Acute chest syndrome is associated with single nucleotide polymorphism-defined beta globin cluster haplotype in children with sickle cell anaemia

Abstract

Genetic diversity at the human β-globin locus has been implicated as a modifier of sickle cell anaemia (SCA) severity. However, haplotypes defined by restriction fragment length polymorphism sites across the β-globin locus have not been consistently associated with clinical phenotypes. To define the genetic structure at the β-globin locus more thoroughly, we performed high-density single nucleotide polymorphism (SNP) mapping in 820 children who were homozygous for the sickle cell mutation (HbSS). Genotyping results revealed very high linkage disequilibrium across a large region spanning the locus control region and the HBB (β-globin gene) cluster. We identified three predominant haplotypes accounting for 96% of the β(S) -carrying chromosomes in this population that could be distinguished using a minimal set of common SNPs. Consistent with previous studies, fetal haemoglobin level was significantly associated with β(S) -haplotypes. After controlling for covariates, an association was detected between haplotype and rate of hospitalization for acute chest syndrome (ACS) (incidence rate ratio 0·51, 95% confidence interval 0·29-0·89) but not incidence rate of vaso-occlusive pain or presence of silent cerebral infarct (SCI). Our results suggest that these SNP-defined β(S) -haplotypes may be associated with ACS, but not pain or SCI in a study population of children with SCA.

Keywords: acute chest syndrome; genetic analysis; haplotype; sickle cell anaemia; β-globin.

Figure 1

Linkage disequilibrium across the β-globin locus in SIT Trial participants with sickle cell anaemia. Haploview Version 4.2 visualization of LD (D′) is shown for 22 SNPs with minor allele frequencies >5% genotyped on the HumanOmni1-Quad BeadChip. The calculated D′ for pairwise comparisons between SNPs is displayed in each box as the decimal value between 0 and 99, and blank boxes represent complete LD (D′ = 1). The relative positions of the β-globin cluster genes compared to the SNPs genotyped along chromosome 11p15.4 are indicated by blue arrows.

Figure 2

Fetal haemoglobin (HbF) levels by haplotype group in SIT Trial participants (n=479). Mean HbF (filled circle) and standard error (horizontal bar) is shown with number of individuals (n) in each haplotype pair group indicated. For statistical analyses, H2,H2 and H1,H2 were grouped together, and H3,H3 and H1,H3 were grouped together. Kruskal-Wallis non-parametric testing demonstrated a significant difference in the sample means (p=0.006). To test the association with haplotype, HbF was log transformed and multiple linear regression models were adjusted for age and gender. Carrying one or two copies of H2 was associated with a decreased HbF (7.4%) compared to the 8.8% level in the H1,H1 reference group (95% confidence interval [CI]: 0.72–0.98; p=0.01). Conversely, carrying one or two copies of H3 was associated with increased HbF (10.5%) compared to the H1,H1 reference group (95% CI: 1.02–1.39; p=0.05).