Β-globin Gene Cluster Haplotypes Research Articles

Beta Globin Gene Cluster Haplotypes in Beta Thalassemia in the Kurdistan Region of Iraq

β-thalassemia is a prevalent inherited red cell disorder in the Kurdistan region of Iraq. To determine the chromosomal background of the frequent β-thalassemia mutations in the latter region, we investigated the β-globin gene cluster haplotypes in 202 β-thalassemia chromosomes. Haplotypes analysis utilized restriction fragment length polymorphism-PCR of seven restriction sites through the β-globin gene cluster. It was observed that IVS-II-1 (G > A) was mainly associated with haplotype III (68.8%), IVS-1-110 (G > A), codon 8/9 (+G) and codon 44 (-C) with haplotype I (in 90.0%, 100%, and 62.5% respectively), IVS-1-6 (T > C) with haplotype VI (97.4%), codon 8 (-AA) with haplotype IV (75%), codon 5(-CT) and IVS1.1 (G > A) with haplotype V (55.6% and 58.3% respectively), while codon 39 (C > T) and IVS1.5 (G > C) were mainly associated with haplotype VII (85.7% and 75% respectively). These observations support the notion that while some mutations may have originated in the Kurdistan region, others were more likely brought in by gene flow from neighboring countries or the Indian subcontinent. The association of some β-thalassemia defects with more than one haplotype may be due to mutations or recombination events.

Association of β-Globin Gene Haplotypes with Haematological Parameters and Foetal Haemoglobin among Patients with Sickle Cell Disorder in Raipur, Chhattisgarh, India

Introduction: Sickle cell disease is caused by a single nucleotide substitution in the β-globin gene. The variations in Foetal Haemoglobin (HbF) levels, β-globin gene cluster haplotype have been used as predictors of disease severity in sickle cell disease patients. Aim: To determine the frequency of β-globin gene haplotypes in sickle cell disease patients and also to establish their association with haematological parameters and HbF. Materials and Methods: The present cross-sectional study was conducted in Department of Biochemistry, Government Medical College, Jagdalpur, Chhattisgarh, India, in collaboration with Department of Biotechnology, Government Nagarjuna PG College of Science, Raipur, Chhattisgarh, India, from April 2021 to May 2022. A total of 100 patients with Sickle Cell Disease (SCD) and 50 with sickle cell traits were included in the study. Haplotypes were identified by Restriction Fragment Length Analysis (RFLP) method for seven polymorphic sites in β-globin gene cluster. Haematological parameters such as Hb, Haematocrit (HCT), Mean Cell Volume (MCV), Mean Cell Haemoglobin (MCH) and HbF levels were estimated. Data was analysed using various statistical tests such as ShapiroWilk test, Levene’s test, student t-test, Mann-Whitney test and Kruskal-Wallis tests as per analysis requirement. Results: In the present study, 51 (51%) males and 49 (49%) females were in sickle cell disease group (SS), while 25 (50%) males and 25 (50%) females were in sickle cell trait group (AS). The mean age of the sickle cell disease patients was 23.84±8.38 years and for sickle cell trait group was 26.3±7.37 years. There was a significant difference (p-value <0.0001) in HbF levels among haplotypes. Additionally, higher HbF concentration was found in Arab-Indian haplotypes in SCD patients. No significant association was observed between the haplotypes and haematological parameters. Conclusion: The findings suggested that haematological parameters were not significantly associated with β-globin gene haplotypes. The β-globin gene haplotypes influence the HbF levels in sickle cell patients.

Haplotype analysis of Bangladeshi β-thalassaemia patients: A pilot study

β-thalassaemia is one of the major genetic disorders in Bangladeshi population. Nevertheless, systematic study on the genetic basis of this disease in Bangladeshi population is very limited. The major aim of this study was to identify and characterize the β-globin gene cluster haplotype in Bangladeshi β-thalassaemia patients. For this, β-thalassaemia patients diagnosed on haematological observations were tested at the genetic level for different β-globin cluster haplotypes. Twenty-eight β-globin gene clusters of fourteen confirmed β-thalassaemia patients were analyzed using PCR amplification and Restriction Fragment Length Polymorphism (RFLP). Type VII haplotype was found to be the most common β-globin gene cluster haplotype in the studied population. Two of the patients had Type VII haplotype in homozygous form. Only one patient had atypical haplotype in one locus. The study reports β-globin cluster haplotype of fourteen Bangladeshi patients for the first time. However, it should be noted that small size precludes the possibility of determining the detailed distribution of different haplotypes and their association with different β-thalassaemia mutations. Dhaka Univ. J. Biol. Sci. 30(3 CSI): 479-486, 2022 (June)

Profiling of 35 Cases of Hb S/Hb E (HBB: c.20A>T/HBB: c.79G>a), Disease and Association with α-Thalassemia and β-Globin Gene Cluster Haplotypes from Odisha, India

Hb S/Hb E (HBB: c.20A>T/HBB: c.79G>A) is an uncommon variant of sickle cell disease resulting from coinheritance of Hb S and Hb E. Clinico-hematological and biochemical parameters of 35 cases of Hb S/Hb E disease were studied and compared with 70 matched cases of homozygous sickle cell disease (Hb SS) and Hb S/β-thalassemia (β-thal) with IVS-I-5 (G>C) (HBB: c.92+5G>C). The influence of α-thal and that of of β-globin gene cluster haplotypes among Hb S/Hb E disease was also studied. Statistical analysis was done using GraphPad InStat version 3.06. Of the 35 cases, 20 (57.14%) had a moderate clinical presentation. Mean lactate dehydrogenase (LDH) level, vaso-occlusive crises (VOCs) per year, and annual blood transfusion requirements were significantly lower in Hb S/Hb E cases than in the other two groups. The hemoglobin (Hb) and packed cell volume (PCV) levels were significantly high in Hb S/Hb E cases with α-thal and these cases were associated with microcytic-hypochromic anemia. α-Thalassemia did not influence clinical presentation in Hb S/Hb E cases. The β-globin gene cluster haplotypes of 70 alleles of Hb S/Hb E revealed an association of five typical haplotypes [Arab-Indian (A-I), Benin, Bantu, Cameroon and Senegal] in 95.71% cases. Hb S/Hb E disease exhibit asymptomatic to moderate phenotypic expression. However, further in-depth studies on Hb S/Hb E will help in reducing the disease burden especially in high-risk countries like India.

Fetal Hemoglobin Mediates the Effect of Beta Globin Gene Polymorphisms on Neurocognitive Functioning in Sickle Cell Disease

Background: Fetal hemoglobin (HbF) is the most influential modifier of the clinical and hematologic phenotype of sickle cell disease (SCD) and is highly heritable. Low HbF is independently associated with increased white matter changes on brain imaging and poorer performance on neurocognitive measures (Ruffiuex, Child Neuropsychology, 2013). Our previous work has shown that 11 SNPs in three genes (BCL11A, MYB, and β-globin), contribute over 20% of the variance in HbF (Rampersaud, Kang. et al., 2020, under review). Clinically, these HbF-associated SNPs are associated with disease severity and frequency of pain events. However, the neurocognitive implications of these SNPs have yet to be explored. As part of a prospective longitudinal cohort study, the Sickle Cell Clinical Research and Intervention Program (SCCRIP), we evaluated the relationship between HbF-associated SNPs and neurocognitive functioning in SCD patients. Methods: We included 257 patients with SCD (69% HbSS/HbSβ0-thalassemia). The median age of participants was 13 years (range 4 - 25). We extracted genotypes for the 11 HbF-associated SNPs from whole genome sequencing data and analyzed them based on an additive genetic model. Following informed consent, patients completed a battery of gold-standard neurocognitive measures, supervised by a psychologist, assessing IQ, verbal and perceptual reasoning, working memory, processing speed, sustained attention, and executive functioning skills. HbF was the average value of measurements collected within 3 months of neurocognitive assessment, or the closest value. In univariate analyses, Kruskal-Wallis rank sum test was used to assess the associations of the 11 HbF-associated SNPs with neurocognitive measures. Linear regression was used to examine these associations adjusting for age, sickle genotype, hydroxyurea exposure, socioeconomic status (index of social vulnerability) and 5 principal components to adjust for population stratification. Benjamini and Hochberg false discovery rate (FDR) was used for multiple corrections and FDR adjusted p (pFDR)<0.05 was considered significant for all analyses. Mediation analyses (Imai, Psychological Methods, 2010) were used to evaluate the indirect effects of HbF-associated SNPs on neurocognitive outcomes via HbF. Results: One SNP in the β-globin gene, rs968857, was associated with performance on measures of IQ, verbal reasoning, working memory, and executive functioning by Kruskal-Wallis rank sum test (Figure 1) and by linear regression adjusting for covariates listed above at pFDR <0.05. HbF expression was positively associated with IQ and verbal reasoning scores at pFDR <0.05 using linear regression adjusting for age, sickle genotype, hydroxyurea exposure, and socioeconomic status. HbF mediated the relationship between rs968857 and scores on IQ and verbal reasoning measures at pFDR <0.05 (Figure 2). The direct effect of rs968857 on neurocognitive functioning remained significant following inclusion of HbF at pFDR <0.05, indicating partial mediation. Full linear regression models with rs968857, HbF, and covariates accounted for 10.8%, 14.5%, 6.4%, and 8.3% of the variance in IQ, verbal reasoning, working memory, and executive functioning measures, respectively. Conclusions: This is the first study to demonstrate a relationship between genetic modifiers of SCD and neurocognitive functioning. Beyond findings on neuroimaging and sociodemographic factors, there is little known about risk for neurocognitive deficits in SCD. The present results suggest an influence of SNP rs968857 on cognitive function, which was partially mediated by expression of HbF. rs968857, is one of four SNPs that defines almost all β-globin gene cluster haplotypes and influences HbF levels in SCD. How this SNP effects HbF and neurocognition is unknown and requires further investigation of its mechanism. The highly heritable nature of HbF may allow for future use of precision medicine. SCD patients could be stratified according to risk for neurocognitive deficits to utilize early intervention strategies, informed by genetic polymorphisms. Correlation with neuroimaging will help further elucidate the relationship between genetic modifiers and neurocognitive functioning. Future trials with larger samples are needed to validate our findings and investigate if the observed relationships differ by age or hydroxyurea treatment status. Disclosures Estepp: Daiichi Sankyo, Esperion, Global Blood Therapeutics: Consultancy; Global Blood Therapeutics, Forma Therapeutics, Pfizer, Eli Lilly and Co: Research Funding; ASH, NHLBI: Research Funding. King:Amphivena Therapeutics: Research Funding; Bioline: Consultancy; Celgene: Consultancy; Cell Works: Consultancy; Incyte: Consultancy; Magenta Therapeutics: Membership on an entity's Board of Directors or advisory committees; Novimmune: Research Funding; RiverVest: Consultancy; Tioma Therapuetics: Consultancy; WUGEN: Current equity holder in private company. Hankins:Novartis: Research Funding; National Heart, Lung, and Blood Institute: Honoraria, Research Funding; UptoDate: Consultancy; Global Blood Therapeutics: Consultancy, Research Funding; MJH Life Sciences: Consultancy, Patents & Royalties; American Society of Pediatric Hematology/Oncology: Honoraria; LINKS Incorporate Foundation: Research Funding.

Interactions of unstable hemoglobin Rush with thalassemia and hemoglobin E result in thalassemia intermedia

ABSTRACTBackground: The clinical consequences and significance of many unstable hemoglobins interacting with other hemoglobinopathies remain unrecognized. Here we first explore molecular and hematological characterizations of previously undescribed compound heterozygosity states for unstable hemoglobin Rush (Hb Rush, Beta 101 Glu > Gln, HBB:c.304G > C) with Hb E and different forms of thalassemia.Methods: Hematological assays, globin gene mutation assays and β-globin gene cluster haplotype were conducted in 11 patients from 8 unrelated Chinese ethnic families with unexplained hemoglobin separation fraction in hemoglobin gel electrophoresis.Results: Hb Rush in various combinations with Hb E, β0-thalassemias and α+-thalassemia were identified. Hb Rush simple heterozygote was generally associated with mild hemolytic anemia, and the compound heterozygotes of Hb Rush and the other β-globin variants led to thalassemia intermedia phenotypes with moderate anemia. Hemoglobin electrophoreses showed that the co-presence of Hb Rush with either Hb E or β0-thalassemias increased proportion of Hb Rush due to relative decrease of other globin chain synthesis. Beta-globin gene cluster haplotype analysis suggested a common origin of the Hb Rush variant in the Chinese families of different ethnic ancestry.Conclusions: Unstable Hb Rush interacting with β-thalassemia result in thalassemia intermedia phenotypes, which demonstrated the clinical significance of Hb Rush and new insights into complex mechanism of clinical heterogeneity of thalassemia.

Time estimations by network of beta globin gene cluster haplotypes linked with Hb D-Los Angeles [β121 (GH4) Glu→Gln GAA→CAA] mutation in the world populations.

Backgroundβ‐Globin gene cluster haplotypes associated with the Hb D‐Los Angeles mutation have been reported in many different locations in different populations including Italy, Iran, Thailand, Belgium, Mexico, Holland, and Turkey. In this study, we have identified genetic relationships and formation periods between the haplotypes reported in the world regarding the Hb D‐Los Angeles.MethodsWe comparatively analyzed the RFLP (restriction fragment length polymorphism) data in Denizli region and world populations using Arlequin 3.5 statistical software program. The data obtained from the Arlequin software were then entered into the Phylogenetic Network software to calculate the age estimates and to discover possible links between the haplotypes.ResultsWe observed the frequencies of the β‐globin gene haplotypes for the seven polymorphic restriction sites around the world and calculated the estimated time of haplotypes using Network software on the basis of ancestral haplotypes. We performed the phylogenetic network analysis of the haplotypes linked with Hb D‐Los Angeles mutation by processing the data of frequency and age estimations with Network software.ConclusionOur period of time results suggests that HAP1 was formed before modern human migration to Asia and/or independent origin of the Hb D‐Los Angeles mutation from other populations. Considering that the population in Denizli region started the Hb D‐Los Angeles mutation past about 40,000 years ago, it can be said that HAP1, HAP15, and HAP21 belong to the gene pool with an external effect. Our period of time results of HAP6 is compatible with published dating results.

Estimating the age of Hb G-Coushatta [β22(B4)Glu→Ala] mutation by haplotypes of β-globin gene cluster in Denizli, Turkey.

BackgroundHb G‐Coushatta variant was reported from various populations’ parts of the world such as Thai, Korea, Algeria, Thailand, China, Japan and Turkey. In our study, we aimed to discuss the possible historical relationships of the Hb G‐Coushatta mutation with the possible migration routes of the world. For this purpose, associated haplotypes were determined using polymorphic loci in the beta globin gene cluster of hemoglobin G‐Coushatta and normal populations in Denizli, Turkey.MethodsWe performed statistical analysis such as haplotype analysis, Hardy–Weinberg equilibrium, measurement of genetic diversity and population differentiation parameters, analysis of molecular variance using F‐statistics, historical‐demographic analyses, mismatch distribution analysis of both populations and applied the test statistics in Arlequin ver. 3.5 software program.ResultsThe diversity of haplotypes has been shown to indicate different genetic origins for two populations. However, AMOVA results, molecular diversity parameters and population demographic expansion times showed that the Hb G‐Coushatta mutation develops on the normal population gene pool. Our estimated τ values showed the average time since the demographic expansion for normal and Hb G‐Coushatta populations ranged from approximately 42,000 to 38,000 ybp, respectively.ConclusionOur data suggest that Hb G‐Coushatta population originate in normal population in Denizli, Turkey. These results support the hypothesis that the multiple origin of Hb G‐Coushatta and indicate that mutation may have been triggered the formation of new variants on beta globin haplotypes.

Association between beta globin haplotypes, HBBP1 and HMOX1 polymorphisms in relation to HbF among sickle cell anemia patients: a study in Southwest Iran

The haplotypes of β-globin gene cluster in patients with sickle cell anemia are associated with different clinical manifestations and fetal hemoglobin (HbF) levels. In addition, SNP in some genes within the β-globin gene cluster (HBBP1) and outside it (HMOX1) has been recently reported to be related to HbF levels. In this study, rs2071348 and rs2071746 polymorphisms in HBBP1 and heme oxygenase 1 (HMOX1) genes associated with different haplotypes and HbF levels in patients with sickle cell anemia were evaluated in comparison with healthy subjects. In this case-control study, 150 patients with sickle cell anemia (90 homozygous and 60 sickle-cell trait) were evaluated and compared with 50 healthy individuals referred to Shafa tertiary hospital in Ahvaz city of Khuzestan Province, Iran. HbF level was measured by alkali and acid electrophoresis. PCR-RFLP and ARMS-PCR methods were used to determine β-globin gene haplotypes and HBBP1 gene polymorphism, respectively. Arab-Indian was the most common genotype found in both homozygous and sickle-cell trait patients with a respective prevalence of 55.5 and 50% followed by homozygous Benin with 11.1 and 18.3% prevalence, respectively. The highest and lowest level of HbF were observed in Arab-Indian (24.1 ± 6.35) and Benin/Benin haplotypes (7.63 ± 2.29), respectively. A significant relationship was found between HbF level with rs2071746 A>T polymorphism of HMOX1 gene (P < 0.019) as well as with rs2071348 polymorphism of HBBP1 gene (P < 0.034). However, there was no significant relationship between haplotypes with gene polymorphisms. Arab-Indian was the most common haplotype in this region. The HbF level was significantly higher in patients with Arab-Indian haplotype, patients with C genotype in rs2071348 polymorphism locus of HBBP1 gene, and patients with T genotype in rs2071746 polymorphism locus of HMOX gene.

\u03b2-globin gene cluster haplotypes in ethnic minority populations of southwest China

The genetic diversity and relationships among ethnic minority populations of southwest China were investigated using seven polymorphic restriction enzyme sites in the β-globin gene cluster. The haplotypes of 1392 chromosomes from ten ethnic populations living in southwest China were determined. Linkage equilibrium and recombination hotspot were found between the 5′ sites and 3′ sites of the β-globin gene cluster. 5′ haplotypes 2 (+−−−), 6 (−++−+), 9 (−++++) and 3′ haplotype FW3 (−+) were the predominant haplotypes. Notably, haplotype 9 frequency was significantly high in the southwest populations, indicating their difference with other Chinese. The interpopulation differentiation of southwest Chinese minority populations is less than those in populations of northern China and other continents. Phylogenetic analysis shows that populations sharing same ethnic origin or language clustered to each other, indicating current β-globin cluster diversity in the Chinese populations reflects their ethnic origin and linguistic affiliations to a great extent. This study characterizes β-globin gene cluster haplotypes in southwest Chinese minorities for the first time, and reveals the genetic variability and affinity of these populations using β-globin cluster haplotype frequencies. The results suggest that ethnic origin plays an important role in shaping variations of the β-globin gene cluster in the southwestern ethnic populations of China.

Phenotypic Diversity of Sickle Cell Disease in Patients with a Double Heterozygosity for Hb S and Hb D-Punjab

Phenotypic heterogeneity for sickle cell disease is associated to several genetic factors such as genotype for sickle cell disease, β-globin gene cluster haplotypes and Hb F levels. The coinheritance of Hb S (HBB: c.20A > T) and Hb D-Punjab (HBB: c.364G > C) results in a double heterozygosity, which constitutes one of the genotypic causes of sickle cell disease. This study aimed to assess the phenotypic diversity of sickle cell disease presented by carriers of the Hb S/Hb D-Punjab genotype and the Bantu [– + – – – –] haplotype. We evaluated medical records from 12 patients with sickle cell disease whose Hb S/Hb D-Punjab genotype and Bantu haplotype were confirmed by molecular analysis. Hb S and Hb D-Punjab levels were quantified by chromatographic analysis. Mean concentrations of Hb S and Hb D-Punjab were 44.8 ± 2.3% and 43.3 ± 1.8%, respectively. Painful crises were present in eight (66.7%) patients evaluated, representing the most common clinical event. Acute chest syndrome (ACS) was the second most prevalent manifestation, occurring in two individuals (16.7%). Three patients were asymptomatic, while another two exhibited greater diversity of severe clinical manifestations. Medical records here analyzed reported a significant clinical diversity in sickle cell disease ranging from the absence of symptoms to wide phenotypic variety. The sickle cell disease genotype, Bantu haplotype and hemoglobin (Hb) levels did not influence the clinical diversity. Thus, we concluded that the phenotypic variation in sickle cell disease was present within a specific genotype for disease regardless of the β-globin gene cluster haplotypes.

Gene frequency and haplotype distribution of hemoglobin E among seven minority groups of Yunnan, China.

The aim of this study was to determine the distribution and origin of hemoglobin E (HbE) in seven minority groups from various geographical regions of the malaria-endemic Yunnan province, southwestern China, which have similar ethnic origins and geographic relationships with HbE-prevalent populations of Southeast Asian countries. By using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) methods, the prevalence of HbE was examined in 1488 individuals from seven native minority groups of Yunnan, and β-globin gene cluster haplotypes were determined on 1420 chromosomes. The prevalence of HbE in the study populations ranged from 1.5 to 39.1%. Higher HbE prevalence was correlated with the minority groups of Tibeto-Burman origin and groups from the Dehong district. The βE -globin genes in Yunnan were mostly associated with three haplotypes [-+++++-], [+----+-], and [-+-+++-] on chromosomes with gene framework 2. Interestingly, the predominant βE associated haplotype in Yunnan minorities was remarkably different from that in other previously reported populations. This study, for the first time, reports population-based data on the heterogeneity of HbE gene frequencies and haplotype distribution in native minorities from southwestern China. Natural selection based on the presence of malaria, ethnic origin, and epistatic interactions may be factors of varying importance for the remarkable variation in HbE frequency among these minority groups. In addition, there appears to be a common origin of the βE -globin gene in populations from Yunnan and Southeast Asia. Am. J. Hum. Biol. 28:927-931, 2016. © 2016Wiley Periodicals, Inc.

Sickle cell disease in western Sudan: genetic epidemiology and predictors of knowledge attitude and practices.

To investigate the epidemiology of sickle cell disease (SCD) and determinants of knowledge, attitudes and practices (KAP) towards SCD in western Kordofan State, Sudan. A community-based, descriptive, cross-sectional study was conducted in three towns. Three hundred and seventy-two households were polled, and blood samples for haemoglobin phenotyping were collected from 1116 individuals. Sociodemographic, socio-economic and KAP data were collected using investigator-administered questionnaires. Descriptive, frequency distribution and multiple regression analyses were performed. About 50.9% of the study population were Misseriya tribes. Consanguineous marriages were reported by 67.5% of the households. The highest percentage of homozygous SCD was 2.8% among children under 5 years of age. About 24.9% were carriers of HbS allele (HbAS). HbS allele frequency was highest in children aged 5-11 years (18.3%, CI: 13.7-22.9%) and lowest in males >15 years old (12.0%, CI: 6.1-17.9%). The average HbS frequency across all age groups was 14.5% (95% CI: 12.2-16.8%). The most frequent β-globin gene cluster haplotype was the Cameroon (30.8%), followed by the Benin (21.8%), the Senegal (12.8%) and the Bantu (2.2%) haplotypes. About 17.0% of all-cause child deaths were due to SCD. The estimated change in log odds of having the SS genotype per year increase in age was (-) 0.0058 (95% CI -0.0359, 0.0242). This represents a non-statistically significant 2.9% increase in 5-year mortality for individuals with the SS genotype relative to those with AS and AA genotypes. About 46.9% of the households had poor knowledge, 26.1% had satisfactory knowledge, and 26.9% had good knowledge about sickle cell disease. Mothers' and fathers' educational levels were significant predictors of good knowledge about SCD (P < 0.05). About 48.0% had a satisfactory attitude towards sickle cell disease while 30.7% had poor attitude and only 21.3 showed good attitudes. Poor knowledge about SCD and low socio-economic status were the strongest positive predictors of poor attitude and practices towards SCD (P < 0.01). Sickle cell disease is a major health problem in West Kordofan, Sudan. Knowledge, attitude and practices towards the disease are not satisfactory. The development of public health programs is highly recommended to control and manage SCD in western parts of Sudan.

Identification of β-globin haplotypes linked to sickle hemoglobin (Hb S) alleles in Mazandaran province, Iran.

Carrier frequency of the βS allele has been reported to be 0.19% in Mazandaran province, northern Iran. Haplotype analysis of the βS allele helps trace the origin of its encoded hemoglobin (Hb) variant, Hb S, in a region. The aim of this study was to investigate the haplotypes associated with βS alleles in Mazandaran province. Capillary electrophoresis was carried out to detect individuals suspected to have a βS allele(s). DNA analysis (PCR-RFLP) was used for final confirmation. To identify 5' to 3' β-globin gene cluster haplotypes associated with βS alleles, family linkage analysis was applied. Six polymorphic sites (HincII 5' to ε, XmnI 5' to Gγ, HindIII in Gγ, HindIII in Aγ, HincII 3' to ψβ and AvaII in β) were investigated using the PCR-RFLP method. Five different haplotypes were linked to βS alleles, while βA alleles were associated with nine haplotypes. Among the βS alleles, 53.9% were associated with the Benin (----++) haplotype, and the Arab-Indian (+++-++) haplotype had the second-highest frequency (23%). Unlike southern provinces, where the Arab-Indian haplotype is prominent, the Benin haplotype is the most frequent haplotype in northern Iran, and this may represent a founder effect. Since the Benin haplotype does not carry the XmnI polymorphism 5' to the Gγ gene, which is responsible for high expression of Hb F, a severe form of sickle cell disease can be anticipated in patients that are homozygous for the βS allele in the northern region.

Polymorphisms Associated with the Arab-Indian Haplotype of Sickle Cell Anemia Are Candidate Fetal Hemoglobin Gene Modulators

Fetal hemoglobin (HbF) inhibits HbS polymerization. Because of this, sufficient HbF in most sickle erythrocytes can lead to a milder disease phenotype. HbF levels differ amongst the β-globin gene (HBB) cluster haplotypes of sickle cell anemia. In the Arab-Indian (AI) haplotype, HbF was about 20% compared with 5-10% in the Bantu, Benin, and Senegal haplotypes. Functional elements linked to the HBB haplotype are likely to regulate the expression of HbF in addition to the effects of trans-acting modulators. To identify cis-acting SNPs in the HBB gene cluster that differentiate the AI haplotype from all others, including the Senegal haplotype-the Senegal haplotype shares some SNPs with the AI haplotype but its carriers have lower HbF-we studied patients with sickle cell anemia who were homozygous for HBB haplotypes by genome-wide SNP association analysis (GWAS; Table). First, we compared the results of GWAS of 42 Saudi AI haplotype homozygotes with GWAS in 71 Saudi Benin haplotype homozygotes. The only variants distinguishing these 2 populations with genome-wide significance (p-values between 9.6E-07 and 2.7E-45) were 223 SNPs in chromosome 11p15 from positions 3.5 to 6.5 mb. This region included the HBB gene cluster, its locus control region (LCR) and the upstream and downstream olfactory receptor gene clusters. The minor allele frequency of SNPs in MYB (chr 6q23), BCL11A (chr 2p16) and KLF1 (chr 19), trans-acting loci that affect expression of the HbF genes, were similar in these 2 cohorts. A novel candidate trans-acting locus was not found, however our power to detect such an association was low. We followed-up these observations by comparing allele frequencies in 303 African American cases homozygous for the haplotypes shown in the Table. Thirteen GWAS-significant SNPs, in addition to rs7482144 and rs10128556, were present in all AI haplotype cases but not in 83 Senegal haplotype chromosomes. The allele frequency of these SNPs was replicated in 62 independent AI haplotype cases. Rs2472530 is in the coding region of OR52A5; rs16912979, rs4910743 and rs4601817 are in the HBB gene cluster LCR; rs16912979 in DNase I hypersensitive site-4 altered motifs for POLR2A, GATA1, and GATA2 binding.The minor allele of rs10837771 causes a missense mutation in OR51B4 an upstream olfactory receptor gene. To see if any of these or other alleles might sometimes be associated with HbF in the Bantu and Benin haplotyes, we selected homozygotes and compound heterozygous for these haplotypes who had unexplained and uncharacteristically high HbF. Thirty-one African Americans, aged ≥5 yrs. who had a HbF of 21% were compared with 350 similar cases who had a mean HbF of 3%. Four additional SNPs on chromosome 11, from positions ranging from 5536415 to 5543705 in the UBQLNL/HBG2, region and present in 45-48% of AI haplotype and 3-13% of other haplotypes, were found at higher frequencies in the high HbF group compared with the low HbF group. These SNPs also altered transcription factor binding motifs. Loci marked by SNPs that distinguish the AI from the Senegal and other HBB haplotypes might contain functionally important polymorphisms and account in part for high HbF in AI haplotype sickle cell anemia, independent of, or in addition to, the effects associated with rs7482144 or rs10128556. They might also be rarely associated with high HbF found in other haplotypes. These observations provide a foundation for mechanistic studies focused on the role of these variants in the expression of their linked HbF genes. Table 1non-codedallelegenomic locationSaudi AI(n=42)Saudi ben.ben(n=71)AA ben.ben(n=264)AA ban.ban(n=31)AA sen.sen(n=8)HbF (%)1711669rs10837771Gexon OR51B410.020.0200rs4601817GLCR10.020.0400rs4910743CLCR10.010.0100rs16912979CLCR00.960.920.111rs10488675Gintron HBE110.01000rs7482144*AHBG210001rs10128556#TIntron HBBP110001rs7935470COR51V110.020.0300rs10837582GOR51V1100.0200rs11036227TOR51V110000rs10734485COR51A1P00.990.9711rs10837461AOR52A110.01000rs2472522GOR52A110.01000rs2472530Gexon OR52A510.01000rs2499948TOR52A510.020.010.020Allele frequencies in haplotypes of sickle cell anemia. * Xmn1 5' HBG 2 restriction site. This SNP, not present on the SNP microarray, was genotyped independently; # LD with rs7482144; AA designates African Americans; ben-Benin; ban-Bantu; sen-Senegal. DisclosuresNo relevant conflicts of interest to declare.

Spectrum of β-Globin Gene Mutations and β-Thalassemia Haplotype Analysis among the Iranian Azeri Turkish Population

Background: A variety of mutations influencing gene transcription, translation, or mRNA processing have been identified in β-thalassemia. Several studies demonstrated a nonrandom linkage of particular RFLP haplotypes with specific β-thalassemia mutations. Linkage analysis using β-globin haplotypes is a valuable tool for indirect mutation detection. Our aim was to determine the spectrum and frequency of β-thalassemia mutations among Northwestern Iranians (Azeri Turkish population) along with determining the heterozygosity and polymorphism information content (PIC) value for seven β-globin markers. Method: We investigated spectrum of β-thalassemia mutations via ARMS-PCR technique followed by sequencing technique. Also β-globin gene cluster haplotypes was determined by PCR-RFLP technique on DNA samples of the patients and his (her) parents or siblings. Result: We detected 36 different mutations among 554 non-identical mutant chromosomes. The most frequent mutation was IVSII-1 (G>A) (23.6%), followed by IVSI-110 (G>A) (11.9%) and CD8 (-AA) (10.5%). Of the various β- globin gene cluster haplotypes, haplotypes I and IV were found to be most common among normal (21.36%) and mutant (15.76%) chromosomes, respectively. The highest observed heterozygosity (48%) was found for the HindIII Gγ and HindII 5'ψs polymorphic sites, whereas the highest expected heterozygosity (50%) was predicted for the HindIII Gγ and HindII sites, which also had the highest PIC value of 0.37. Conclusion: The current study implies mutational heterogeneity among investigated population. Haplotype study results (heterozygosity and PIC), clarifies β-globin markers usefulness for tracking mutant alleles as a complementary method to confirm the genotype in prenatal diagnosis (PND) among investigated population.

β-Globin gene cluster haplotypes of Hb D-Los Angeles in Mazandaran Province, Iran.

Several types of hemoglobin D (Hb D) are distinguishable by DNA analysis, and the aim of this study was to identify the types of Hb D variant and β-globin gene haplotypes linked to Hb D in Mazandaran Province, northern Iran. Fifty five individuals were identified as Hb D carriers, and PCR-RFLP analysis revealed that all 55 had the Hb D-Los Angeles type. To identify haplotypes associated with the β(D) allele, family linkage analysis, using the PCR-RFLP method for seven polymorphisms in the β-globin gene cluster, was carried out on families of 23 of these 55 individuals. We observed three different haplotypes in association with Hb D-Los Angeles. In most cases (91.4%) β(D) alleles were linked to haplotype I [+ - - - - + +]. Haplotype II [- + + - + + +] and an atypical haplotype [- + + - - + -] were each in association with the β(D) allele in only one case (4.3%). This is the first report worldwide of the [- + + - - + -] haplotype in association with Hb D-Los Angeles. We conclude that more than 90% of the evaluated Hb D-Los Angeles alleles in Mazandaran have the same origin, and the two rare haplotypes may represent different genetic origins and/or other molecular events, such as gene conversion or recombination, in the region.

Fetal Hemoglobin In Sickle Cell Anemia: A Glass Half Full?

HbF modulates the phenotype of sickle cell anemia by inhibiting deoxyHbS polymerization. HbF is confined to erythrocytes called F-cells that can be detected by FACS when these cells contain sufficient HbF. Measuring the amount of HbF/F-cell is difficult and not clinically available. African-Americans with sickle cell anemia have 2-80% F-cells with an average HbF/F-cell of 6.4±1.6 pg. The distribution of HbF/F-cell is highly individual regardless of HbF level. People with HbS-gene deletion hereditary persistence of HbF (HPFH) have a mean HbF of 30%, and HbF is evenly distributed among their erythrocytes. Polymer is not present in these cells either experimentally or after calculating the HbS polymer fraction at 70% O2 saturation. Therefore, each cell contains about 10 pg. of HbF. DeoxyHbS polymerization is prevented at physiologic venous and capillary O2 saturations of 40-70% when HbF/F-cell is 9-12 pgs. We call this the “protective” level of HbF. F-cells need not contain “protective” levels of HbF. Some β-globin gene cluster haplotypes are associated with high HbF. Carriers of these haplotypes can have milder disease. Nevertheless, even patients with high HbF can have frequent painful episodes, acute chest syndrome and osteonecrosis. Patients with HbS-δβ thalassemia have 15 to 25% HbF but are anemic and have vasoocclusive complications, albeit less often than in sickle cell anemia. Hydroxyurea reduces the morbidity and mortality of sickle cell anemia, an effect likely to be mediated by its induction of HbF. Patients treated with hydroxyurea are better and probably live longer, but adults are anemic and rarely asymptomatic. In all these patient groups, HbF is unevenly distributed among erythrocytes. In contrast, people with HbS-HPFH are nearly asymptomatic and not anemic. The failure of HbF to modulate uniformly all complications of sickle cell disease might be related to the heterogeneous concentration of HbF in sickle erythrocytes. HbF is associated with protection from the development of certain disease subphenotypes but has limited prognostic value in individuals. In many cross-sectional studies, high HbF was associated with a reduced rate of acute painful episodes, fewer leg ulcers, less osteonecrosis, less frequent acute chest syndromes and reduced disease severity. HbF had a weak or no clear association with priapism, urine albumin excretion, stroke and silent cerebral infarction, systemic blood pressure and tricuspid regurgitant velocity. Perhaps this is because intravascular hemolysis of cells with little or no HbF causes nitric oxide scavenging, or because these complications are less dependent on HbS polymerization. No study provides information on the concentration of HbF/F-cell other than providing the relatively meaningless calculated mean value. Rather than the total number of F-cells or the concentration of HbF in the hemolysate, HbF/F-cell and the proportion of F-cells that have “protective” HbF is the most critical predictor of the likelihood of some disease subphenotypes. Hypothetical distributions of HbF-cells with different levels of HbF/F-cell can be plotted for different concentrations of HbF. With mean HbF levels of 5%, 10% and 20%, and HbF content per cell of 1.5, 3 and 6 pg., assuming a fixed mean, the variance was changed to show how the distribution of HbF per cell can greatly vary, even if the mean is constant. For example, with 20% HbF, as few as 1% and as many as 24% of cells have “protective” HbF. When HbF is lower, few or no “protected” cells can be present. Due to the heterogeneous concentrations of HbF, HbS can polymerize in some F-cells that have sub-polymer inhibiting concentrations of HbF. Inducing high levels of HbF is one approach to treating sickle cell disease. Inactivating BCL11A, a repressor of γ-globin gene expression, abrogates sickle cell disease in transgenic sickle mice. Their HbF was distributed homogeneously, and their phenotype mimicked HbS-HPFH. If it becomes possible in humans to target BCL11A or its pathway with agents that affect gene transcription, will it result in pancellular HbF? Broadening the distribution of HbF amongst sickle erythrocytes with drugs like hydroxyurea that effect the kinetics of erythropoiesis, coupled with an agent whose primary mechanism of action is to increase the transcription of the γ-globin genes, might be the most fruitful approach to HbF induction therapy and more efficacious than single agent treatment. Disclosures: No relevant conflicts of interest to declare.

Fetal hemoglobin in sickle cell anemia: Genetic studies of the Arab-Indian haplotype

Sickle cell anemia is common in the Middle East and India where the HbS gene is sometimes associated with the Arab-Indian (AI) β-globin gene (HBB) cluster haplotype. In this haplotype of sickle cell anemia, fetal hemoglobin (HbF) levels are 3-4 fold higher than those found in patients with HbS haplotypes of African origin. Little is known about the genetic elements that modulate HbF in AI haplotype patients. We therefore studied Saudi HbS homozygotes with the AI haplotype (mean HbF 19.2±7.0%, range 3.6 to 39.6%) and employed targeted genotyping of polymorphic sites to explore cis- and trans- acting elements associated with high HbF expression. We also described sequences which appear to be unique to the AI haplotype for which future functional studies are needed to further define their role in HbF modulation. All cases, regardless of HbF concentration, were homozygous for AI haplotype-specific elements cis to HBB. SNPs in BCL11A and HBS1L-MYB that were associated with HbF in other populations explained only 8.8% of the variation in HbF. KLF1 polymorphisms associated previously with high HbF were not present in the 44 patients tested. More than 90% of the HbF variance in sickle cell patients with the AI haplotype remains unexplained by the genetic loci that we studied. The dispersion of HbF levels among AI haplotype patients suggests that other genetic elements modulate the effects of the known cis- and trans-acting regulators. These regulatory elements, which remain to be discovered, might be specific in the Saudi and some other populations where HbF levels are especially high.

Fetal Haemoglobin and β-globin Gene Cluster Haplotypes among Sickle Cell Patients in Chhattisgarh.

Foetal Haemoglobin (HbF) is the best-known genetic modulator of sickle cell anaemia, which varies dramatically in concentration in the blood of these patients. The patients with SCA display a remarkable variability in the disease severity. High HbF levels and the β-globin gene cluster haplotypes influence the clinical presentation of sickle cell disease. To identify the genetic modifiers which influence the disease severity, we conducted a β-globin haplotype analysis in the sickle cell disease patients of Chhattisgarh. The foetal haemoglobin and the β-globin gene haplotypes of the sickle cell trait and the sickle cell disease patients from Chhattisgarh were investigated. A total of 100 sickle cell patients (SS), 50 sickle cell trait patients (AS) and 50 healthy control individuals were included in the present study. The distribution of the β-globin gene haplotype was done by the PCR-RFLP method. PCR-RFLP showed that the homozygous Arab-Indian haplotype (65%) was the most frequent one, followed by the heterozygous Arab-Indian haplotype (11%) in the sickle cell patients (SS), while the AS patients had a higher frequency of the heterozygous Arab-Indian haplotype (38%) in comparison to homozygous one (32%). Four atypical haplotypes, 3 Benin and 1 Cameroon were also observed, although they were in lower frequencies. In the present study, the HbF levels were higher in the AS and the SS patients, with one or two Arab-Indian haplotypes as compared to the other haplotypes. The presence of the Arab-Indian haplotype as the predominant haplotype might be suggestive of a gene flow to/from Saudi-Arabia or India and it was associated with higher HbF levels and a milder disease severity.