Homozygosity for a haplotype in the HBG2‐OR51B4 region is exclusive to Arab‐Indian haplotype sickle cell anemia
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To the Editor: Homozygosity for rs334 (GAG-GTG, glu6val) or sickle cell anemia is common in Saudi Arabia. In the Eastern Province the sickle hemoglobin (HbS) gene is usually on the autochthonous Arab Indian (AI) β-globin gene (HBB) haplotype 1. The higher fetal hemoglobin (HbF) level in the AI haplotype is often associated with milder disease compared with other HbS-associated haplotypes, especially in children 2, 3. The Xmn1 G-A (C-T) polymorphism (rs7482144) is present in both the AI haplotype and the Senegal haplotype. Rs10128556, which is in linkage disequilibrium (LD) with rs7482144, could be the functional SNP of the Senegal haplotype 4. The minor alleles of these SNPs also characterize the AI haplotype where adults had ∼20% HbF compared with ∼10% HbF in the Senegal haplotype. This suggests that elements linked to rs10128556 and rs7482144 in the AI but not the Senegal haplotype might affect HbF gene expression. We compared the genome-wide distribution of SNPs in Saudi patients with the AI haplotype and Benin haplotype. Variants distinguishing these populations were limited to chromosome 11p15.5. Annotation of these SNPs narrowed the selection to three that we analyzed jointly using haplotype analysis. Homozygosity for a T/A/T haplotype of rs16912979 (in HS-4 of the LCR), rs7482144 and rs10128556 was exclusive to the AI haplotype. The AI haplotype might include a functionally important sub-haplotype that accounts for high HbF. We recruited 245 sickle cell disease patients from the Eastern and Southwestern Provinces of Saudi Arabia for a genome-wide association study (GWAS). Forty-two AI (cohort 1) and 71 Benin cases were compared. Sixty-two additional 62 AI Saudi cases (cohort 2) and 41 Indian AI haplotype cases were studied by GWAS or targeted SNP analysis 5, 6. Fourteen Saudi AI haplotype homozygotes had whole genome sequencing (WGS) including seven AI homozygotes with high and seven with low HbF, three Indian AI homozygotes, three African American Benin haplotype homozygotes selected because of unusually high HbF 7, and one African American Senegal haplotype homozygote. GWAS in 339 African American HbS homozygotes of diverse haplotypes examined the presence of SNPs found in the Saudi cohorts 8. (Tables 1 and 2). The AI haplotype was ascertained directly by genotyping rs7482144, rs3834466, and rs549964658; other haplotypes were determined as described 6, 10, 11. GWAS: Genotyping used Illumina SNP arrays 8. To capture all SNPs in the HBB gene cluster region, SHAPEIT and IMPUTE2 were used to impute non-genotyped SNPs using reference files from the 1000 Genome phase I database 12. Only variants with a quality score threshold of ≥0.90, a minor allele frequency (MAF) difference >0.85 between the Saudi AI cohort1 and Saudi Benin haplotype cohorts, and SNPs annotated with RegulomeDB that were examined only in blood cells were included in our final analysis (Fig. S1 Supporting Information). Paired-end 100 bp reads were sequenced on the Illumina HiSeq 2000 platform to a depth of 40× per individual (Supporting Information) 13, 14. Amplification refractory mutation system (ARMS) was used to genotype rs16912979 in 41 AI haplotype Indian HbS homozygotes (Supporting Information). Transcription factor binding data sets from the RegulomeDB of the ENCODE Consortium and Roadmap Epigenomics Project were searched for enhancer marks and transcription factor binding in blood cells 15. Analysis was done in PLINK using logistic regression with additive coding of the SNPs 16. Genomic control (GC) approach corrected the genomic inflation caused by sub-population stratification. QQ plots and genomic control estimates were generated using R (Fig. S2 Supporting Information). Regional association plots were generated by the LocusZoom 17. Haplotype analysis was conducted using the haplostats package in the R software as described 18 (Supporting Information). Two hundred-twenty three variants in chromosome 11p15.5 from positions 3.5–6.5 mb distinguished Saudi AI (cohort 1) and Benin cases (P-values 9.6E-07-2.7E-45). (Fig. 1A and Table SI Supporting Information). Thirteen SNPs were present in all Saudi AI haplotype but rare in the Saudi Benin haplotype (allele frequency < 0.05) (Table SII and Fig. S3 Supporting Information). These results were replicated in the 62 AI haplotype cohort 2 cases and in 14 Saudi and three Indian cases genotyped by WGS. The 13 SNPs were not present in the three high HbF African American Benin and 1 Senegal haplotype samples and were rare or absent in 93 Senegal and 606 Benin haplotype chromosomes. A regional LD plot for rs16912979 is shown in Fig. S4 Supporting Information. MAF of SNPs in MYB, BCL11A and KLF1 were similar in AI and Benin haplotype cohorts. A: Manhattan plot from the GWAS comparing Saudi Eastern AI versus Saudi Southwestern Benin haplotype patients. P-values (−log10 P) of 599,131 SNPs after correction by Genomic Control is plotted against its physical chromosomal position. Odd chromosomes
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The AI haplotype in Saudi patients is associated with a unique pattern of SNPs in putative cis-acting globin regulatory elements and is linked to a novel variant in ANTXR1.
“The AI haplotype in Saudi patients is associated with a unique pattern of SNPs in putative cis-acting globin regulatory elements and is linked to a novel variant in ANTXR1.40,41”
From Fetal hemoglobin in sickle cell anemia (2020) · cites this paper as [40]
The Results (“A unique AI haplotype”) and Discussion describe a distinctive SNP haplotype in Saudi AI patients that may involve cis-acting globin regulatory elements. The paper does not report a link to a novel ANTXR1 variant; a search for ANTXR1 found no matching passage in our copy. Page numbers were not provided. (LLM, conf=0.88)
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- Authors
- Vathipadiekal, V., Alsultan, A., Baltrusaitis, K., Farrell, J. J., Al‐Rubaish, A. M., Al‐Muhanna, F., Naserullah, Z., Suliman, A., Patra, P. K., Milton, J. N., Farrer, L. A., Chui, D. H. K., Al‐Ali, A. K., Sebastiani, P., & Steinberg, M. H.
- Affiliations
- Boston University (US)
- King Saud University (SA)
- Imam Abdulrahman Bin Faisal University (SA)
- Maternity and Children's Hospital (SA)
- King Faisal University (SA)
- Pt. Jawahar Lal Nehru Memorial Medical College (IN)
- Department of Biostatistics Boston University School of Public Health Boston Massachusetts
- Corresponding author
- Steinberg, Martin. H.
- ORCID
- Venue
- American Journal of Hematology
- Publisher
- Wiley
- Published
- 2016-04-28
- Volume
- 91
- Issue
- 6
- Pages
- E308-11
- ISSN
- 0361-8609 (ISSN-L)
- 1096-8652
- PMC
- PMC4874527
- OpenAlex
- W2298548348
- Cited by
- 15
- References
- 34
- Citations by year
- 2024: 1 · 2022: 3 · 2021: 1 · 2020: 3 · 2019: 1 · 2018: 1 · 2017: 3 · 2016: 2
- FWCI
- 1.69
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- American Journal of Hematology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Heart, Lung, and Blood Institute (R01HL087681, R01HL068970, RC2HL101212, U01HL107443, T32HL007501)
- National Institute of General Medical Sciences (T32GM074905)
- Topics
- Health Sciences › Medicine › Genetics › Hemoglobinopathies and Related Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Hemoglobin structure and function
- Keywords
- sickle cell disease, fetal hemoglobin, haplotype homozygosity, linkage disequilibrium, Saudi Arabia, haplotype analysis, genome-wide association study
- MeSH terms
- Adolescent, Adult, Anemia, Sickle Cell, Fetal Hemoglobin, Haplotypes, Homozygote, Humans, Arabs, Polymorphism, Single Nucleotide, Genome-Wide Association Study, gamma-Globins, Young Adult
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