Beta-globin gene cluster haplotypes in the Corsican and Sardinian populations

The distribution of beta-globin cluster haplotypes has been studied in the populations of Corsica (France) and Sardinia (Italy). The analysis was carried out using five restriction fragment length polymorphism markers on chromosome 11 inside the beta-globin cluster using the restriction enzymes HincII and HindIII. The results show a remarkable heterogeneity within the two islands. However, the presence of rare haplotypes common to the most conservative areas (Nuoro and Corte) of the two islands is particularly interesting. These data support the hypothesis of a common origin of the populations of Sardinia and Corsica during the middle and upper Paleolithic periods and could be interpreted as a founder effect.     

Beta-globin gene cluster haplotypes in two North American indigenous populations

Haplotypes derived from five polymorphic restriction sites were determined in 50 Carrier-Sekani and 70 Mvskoke chromosomes, and the results were integrated with those previously obtained for 11 South American Indian populations. Eleven haplotypes were identified in the Mvskokes, while five were observed in the Carrier-Sekani. As in South American natives, haplotype 2 (+----) and 6 (-++ -+) were the most prevalent among the Mvskoke (46% and 30%, respectively). In the Carrier-Sekani, haplotype 2 was also the most common, but haplotype 5 (-+ -++) was somewhat more frequent (18%) than 6 (12%). High heterozygosities, as well as genetic differentiation, were observed among these two North American and two other South American groups (Mapuche and Xavante). They could be due to non-Indian admixture in the Mvskoke and Mapuche, but the findings in the other two populations require some other type of explanation.     

Beta-globin gene haplotypes in Polynesians are predominantly southern Chinese in type

beta-Globin gene haplotypes obtained in Polynesian Samoans were similar to those described in Southern Chinese. An atypical HindIII restriction fragment length polymorphism detected with pRK29, a 3' beta-globin gene probe, was present at a gene frequency of 7% in Samoans. Haplotype patterns suggest that this polymorphism may have arisen by 1 or 2 mutational events. DNA haplotypes derived from the beta-globin gene cluster confirm nuclear and mitochondrial DNA data that Polynesian precursor populations were East Asian in origin.     

Beta-globin gene haplotypes and alpha-thalassemia analysis in Babinga pygmies from Congo-Brazzaville

We analyzed beta-globin gene cluster haplotypes and deletional alpha+-thalassemia (-alpha3.7kb) in 54 Babinga pygmy subjects from Congo-Brazzaville. The beta(S)-globin gene frequency was 0.065 and that of the deletional alpha-globin gene (-alpha3.7kb) was 0.29. Eighty-five percent of the beta(S) chromosomes and 13% of the beta(A) chromosomes were associated with the Bantu haplotype, 10% of beta(A) chromosomes with the Senegal haplotype, and the remaining beta chromosomes with atypical haplotypes. None of the chromosomes were of the Benin haplotype. These results are clearly of anthropological and evolutionary interest. They also support earlier observations that alpha+-thalassemia is prevalent at a high frequency in African populations.     

Hepatic sequestration in sickle cell anaemia.

Several episodes of acute hepatic enlargement associated with a dramatic fall in haemoglobin concentration were observed in two patients with sickle cell anaemia. No appreciable disturbances of liver function or signs of cardiac failure were evident. The most likely mechanism was sequestration of sickled erythrocytes in the liver. This complication, which may have a basis similar to that of splenic sequestration and the sickle lung syndrome, may be easily overlooked unless the size of the liver is regularly monitored in patients with sickle cell crisis.     

Biochemical and Molecular analysis of the beta-globin gene on Saudi sickle cell anemia

Sickle cell anemia (SCA) is one of the most common hematologic diseases affecting humans. Detection of a single base pair mutation at 6th codon of β-globin gene is important for the diagnosis of SCA. The aim was to study the nucleotide sequences and the molecular survey of β-globin gene in Saudi patients.Blood samples from 77 unrelated SC patients were obtained from the KKUH, between 2015 and 2017. In this study, DNA was extracted then PCR was performed. Twelve overlapping fragments covering β-globin gene, have been generated by PCR.A total of 47 alterations have been recognized in β-globin gene. These alterations composed of: deletions, insertion or substitutions as follows:- one mutation identified on the 1st segment; three alterations on 2nd fragment; two alterations on 3rd segment; seven alterations on 4th segment; three substitution on 5th fragment; two changes on 6th fragment; five alterations on 7th fragment; seven substitution changes on 8th fragment; two heterozygous substitution changes on 9th fragment; three changes on 10th fragment and eight substitution changes on 11th fragment, and four changes on 12th fragment.SCA had profound negative effects on many organs, causing many complications. The results should be taken further to set up management strategies to improve outcomes.     

Experimental generation of SNP haplotype signatures in patients with sickle cell anaemia

Background

Sickle cell anemia is caused by a single type of mutation, a homozygous A→T substitution in the ß globin gene. Clinical severity is diverse, partially due to additional, disease-modifying genetic factors. We are studying one such modifier locus, HMIP (HBS1L-MYB intergenic polymorphism, chromosome 6q23.3). Working with a genetically admixed patient population, we have encountered the necessity to generate haplotype signatures of genetic markers to label genomic fragments with distinct genealogical origin at this locus. With the goal to generate haplotype signatures from patients experimentally, we have investigated the suitability of an existing nanofluidic assay platform to perform phase alignment with single-nucleotide polymorphism alleles.

Methodology/Principal Findings

Patient DNA samples were loaded onto Fluidigm Digital Arrays and individual DNA molecules were assayed with allele-specific probes for SNP markers. Here we present data showing the utility of the nanofluidic approach, yielding haplotype data identical to those obtained with a family-based method. We then determined haplotype composition in a group of patients with sickle cell disease, including in those where a mathematical inference approach gave ambiguous or misleading results. Experimental phasing of genotypes across 3.8 kb for rs9399137, rs9402685, and rs11759553 created unequivocal haplotype signatures for each of the patients. In 68 patients, we found 8 copies of a haplotype signature (‘C-C-T’), which is known to be prevalent in Europeans but to be absent in West African populations. We have confirmed the identity of our phased allele pairs by single-molecule sequencing and have demonstrated, in principle, that three-allele phasing (using three colors) is a potential extension to this method.

Conclusions/Significance

Phased haplotypes yield more information than the individual marker genotypes. Procedures such as the one described here would therefore benefit genetic mapping and functional studies as well as diagnostic procedures where the identity or parental origin of short genetic fragments is of importance.     

Implications of the genetic epidemiology of globin haplotypes linked to the sickle cell gene in southern Iran

To determine the origin of sickle cell mutation in different ethnic groups living in southern Iran, we studied the haplotype background of the betaS and betaA genes in subjects from the provinces of Fars, Khuzestan, Bushehr, Hormozgan, and Kerman and from the islands of Khark and Qeshm. beta-globin gene cluster haplotypes were determined using the PCR-RFLP technique. Detection of -alpha 3.7 deletion and beta-thalassemia mutations were defined by PCR and reverse dot blot techniques, respectively. The framework of the beta-globin gene was determined using denaturing gradient gel electrophoresis. We found that the betaS mutation in southern Iran is associated with multiple mutational events. Most of the patients were from two ethnic groups: Farsi speakers (presumably Persian in origin) from Fars province and patients of Arab origin from Khuzestan province. In both ethnic groups the Arab-Indian haplotype was the most prevalent. The frequencies of the Arab-Indian and African haplotypes in sickle cell anemia patients from the provinces of Fars and Khuzestan were similar. Among betaA chromosomes the Bantu A2 haplotype was the most prevalent. The decrease in alpha-globin production in SS patients and AS individuals appeared to be related to the reduction in mean cell volume and mean cell hemoglobin. The Arab-Indian haplotype gene flow into this region of Iran can be traced to the Sassanian Empire. It is likely that the influx of betaS genes linked to the Benin and Bantu haplotypes, of African origin, must have occurred during the Arab slave trade.     

Some atypical and rare sickle cell gene haplotypes in populations of Andhra Pradesh, India.

We have investigated the clinical, hematological, and molecular genetic characteristics of sickle cell anemia patients from 6 populations of Andhra Pradesh, South India. Of 72 sickle cell chromosomes (HBB*S) 60 belong to characteristic Arab-Indian haplotypes, 6 to variant Arab-Indian haplotypes, 1 to a Bantu haplotype, 2 to a Cameroon haplotype, and 3 to rare haplotypes. This is the first report of a Bantu haplotype in an Indian population. Some information on haplotype characteristics of normal chromosomes (HBB*A) is also presented. The average hemoglobin level was 7.3 g% and mean fetal hemoglobin (HbF) level was 12.6%. The higher HbF levels corroborate earlier observations in sickle cell homozygotes from India. Clinical investigations have revealed splenomegaly and painful crises as the most common features in these patients.     

Balance control is impaired in adults with sickle cell anaemia

Abstract

Background: Musculoskeletal involvement and cerebrovascular disease are common in sickle cell anaemia (SCA). These changes are potentially important factors that modify the control of balance in this population.

Objective: To assess balance control in adults with SCA and investigate the associations among balance, posture and muscle function.

Methods: Twenty neurologically intact (i.e. without previous episodes of overt stroke or transient ischaemic attack) adults with SCA and 18 controls were evaluated. All participants underwent static balance measurement through stabilometry, postural evaluation through photogrammetry and assessment of muscle function through handgrip and respiratory muscle strength.

Results: Compared to the controls, the adults with SCA exhibited greater displacement of the centre of mass, particularly in the mediolateral direction. Moreover, the adults with SCA exhibited greater postural deviations for the following variables: angles of the right and left hip, horizontal asymmetry of the scapula in relation to T3, angles of the right and left leg-heel and horizontal alignment of the pelvis. Handgrip strength, respiratory muscle strength and haemoglobin (Hb) levels were significantly correlated with postural balance measurements. Significant correlations between balance and posture were only observed between the variables of balance and the postural parameters that involved the angulations calculated from the vertical alignment of the pelvis, hip and ankle.

Conclusions: Neurologically intact adults with SCA exhibit damage in static balance, particularly in the mediolateral direction. These patients present postural deviations due to changes in the hip and ankle joints. In addition, balance control is related to posture, Hb level and muscle function.     

Environment change, geographic migration and sickle cell anaemia

The classic model describing the interaction between sickle cell anaemia and malaria is one of the most notable achievements of population genetics. Nevertheless, only panmictic populations in steady environments have been studied theoretically to date. In this paper, environment change and geographic inhomogeneity are introduced. The rate of decrease of mutation after environment improvement is obtained. The kinetics of the spread of disease after the initial mutation, together with the genetic composition profile near the borders of malaria areas, are calculated. The results are compared with the empirical data on the mutation level in African and African-American populations. It is shown that the spread of disease and decrease in mutation are highly asymmetric: the mutation level increases exponentially and decreases much more slowly (as a power function). The mathematical and biological reasons for this behaviour are discussed.     

Aspects of sickle cell gene in Saudi Arabia—interaction with glucose-6-phosphate dehydrogenase deficiency

Summary Glucose-6-phosphate dehydrogenase (G-6-PD) deficiency and sickle cell haemoglobin (Hb S) are red cell genetic abnormalities that occur at a high frequency in several areas of the world including several areas of Saudi Arabia. Genetic and clinical interactions between these two disorders are reported to occur in some populations.In the present investigations, samples from affected individuals were studied for the prevalence of G-6-PD deficiency and Hb S genes. The results of haematological parameters and common clinical findings in the Hb S homozygotes with and without G-6-PD deficiency are presented and the possibility that the two conditions interact beneficially is discussed.     

New mutations of locus control region in Saudi sickle patients

Sickle cell anemia (SCA) is a common hematological disease affecting humans. Detection of a single base pair mutation in β-globin gene is an important diagnostic tool for SCA. The aim was to study the molecular survey of locus control regions (LCR) in Saudi patients with sickle cell anemia, and to identify the genetic variables and their clinical manifestations.MethodologyBlood samples from 69 unrelated sickle cell disease patients were obtained from the KKUH, Riyadh between 2017–2019. In this study, the DNA was extracted and PCR was performed. Additional PCR amplifications reactions covering the LCR were performed by using another different set of primers. Seven specific primer pairs were used to amplify seven regions in the locus control region (LCR) of β globin family. The generated fragments were sequenced to identify the possible alterations in this region.ResultsThe results gained from sequencing experiments revealed a wide range of genomic alterations. A total of 69 gene alterations have been recognized in the locus control region;- The first fragment LCR-HS1 shows 20 alterations; The second fragment LCR-HS2 revealed six changes; The third fragment LCR-HS3 shows many changes; The fifth LCR-HS5 region revealed four changes; The sixth fragment LCR-HS6 revealed eight changes; The seventh LCR-HS7 fragment demonstrates ten changes.ConclusionIt clear that this study has successfully identified LCR mutations for random Saudi patients with SCD. The above results should be taken further to set up management strategies to improve outcomes.     

Deficiency of factor B of the complement system in sickle cell anaemia.

Factors B and D as well as the total activity of the alternative pathway of complement activation were measured using a functional assay in sera from 29 patients with sickle cell anaemia and 18 normal controls. Total alternative pathway activity was reduced in the patients compared with controls. In patients with abnormally low total alternative pathway activity factor D levels were normal, whereas factor B levels were significantly depressed to a mean level of about half of normal. Regression analysis in patients also showed a significant relation between total alternative pathway activity and factor B levels. A deficiency of factor B is the likely cause of the defect in the complement system in patients with sickle cell anaemia. Such a defect may contribute to the excessive proneness of such patients to severe infection.     

An explanation for the efficacy of procaine in the treatment of sickle cell anaemia

A study has been carried out into the effects of procaine on the activities (Na+,K+)- and (Ca2+,Mg2+)-ATPases of the human erythrocyte membrane. In general, procaine inhibited both types of ATPases activities but with characteristic inhibition profiles and varying degrees of efficacy. In addition, the effects of procaine on the transport of K+ and phosphate ions across the membrane of the human erythrocyte were monitored and compared. Procaine was found to stimulate K+ release and to inhibit phosphate uptake. At low concentrations, both processes were found to be concentration dependent. Stimulation of K+ release and inhibition of phosphate uptake reached plateaus at concentrations of 50 and 150 mM, respectively. The antisickling effect of procaine was explained mainly in the light of the changes it induces in the activities of membrane bound ATPases and the permeability properties of the erythrocyte membrane to cations and anions.     

Single tube genotyping of sickle cell anaemia using PCR-based SNP analysis

Allele-specific amplification (ASA) is a generally applicable technique for the detection of known single nucleotide polymorphisms (SNPs), deletions, insertions and other sequence variations. Conventionally, two reactions are required to determine the zygosity of DNA in a two-allele system, along with significant upstream optimisation to define the specific test conditions. Here, we combine single tube bi-directional ASA with a ‘matrix-based’ optimisation strategy, speeding up the whole process in a reduced reaction set. We use sickle cell anaemia as our model SNP system, a genetic disease that is currently screened using ASA methods. Discriminatory conditions were rapidly optimised enabling the unambiguous identification of DNA from homozygous sickle cell patients (HbS/S), heterozygous carriers (HbA/S) or normal DNA in a single tube. Simple downstream mathematical analyses based on product yield across the optimisation set allow an insight into the important aspects of priming competition and component interactions in this competitive PCR. This strategy can be applied to any polymorphism, defining specific conditions using a multifactorial approach. The inherent simplicity and low cost of this PCR-based method validates bi-directional ASA as an effective tool in future clinical screening and pharmacogenomic research where more expensive fluorescence-based approaches may not be desirable.     

Killer cell immunoglobulin-like receptor gene diversity in the Saudi population

Killer cell immunoglobulin-like receptors (KIRs) influence the outcome of haematopoetic stem cell transplantation by modulating the cytotoxic ability of natural killer (NK) cells and a subset of T cells. KIRs are also highly polymorphic and could therefore be good population genetic markers, much like their human leukocyte antigen (HLA) ligands. This study represents the first report on distribution of 16 KIR genes in 162 unrelated healthy Saudi individuals. All the 16 KIR genes were observed in the studied population and the four framework genes (KIR2DL4, 3DL2, 3DL3 and 3DP1) were present in all individuals. Forty- one distinct KIR profiles were expressed in our population, 11 of which had not been previously described in other populations including the Middle Eastern population. AA1, the most common genotypic profile was observed at a frequency of 26.5%. The group A haplotype was more frequent (53%) in the Saudi population compared to the group B haplotype (47%). The pattern of the inhibitory KIR/HLA ligands were also analyzed and 52.3% of the Saudi population was found to express two pairs of the inhibitory KIR/HLA-C. The KIR gene frequencies suggests that the Saudi population shares common general features with the Middle Eastern and other populations, but still has its own unique frequencies of several KIR loci.     

Socioeconomic status dependent medical complexities in children with sickle cell disease in Saudi Arabia

A look into the associations of socioeconomic status (SES) with prevalence of various complications in sickle cell disease (SCD) is necessary, for an improvement of societal norms, governmental health policies and strategies. We therefore studied the influence of SES indices on certain hematological and clinical parameters in children with SCD in Saudi Arabia. We included 32 female and 33 male patients aged 5–16 years, who were classified based upon their family income. Family monthly income was divided into 4 categories from lowest to highest, with socioeconomic class1 having low earnings of <5000 SAR; the middle income class divided further into class 2 with earnings >5000–10,000 SAR, and class 3 with earnings >10,000–15,000 SAR; and the higher income class 4 with earnings of >15,000 SAR. The assessment indices used were, the frequency of vaso-occlusive crisis (VOC), adverse events, and hematological parameters. A higher percentage of children affected with the disease were from class1, which is the low socio-economic class. It was found that the percentage of frequency of VOC pain crisis, and adverse events was higher in social class 1 patients than in the classes 2, 3, and 4. Also, the age group 5–10 years appeared more susceptible to adverse events and VOC. Our findings suggest the need to conduct future larger studies, to deduce the modifying influence of disparity in SES on certain clinical and hematological indices in children with SCD.     

Glutathione reductase deficiency in association with sickle cell and thalassaemia genes in Saudi populations

Glutathione reductase (GR) deficiency is reported to occur with a variable frequency in some populations of the world. In this study, the populations of two regions of Saudi Arabia which have a high frequency of sickle cell, thalassaemia and glucose-6-phosphate dehydrogenase (G-6-PD) deficiency, were screened for GR deficiency. Studies were also carried out to investigate the frequency of GR deficiency with other genetic blood disorders. The frequencies of complete GR deficiency were 0.0065 and 0.006, while those of partial deficiency were 0.146 and 0.074 in Al-Hafouf and Khaiber, respectively. GR deficiency was encountered in combination with the sickle gene, the G-6-PD deficiency gene and the thalassaemia gene in both regions. Individuals with GR deficiency showed slightly reduced haematological parameters. In thalassaemic/GR-deficient subjects, mean cell volume and mean cell haemoglobin were low, while in sickle cell anaemia patients with GR deficiency the haematological parameters were higher than in sickle cell anaemia patients without GR deficiency.