Genome-wide association study identifies genetic loci associated with iron deficiency

Abstract

The existence of multiple inherited disorders of iron metabolism in man, rodents and other vertebrates suggests genetic contributions to iron deficiency. To identify new genomic locations associated with iron deficiency, a genome-wide association study (GWAS) was performed using DNA collected from white men aged≥25 y and women≥50 y in the Hemochromatosis and Iron Overload Screening (HEIRS) Study with serum ferritin (SF)≤12 µg/L (cases) and iron replete controls (SF>100 µg/L in men, SF>50 µg/L in women). Regression analysis was used to examine the association between case-control status (336 cases, 343 controls) and quantitative serum iron measures and 331,060 single nucleotide polymorphism (SNP) genotypes, with replication analyses performed in a sample of 71 cases and 161 controls from a population of white male and female veterans screened at a US Veterans Affairs (VA) medical center. Five SNPs identified in the GWAS met genome-wide statistical significance for association with at least one iron measure, rs2698530 on chr. 2p14; rs3811647 on chr. 3q22, a known SNP in the transferrin (TF) gene region; rs1800562 on chr. 6p22, the C282Y mutation in the HFE gene; rs7787204 on chr. 7p21; and rs987710 on chr. 22q11 (GWAS observed P<1.51×10(-7) for all). An association between total iron binding capacity and SNP rs3811647 in the TF gene (GWAS observed P=7.0×10(-9), corrected P=0.012) was replicated within the VA samples (observed P=0.012). Associations with the C282Y mutation in the HFE gene also were replicated. The joint analysis of the HEIRS and VA samples revealed strong associations between rs2698530 on chr. 2p14 and iron status outcomes. These results confirm a previously-described TF polymorphism and implicate one potential new locus as a target for gene identification.

Figure 1. Manhattan plots displaying results from GWAS for eight iron outcomes.

(A) iron deficient case-control status, (B) body iron (C) serum iron, (D) Log_e(SF), (E) Log_e(TfS), (F) Log_e(sTfR), (G) TIBC, and (H) UIBC.

Figure 2. High resolution association analysis of GWAS samples for chromosome 2p14.

Analysis includes measured genotypes from 21 SNPs and imputed genotypes from 108 SNPs. A. Genome-wide statistical significance is represented by the dashed line corresponding to an observed p-value of 1.51×10⁻⁷. For unsaturated iron-binding capacity (UIBC), the most significant association was with rs2698530 (▴) with an observed p-value = 8.31×10⁻⁸. For total iron-binding capacity (TIBC), the most significant association was with rs2698527 (•) with an observed p-value = 2.73×10⁻⁷. B. The heat graph was generated from pairwise LD coefficients D', calculated from the HapMap genotype data for all 129 SNPs. Recombination hotspots are indicated by black bars. C. The location of the region on chromosome 2p14, with approximate position and size of neary genes is shown.

Figure 3. High resolution association analysis of GWAS samples for chromosome 3q22.

The analysis includes measured genotypes from 40 SNPs and imputed genotypes from 220 SNPs. The location and structure of the TF gene is shown along the top of the figure. The most significant associations with total iron-binding capacity (TIBC, •) and unsaturated iron-binding capacity (UIBC, ▴) were observed with the measured SNP rs3811647, with observed p-values of 9.55×10⁻⁹ and 7.28×10⁻⁶ for TIBC and UIBC, respectively. The most statistically significant associations were observed at five SNPs across the 7 kbp region (delineated) which includes exons 9, 10, and 11 of the transferrin gene, TF.