A functional promoter polymorphism of the δ‐globin gene is a specific marker of the Arab‐Indian haplotype

Abstract

Most sickle cell anemia (SCA) patients indigenous to the Eastern Province of Saudi Arabia have their HbS gene on the Arab-Indian (AI) HBB gene cluster haplotype. Their fetal hemoglobin (HbF) levels are near 20% and they have milder disease compared with SCA where the HbS gene is on African origin HBB haplotypes [1][2][3][4][5][6][7][8][9]. The AI haplotype is characterized by an Xmn1 restriction site at position 2158 5 0 to HBG2 (rs7482144), a Hinc2 site 5 0 to HBE (rs3834466) and other polymorphisms [10]. The causal elements that modify HbF might be in linkage disequilibrium with the b S globin gene in this Saudi population. We first performed homozygosity mapping using genome-wide single nucleotide polymorphisms (SNPs) in AI HbS homozygotes [11,12] and identified a single large autozygous region including the HBB cluster and surrounding genes. By next generation sequencing, we examined this region in these same individuals and identified several variants that included a SNP in the HBD promoter region at position 268 bp 5 0 to HBD (CCAAC > TCAAC). We found this SNP only when the HbS gene was on an AI haplotype and not in SCA with other haplotypes. This SNP was functional in reporter assays in K562 cells and is an AI haplotype-specific marker. Table I summarizes the patient characteristics. Using genome-wide SNP data from a limited number of cases, a region of autozygosity was found only in AI HbS homozygotes on chromosome 11 (coordinates 5,196,450-5,323,071). The region contains HBD, HBG1, HBG2, HBE1, and the Xmn1 5 0 HBG2 restriction site (rs7482144). By targeted deep sequencing of 400 kb of chromosome 11 (coordinates 5,143,424-5,543,424; average coverage 42x) in 4 AI patients 1,195 variants were found. A homozygous C-T variant 268 bp 5 0 HBD with high genotyping and mapping quality that was not in dbSNP build 135 or 1,000 Genomes, was present. Resequencing of 15.9 kb of chr11 (coordinates 5,253,531-5,269,435) by Sanger sequencing detected three new SNPs of which one was the 268 C > T SNP. We focused on this SNP because of its location within the Corfu deletion region and its location in the HBD promoter.The C > T SNP in the HBD promoter was found only in individuals with the AI haplotype. Saudi sickle cell trait carriers with the AI haplotype were heterozygous for this SNP; while siblings without HbS did not carry this mutation. Among 25 AI HbS-b 0 thalassemia patients, 16 were heterozygous at this site (C/T) and 9 were homozygous (T/T). All AI HbS-b 0 thalassemia patients who were homozygous T/T were also homozygous for the AI haplotype (Table I). Fifteen African American SCA patients with unusually high HbF, 54 Saudi SCA patients from the Southwestern Province (SW)-mainly Benin but including subjects with the Senegal haplotype-19 SW HbS-b 0 thalassemia patients, 16 SW sickle cell trait cases, and 25 normal Saudi controls did not carry the 268 HBD SNP. This SNP was not found in 1,094 individuals in 1,000 Genomes May 2011 release. It is important to note that hemoglobin electrophoresis results in Table I wer...

Phyto-Medicine in Gene(s) Targeting Future Direction for Sickle Cell Disease Management

“…Further, the AI haplotype is characterized by the presence of both Xmn1, Hinc2 restriction endonuclease site and, insertion-deletion polymorphism [19]. Moreover, association between the XmnI polymorphism (rs7482144) in the proximal promoter of the Gα-globin (HBG2) gene and HbF levels is well established in SCD patients [24,25].…”

“…Some other study on the AI haplotype, genetic association protocol [25,26] was used to pinpoint HbF variant (rs4671393) in an intron of the BCLIIA gene (B-cell lymphoma/leukemia IIA), a gene expressed in erythrocyte precursors and implicated in lymphoid malignancies [15,26,27], have the strongest effect bearing, its importance in the control switching of HbF to HbA. Further AI haplotype mapping had long revealed three other single nucleotide polymorphisms (SNPs) (rs28384513, rs9399137 and rs4895441) located in the intergenic region 5' to HBS1L and the MYB (family of transcription factors operational e.g.…”

“…Common variant within these three blocks had been shown to account for levels of fetal cell (FC) counts. This was mapped to the 6q23 locus, as seen in a European sample study [14,[25][26][27]. However, LD patterns at this genomic region seem different between populations of different race (European and African), origin [26,[28][29][30][31].…”

“…However, LD patterns at this genomic region seem different between populations of different race (European and African), origin [26,[28][29][30][31]. Using such findings, insights can be gained from populations of different race, replicate and refine genetic association signals [25,26,28]. This strategy was instrumental, for the identification of an additional SNP (rs4895441) with good predictive power for pain crisis combined with acute chest syndrome (ACS) rates in SCD [25].…”

“…Using such findings, insights can be gained from populations of different race, replicate and refine genetic association signals [25,26,28]. This strategy was instrumental, for the identification of an additional SNP (rs4895441) with good predictive power for pain crisis combined with acute chest syndrome (ACS) rates in SCD [25]. The MYB gene is well studied for its role in hematopoiesis; however, HBS1L is a poorly characterized gene with yet unknown biological functions [26,28,31].…”