High-density SNP genotyping to define β-globin locus haplotypes

Abstract

Five major β-globin locus haplotypes have been established in individuals with sickle cell disease (SCD) from the Benin, Bantu, Senegal, Cameroon, and Arab-Indian populations. Historically, β-haplotypes were established using restriction fragment length polymorphism (RFLP) analysis across the β-locus, which consists of five functional β-like globin genes located on chromosome 11. Previous attempts to correlate these haplotypes as robust predictors of clinical phenotypes observed in SCD have not been successful. We speculate that the coverage and distribution of the RFLP sites located proximal to or within the globin genes are not sufficiently dense to accurately reflect the complexity of this region. To test our hypothesis, we performed RFLP analysis and high-density single nucleotide polymorphism (SNP) genotyping across the β-locus using DNA samples from either healthy African Americans with normal hemoglobin A (HbAA) or individuals with homozygous SS (HbSS) disease. Using the genotyping data from 88 SNPs and Haploview analysis, we generated a greater number of haplotypes than that observed with RFLP analysis alone. Furthermore, a unique pattern of long-range linkage disequilibrium between the locus control region and the β-like globin genes was observed in the HbSS group. Interestingly, we observed multiple SNPs within the HindIII restriction site located in the Gγ-globin intervening sequence II which produced the same RFLP pattern. These findings illustrated the inability of RFLP analysis to decipher the complexity of sequence variations that impacts genomic structure in this region. Our data suggest that high density SNP mapping may be required to accurately define β-haplotypes that correlate with the different clinical phenotypes observed in SCD.

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

“…In the present study of over 800 individuals homozygous for the sickle mutation, we used high density SNP mapping to perform a detailed analysis of this region in individuals participating in a clinical trial. We observed a striking pattern of very high LD across a large region of the β S ‐globin locus, supporting the idea that β S ‐haplotypes are conserved over long genomic distances due to selective pressure (Hanchard et al , ; Liu et al , ). In spite of typing over one hundred SNPs at the β‐globin locus, we identified three predominant haplotypes that accounted for the majority of the β S ‐chromosomes in this population, similar to previous RFLP studies that report Benin, CAR, and Senegal as the most prevalent haplotypes in populations in the United States (Hattori et al , ; Schroeder et al , ; Powars, ).…”

“…Previous reports of high‐density genomic analysis of the HBB cluster were performed in small numbers of individuals with HbSS and did not consider disease severity (Hanchard et al , ; Liu et al , ). In the present study of over 800 individuals homozygous for the sickle mutation, we used high density SNP mapping to perform a detailed analysis of this region in individuals participating in a clinical trial.…”

Beta-Globin Gene Haplotypes Among Cameroonians and Review of the Global Distribution: Is There a Case for a Single Sickle Mutation Origin in Africa?

“…More recently, a specific atypical haplotype in Tunisia was considered by authors as specific to the Tunisian chromosome b(S) (Imen et al, 2011). In the case of the Cameroon and Tunisia, these specific haplotypes were likely generated by a variety of genetic mechanisms including (a) isolated nucleotide changes in one of the polymorphic restriction sites, (b) simple and double crossovers between two typical b(S) haplotypes, or much more frequently between a typical b(S) haplotype and a different b(A)-associated haplotype that was present in the population, and (c) gene conversions (Zago et al, 2000)-all of which have been observed at the beta-globin locus (Borg et al, 2009;Holloway et al, 2006;Liu et al, 2009;Neumann et al, 2010;Patrinos et al, 2005;Sankaran et al, 2011).…”

Evolutionary Constraints in the β-Globin Cluster: The Signature of Purifying Selection at the δ-Globin (HBD) Locus and Its Role in Developmental Gene Regulation

“…One possible explanation for this apparent inconsistency could be that genetic variation has been more exhaustively assessed for HBB than for HBD . Even though the β-globin cluster is among the most extensively studied regions in the human genome, current genetic diversity estimates for the HBD and HBB genes across human populations are likely to be biased, because the genetic analysis of HBD and HBB has been performed mainly for diagnostic purposes and often based on a set of pre-ascertained single nucleotide polymorphisms (SNPs) (Morgado et al 2007; Lacerra et al 2008; Liu et al 2009; Phylipsen et al 2011). …”