and conditionally independent SNPs from combined-phenotype analysis of total study population show shared genetic architecture directionally consistent with correlation structure. Colored circles to the right of figure correspond to trait-specific associations. X-axis: rsid (bottom) sorted by chromosome (top) and position; y-axis: significance of association and direction of effect, represented by t-value (scaled to a maximum of t = |15|). Size of circles is exponentially proportional to effect size standardized to trait means (3^Z) to demonstrate differences in average effect size at lead SNPs by trait. Dashed gray lines correspond to genome-wide-significance threshold of a = 5E-09. b RBC trait pair partial correlations among MEGA-genotyped participants adjusted for linear regression model covariates (n = 29,090 for HCT, HGB, and MCHC measurements; n = 22,330 for MCH, MCV, and RBCC; n = 19,573 for RDW). c. Low-frequency and rare alleles exhibit larger magnitude of effect across RBC traits in the total multi-ethnic study population. X-axis: minor allele frequency; y-axis: effect size standardized to trait mean (|Z|). Filled circles represent variants present in all ancestry sub-populations; open circles are monomorphic in one or more ancestries

Fig. 2

Multiple independent associations with MCH demonstrate complex genetic architecture at HBA1/HBA2 locus. All plots: each point represents one SNP; x-axis: increasing position on chromosome 16 left to right; y-axis: -log₁₀(p-value) of the association with MCH. a Regional association plot of 14 independent associations in unadjusted analysis of multi-ethnic study population (n = 41,317). Large circles represent conditionally independent lead SNPs, labeled by rsid (order of conditioning is shown in Table 1); small colored SNPs represent variants in high LD (r² > 0.8 in LD in pooled MEGA subpopulation) with the lead SNP of the corresponding color. b-d Locus-Zoom regional association plots of MCH association with rs60125383 (11th round of conditioning, purple diamond) in African Americans on an African American LD background (b n = 8703), Hispanics/Latinos on a Hispanic/Latino LD background (c, n = 17,380), and European Americans on a European LD background (d n = 14,707). SNP correlation with the lead SNP (r²) is colored according to the legend in (b). Annotated Refseq genes proximal to the lead SNP are shown by position above the X axis