Genetic modifiers of Hb E/[beta].sup.0 .sup.thalassemia identified by a two-stage genome-wide association study

First, we estimated and compared the allele frequencies of approximately 110,000 gene-based single nucleotide polymorphisms (SNPs) in pooled DNAs from different severity groups. The 756 SNPs that showed reproducible allelic differences at P [less than] 0.02 by pooling were selected for individual genotyping. After adjustment for age, gender and geographic region, logistic regression models showed 50 SNPs significantly associated with disease severity (P [less than] 0.05) after Bonferroni adjustment for multiple testing. Forty-one SNPs in a large LD block within the [beta]-globin gene cluster had major alleles associated with severe disease. The most significant was bthal_bg200 (odds ratio (OR) = 5.56, P = 2.6 x 10.sup.-13.sup.). Seven SNPs in two distinct LD blocks within a region centromeric to the [beta]-globin gene cluster that contains many olfactory receptor genes were also associated with disease severity; rs3886223 had the strongest association (OR = 3.03, P = 3.7 x 10.sup.-11.sup.). Several previously unreported SNPs were also significantly associated with disease severity. These results suggest that there may be an additional regulatory region centromeric to the [beta]-globin gene cluster that affects disease severity by modulating fetal hemoglobin expression.