Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits

Abstract

Red blood cell (RBC) traits are important heritable clinical biomarkers and modifiers of disease severity. To identify coding genetic variants associated with these traits, we conducted meta-analyses of seven RBC phenotypes in 130,273 multi-ethnic individuals from studies genotyped on an exome array. After conditional analyses and replication in 27,480 independent individuals, we identified 16 new RBC variants. We found low-frequency missense variants in MAP1A (rs55707100, minor allele frequency [MAF] = 3.3%, p = 2 × 10(-10) for hemoglobin [HGB]) and HNF4A (rs1800961, MAF = 2.4%, p < 3 × 10(-8) for hematocrit [HCT] and HGB). In African Americans, we identified a nonsense variant in CD36 associated with higher RBC distribution width (rs3211938, MAF = 8.7%, p = 7 × 10(-11)) and showed that it is associated with lower CD36 expression and strong allelic imbalance in ex vivo differentiated human erythroblasts. We also identified a rare missense variant in ALAS2 (rs201062903, MAF = 0.2%) associated with lower mean corpuscular volume and mean corpuscular hemoglobin (p < 8 × 10(-9)). Mendelian mutations in ALAS2 are a cause of sideroblastic anemia and erythropoietic protoporphyria. Gene-based testing highlighted three rare missense variants in PKLR, a gene mutated in Mendelian non-spherocytic hemolytic anemia, associated with HGB and HCT (SKAT p < 8 × 10(-7)). These rare, low-frequency, and common RBC variants showed pleiotropy, being also associated with platelet, white blood cell, and lipid traits. Our association results and functional annotation suggest the involvement of new genes in human erythropoiesis. We also confirm that rare and low-frequency variants play a role in the architecture of complex human traits, although their phenotypic effect is generally smaller than originally anticipated.

Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals

“…18 showed association with WBC-related traits (p < 0.0001) ( Table 4). To explore possible shared genetic associations of platelet size/number with platelet reactivity, we examined the association of PLT/MPV-associated SNVs with platelet reactivity to collagen, epinephrine, and ADP in GeneSTAR and FHS.…”

“…As the BCX is interested in the genetics of common hematological measures, our collaborative group is divided into three main working groups: RBC, WBC, and platelet. 18,19 For the platelet working group, our sample is comprised of 157,293 participants from 26 discovery and replication cohorts of five ancestries: European (EA), African American (AA), Hispanic, East Asian, and South Asian. Detailed descriptions of the participating cohorts are provided in the Tables S1-S4.…”

Large-Scale Exome-wide Association Analysis Identifies Loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases

“…Similarly, to assess whether the WBC variants were associated with other blood cell traits, we obtained effect sizes and p values for these variants from RBC-and platelet-related traits exome array analyses within the BCX consortium. 32,33 …”

An erythroid-specific ATP2B4 enhancer mediates red blood cell hydration and malaria susceptibility

“…Well-established cell-culture protocols exist to monitor proliferation and differentiation. Furthermore, GWAS have already revealed more than 100 loci associated with the number, size, or hemoglobin content of rbc (6,7). Fine mapping these genetic associations with rbc traits promises not only to provide new illustrations of how noncoding variants influence complex phenotypes through effects on gene expression, but to also reveal genes that control rbc biology in health and disease.…”