Spectrum of beta-thalassemia in Jordan: identification of two novel mutations

Prevalence and Molecular Characterization of β-Thalassemia in Kirkuk Province of Northern Iraq

To determine the prevalence and molecular basis of β-thalassemia in the Northeastern Iraqi province of Kirkuk, a total of 3954 individuals attending the provincial premarital screening center were recruited. The prevalence of β-thalassemia minor among the screened individuals was found to be 3.0%, while those of Hemoglobin E, and δβ-thalassemia carrier states were 0.05%, and 0.03% respectively. Molecular characterization of the β-thalassemia mutations was achieved by multiplex PCR and reverse hybridization, followed by next generation sequencing for those left uncharacterized by the former technique. Among 19 β-thalassemia mutations identified, seven were the most frequent, namely: IVS-II-1 (G > A), codon 8/9 (+G), IVS-I-6 (T > C), IVS-I-110 (G > A), IVS-I-I (G > A), IVS-I-5 (G > C) and codon 44 (-C) accounting for 78.5% of the mutations. This study further illustrates the heterogeneity of the spectrum of β-thalassemia in different parts of Iraq, and provides an essential step to facilitate prenatal diagnosis in the setting of a future national thalassemia prevention program.

Functional categorization of gene regulatory variants that cause Mendelian conditions

Much of our current understanding of rare human diseases is driven by coding genetic variants. However, non-coding genetic variants play a pivotal role in numerous rare human diseases, resulting in diverse functional impacts ranging from altered gene regulation, splicing, and/or transcript stability. With the increasing use of genome sequencing in clinical practice, it is paramount to have a clear framework for understanding how non-coding genetic variants cause disease. To this end, we have synthesized the literature on hundreds of non-coding genetic variants that cause rare Mendelian conditions via the disruption of gene regulatory patterns and propose a functional classification system. Specifically, we have adapted the functional classification framework used for coding variants (i.e., loss-of-function, gain-of-function, and dominant-negative) to account for features unique to non-coding gene regulatory variants. We identify that non-coding gene regulatory variants can be split into three distinct categories by functional impact: (1) non-modular loss-of-expression (LOE) variants; (2) modular loss-of-expression (mLOE) variants; and (3) gain-of-ectopic-expression (GOE) variants. Whereas LOE variants have a direct corollary with coding loss-of-function variants, mLOE and GOE variants represent disease mechanisms that are largely unique to non-coding variants. These functional classifications aim to provide a unified terminology for categorizing the functional impact of non-coding variants that disrupt gene regulatory patterns in Mendelian conditions.

The Spectrum of β-Thalassemia Mutations in the Population Migration in Lebanon: A 6-Year Retrospective Study

β-Thalassemia (β-thal) is highly prevalent among the Mediterranean populations. In Lebanon, the carrier rate of the disease is estimated to be around 2.0-3.0%. In this retrospective study, we determined the spectrum of β-thal mutations in a total of 170 individuals from a sample of 140 Lebanese, Iraqi and Syrian refugee families in Lebanon, over a period from 2012 to 2018. Twenty-eight different β-globin gene mutations were identified. The most prevalent mutations were IVS-I-110 (G>A) (HBB: c.93-21G>A), IVS-II-1 (G>A) (HBB: c.315+1G>A), IVS-I-6 (T>C) (HBB: c.92+6T>C) and IVS-I-1 (G>A) (HBB: c.92+1G>A), accounting for the majority of mutations found in HBB mutations analysed in 250 alleles. Ten different β-globin gene mutations that were not previously described in Lebanon were identified in our study. These mutations include the IVS-II-848 (C>A) (HBB: c.316-3C>A), codons 9/10 (+T) (HBB: c.30_31insT), codon 15 (-T) (HBB: c.46delT), -86 (C>G) (HBB: c.-136C>G), Cap +22 (G>A) (HBB: c.-29G>A), -28 (A>C) (HBB: c.-78A>C), codon 7 (GAG>TAG) (HBB: c.22G>T), codon 26 (GAG>TAG) (HBB: c.79G>T), codons 41/42 (-TTCT) (HBB: c.126_129delCTTT), and codons 82/83 (-G) (HBB: c.250delG). Of these, six mutations [codons 9/10, codon 15 (-T), -86, codon 7, codon 26, codons 82/83) were identified in Lebanese samples only; one mutation (IVS-II-848) was identified in both Lebanese and Iraqis; and three mutations (Cap +22, -28, codons 41/42) were identified in Iraqi samples only. Further studies will help better delineate the spectrum of β-thal mutations among different ethnic groups, and provide crucial prevention strategies.

A large-scale study exploring understanding of the national premarital screening program among Jordanians: Is an at-risk marriage a valid option for Jordanians?

Detecting carrier couples through premarital screening implementation is an effective way of controlling thalassaemia. The aim of this study was to investigate the knowledge of university students towards premarital screening and their possible involvement in an at-risk marriage. Students (n = 976) were chosen randomly from Jordanian universities. The questionnaire consisted of three sections: socio-demographical data, the students' knowledge about the screening programme, and finally their beliefs and future decisions related to it. Most (90%) participants were aware of the premarital screening availability. Females had significantly better understanding of premarital screening compared to males. Despite the majority of the participants not wanting to go ahead with at-risk marriages, 23% would not be deterred from marrying their anticipated partner and believed engaging in at-risk marriage was a valid idea. We suggest providing more effective educational programmes, genetic counselling and free prenatal diagnosis for at-risk couples.

Sickle Cell Disease in Jordan: The Experience of a Major Referral Center

Introduction

Sickle cell disorders are the most frequently encountered hemoglobin variants in Jordan. Both alpha and beta thalassemias are also prevalent in this population. However, studies on the interaction between these hemoglobin disorders are lacking.

Aim

To determine the genotypes responsible for Sickle cell disease in Jordan, by retrospectively reviewing the data from a major referral center in the country's capital.

Methods

A total 29,712 peripheral blood samples referred and investigated for hemoglobinopathies over a 10-year period at Princess Iman Center at Amman, Jordan were retrospectively reviewed. In addition to full blood counts, high performance liquid chromatography, those who were identified with sickle cell hemoglobin were studied using polymerase chain reaction and reverse hybridization to determine the various sickle cell disease genotypes.

Results

Out of the (29,712) blood samples, 450 were sickle cell trait, while 216 had sickle cell disease. Of the latter: 120 were found to be cases of Sickle cell anemia (Hb SS), 66 were compound heterozygous for Sickle cell and a beta thalassemia mutation (Sickle/β-thalassemia), while 30 had concomitant alpha thalassemia (HbSS/alpha thalassemia). The most frequent genotype associated with sickle/β-thalassemia was HbS/ IVS-110 (G>A), followed by Hb S/IVS-I-6 (T>C), HbS/IVS-II-745 (C>G) and HbS/ IVS-II-1 (G>A). While the most frequent alpha genotype detected in HbSS/α-thalassemia samples was (-α^3.7/αα) followed by (-α^3.7/-α^3.7). Hb SS patients had the severest hematological phenotype compared to those with sickle/β-thalassemia and sickle/ α-thalassemia. Furthermore, within the sickle/β-thalassemia subgroup the least severe hematological phenotype was encountered in HbS/IVS-1-6 (T>C), while the most severe in HbS/IVS-II-1 (G>A) genotype.

Conclusion

The most frequent Sickle cell disease genotype in Jordanians is Sickle cell anemia (HbSS), followed by Sickle/β-thalassemia and least frequent is HbSS/alpha thalassemia. The concomitant identified thalassemia mutations were consistent with their spectrum among the Jordanian population.

The spectrum of beta-thalassemia mutations in the 22 Arab countries: a systematic review

OBJECTIVES

To investigate the mutational spectrum in the HBB gene in Arab patients with β-thal.

METHODS

Authors searched five databases (PubMed, Science Direct, Scopus, Web of Science, and Google Scholar) from the time of inception until March 2020.

RESULTS

The authors search strategy yielded 3,229 citations, of which 48 eligible studies captured. 105 mutations were captured, of these, 99 were shared between Arabs and other ethnic groups, six mutations were unique to Arabs (c.92 + 2 T > G, c.-240 G > A, c.150delC, c.420dupT, deletion of 192 bp spanning exon 1, intron 1, and the first two bases of exon 2 of HBB gene, and deletion of 9.6 kb, including exon 1 and intron 2 of HBB gene). The most common HBB gene mutations among Arabs were c.93-21 G > A, c.118 C > T, c.92 + 1 G > A, c.92 + 6 T > C, c.92 + 5 G > C, c.315 + 1 G > A, and c.27dupG. Consanguinity is high among Arab patients with β-thal. Migration into Arab countries led to allelic heterogeneity among Arab patients with β-thal.

CONCLUSION

Our findings present a platform for further genetic epidemiological studies for Arab patients with β-thal.

Molecular characterization of β-thalassemia intermedia in the West Bank, Palestine

BACKGROUND

We aimed to investigate the molecular basis of β-Thalassemia intermedia (TI) in the West Bank region and its management practices.

METHODS

This was a case series multi-center study and included 51 cases of TI. DNA sequencing was used to analyze β-globin gene mutations. Common α-globin gene mutations were screened by Gap-PCR (-α3.7, -α4.2, --MED, αααanti3.7) or DNA sequencing (α2-IVS II 5 nt del). XmnI -158 C > T polymorphisms of Gγ-globin gene was determined by RFLP-PCR.

RESULTS

Seven β-globin gene mutations were observed, namely IVS-I -6 C > T, IVS-I-110 G > A, IVS-II-1 G > A, IVS-I-1 G > A, Codon 37 Trp > Stop, beta - 101 and IVS-II-848 C > A. Ten genotypes were observed. Homozygosity for IVS-I-6 accounted for the majority of TI cases with a frequency of 74.5%. The second common β-globin gene genotype was homozygote IVS-I-110 G > A (5.8%) and homozygote IVS-II-1 G > A (5.8%). The remaining seven genotypes were each detected in about 2% of patients. α-Thalassemia mutations were seen in five patients (9.8%), and included (-α3.7, αααanti3.7 and α2-IVSII-5 nt del). XmnI polymorphism was observed in four patients (7.8%), three homozygotes and one heterozygote.

CONCLUSIONS

Homozygosity for the mild β-globin gene IVS-I-6 allele was the major contributing factor for the TI phenotype among the study subjects. The role of XmnI SNP and α-thalassemia mutations in ameliorating the TI phenotype was observed in few patients for each factor. The beta - 101 C > T mutation was diagnosed in one patient in homozygote state for the first time in Palestine.

β-Thalassemia Haplotypes in Romania in the Context of Genetic Mixing in the Mediterranean Area

The purpose of this meta-study was to investigate β-thalassemia (β-thal) mutations and their chromosomal background in order to highlight the origin and spread of thalassemia alleles in the European and Mediterranean areas. Screening of more than 100 new Romanian β-thal alleles was also conducted. The results suggest an ancient introduction of mutations at codon 39 (C > T) (HBB: c.118C > T) and IVS-I-6 (T > C) (HBB: c.92 + 6T > C) in Romania. A comparative study was performed based on restriction fragment length polymorphism (RFLP) haplotypes associated with β-thal mutations in Romania and in Mediterranean countries. Each common β-thal allele from different populations exhibits a high degree of haplotype similarity, a sign of a clear unicentric origin for the IVS-I-110 (G > A) (HBB: c.93-21G > A), IVS-I-6, IVS-II-745 (C > G) (HBB: c.316-106C > G) and codon 39 mutations (the 17a [+ - - - - + +], 13c [ - + + - - - +], 17c [ + - - - - - +] and 14a [- + + - + + + ] ancestral RFLP background, respectively), followed by recurrent recombination events. This study also showed that geographic distances played a major role in shaping the spread of the predominant β-thal alleles, whereas no genetic boundaries were detected between broad groups of populations living in the Middle East, Europe and North Africa. The analyses revealed some discrepancies concerning Morocco and Serbia, which suggest some peculiar genetic flows. Marked variations in β(A) were observed between Southeast Asia and the Mediterranean, whereas a relative genetic homogeneity was found around the Mediterranean Basin. This homogeneity is undoubtedly the result of the high level of specific historic human migrations that occurred in this area.

Molecular Characterization of β-Thalassemia in Nineveh Province Illustrates the Relative Heterogeneity of Mutation Distributions in Northern Iraq

Beta thalassemia is an important health problem in Nineveh province, a large province in Northwestern Iraq. No previous study of significance had focused on the spectrum of β-thalassemia mutations in this part of the country. A total of 94 unrelated β-thalassemia minor subjects from the latter province were recruited. Their carrier status was confirmed by full blood count, Hb A2 and F estimation. Thereafter their DNA was subjected to multiplex polymerase chain reaction and reverse hybridization to detect 20 β-thalassemia mutations. A total of eleven different β-thalassemia mutations were documented. The most frequent mutation was IVS-I-110 (G>A) documented in 34 %, followed by IVS-I-6 (T>C) in 9.6 %, IVS-I-5(G>C) in 8.5 %, codon 39 (C>T) and codon 44 (-C) in 7.4 % each, while IVS-I-1(G>A) and IVS-II-1(G>A) were encountered in 6.4 % each. Other mutations were less frequent including codon 8 (-AA), IVS-I-130 (G>C), codon 5 (-CT) and IVS-II-745(C>G). The current study revealed notable differences in the relative frequencies of several β-thalassemia mutations in Nineveh province as compared to other parts of Northern Iraq. Such an observation may be reflective of different ethnic backgrounds and varying historical population interactions. It is believed that these findings complement those of earlier studies on β-thalassemia mutations from the country, and are quite essential in the setting of a proposed national preventive program.

A novel promoter mutation (HBB: c.-75G>T) was identified as a cause of β(+)-thalassemia

We report a novel β-globin gene promoter mutation in a Chinese family identified using fluorescence resolution melting curve analysis and gene sequencing. The proband, who showed the phenotype of β-thalassemia intermedia (β-TI), was found to be a compound heterozygote for the novel mutation -25 (G>T) (HBB: c.-75G>T) and a codon 17 (HBB: c.52A>T) mutation. Moreover, conservation analysis using phyloP and phastCons indicated that the mutated base in the proband was conserved. This novel point mutation on the β-globin gene is in close proximity to the conserved ATAA sequence located at position -25 relative to the mRNA Cap site. We performed a further comparative analysis of the clinical phenotypes and hematological parameters in this pedigree and found that the father was a carrier of the novel point mutation and showed low levels of hemoglobin (Hb), mean corpuscular volume (MCV) and mean corpuscular Hb (MCH). Thus, the available evidence suggests that this novel mutation, -25, results in β(+)-thalassemia (β(+)-thal).

Epidemiological profile of common haemoglobinopathies in Arab countries

Haemoglobinopathies including the thalassemias and sickle cell disease are known to be prevalent inherited disorders in most Arab countries with varying prevalence rates and molecular characterisation. β-thalassemia is encountered in polymorphic frequencies in almost all Arab countries with carrier rates of 1-11 % and a varying number of mutations. The most widespread mutation in Lebanon, Egypt, Syria, Jordan, Tunisia and Algeria is the IVS-I-110 (G>A). In the Eastern Arabian Peninsula, the Asian Indian mutations (IVS-I-5 (G>C), codons 8/9 (+G) and IVS-I (-25 bp del)) are more common. The α-thalassemias are encountered in the majority of Arab countries in frequencies ranging from 1 to 58 % with the highest frequencies reported from Gulf countries. The (-α(3.7)) mutation is the most frequent followed by the non-deletional α2 polyadenylation signal mutation (AATAAA>AATAAG) and the α2 IVS1 5-bp deletion. The rates of sickle cell trait in Arab countries range from 0.3 to 30 %, with the Benin, the Arab-Indian and the Bantu haplotypes constituting the bulk of the haplotypes, leading to two major phenotypes; a mild one associated with the Arab-Indian and a severe one with the Benin and Bantu haplotypes. Public health approaches targeting prevention of haemoglobinopathies in Arab countries include newborn screening for sickle cell disease, and premarital screening for carriers of β-thalassemia and sickle cell disease. These services are still patchy and inadequate in many Arab countries recommending the upgrade of these services with strengthening of the education and training of health care providers and raising public awareness on the feasibility of prevention and care for haemoglobinopathies.

Global burden, distribution and prevention of β-thalassemias and hemoglobin E disorders

The β-thalassemias, including the hemoglobin E disorders, are not only common in the Mediterranean region, South-East Asia, the Indian subcontinent and the Middle East but have now become a global problem, spreading to much of Europe, the Americas and Australia owing to migration of people from these regions. Approximately 1.5% of the global population are heterozygotes or carriers of the β-thalassemias. While the overall frequencies of carriers of these disorders are known in most countries, there have been few attempts at micromapping and wherever this has been done, significant variations are seen even within small geographic regions. Thus, the figures for the estimated numbers of births each year of homozygous β-thalassemia and the severe compound states involving other hemoglobin disorders may be an underestimate. Screening strategies have varied from premarital to antenatal in different countries depending on socio-cultural and religious customs in different populations. Prenatal diagnosis programs are ongoing in many countries and the knowledge of the distribution of mutations has facilitated the establishment of successful control programs. Many of these were through North-South partnerships and networking. Yet, there are many countries in Asia where they are lacking, and South-South partnerships are now being developed in South-East Asia and the Indian subcontinent to link centers with expertise to centers where expertise needs to be developed. Although the carrier frequencies will remain unaltered, this will eventually help to bring down the burden of the birth of affected children with β-thalassemias and hemoglobin E disorders in Asia.

β-Thalassemia mutations in the Kurdish population of northeastern Iraq

A random 123 carriers of β-thalassemia (β-thal), identified by the Sulaimaniyah Provincial Premarital Screening Program in northeastern Iraq, were screened for β-thal mutations using multiplex polymerase chain reaction followed by reverse hybridization StripAssay and direct sequencing. A total of 11 different β-thal mutations was identified in the studied samples, of which eight represented 96% of the mutated β-globin genes. These were IVS-II-1 (G>A), IVS-I-110 (G>A), codon 8 (-AA), codons 8/9 (+G), IVS-I-5 (G>C), codon 5 (-CT), IVS-I-6 (T>C) and IVS-I-1 (G>A). Other mutations were less common or sporadic. There were some notable differences in frequencies of various mutations in comparison to other eastern Mediterranean populations, as well as with previous studies of Iraqi Kurds. The latter illustrate the relative heterogeneity of the mutations distributed in Iraq, and the need to screen other areas of the country, to ensure the establishment of an effective prenatal diagnosis program.

β-Thalassemia Mutations among Transfusion-Dependent Thalassemia Major Patients in Northern Iraq

Molecular defects responsible for β-thalassemias (thal) were investigated among 254 chromosomes from 127 transfusion-dependent unrelated thalassemic patients from two provinces in Northern Iraq. Among fourteen identified mutations, the seven most common found in 88.2% of the thal chromosomes were: IVS-II-1 (G → A), IVS-I-1 (G → A), codon 8 (−AA), codon 39 (G → T), codon 8/9 (+G), codon 44 (−C), and codon 5 (−CT). There were some notable differences in frequencies of various mutations in comparison to other Eastern Mediterranean populations, as well as between the two provinces studied. The latter illustrates the relative heterogeneity of the mutations distribution in Iraq, and the need to screen other areas of the country, to ensure establishing an effective prenatal program.

Molecular updating of β-thalassemia mutations in the Upper Egyptian population

We have updated the dataset of the molecular spectrum of the β-thalassemia (β-thal) in Upper Egypt. Buccal swabs were analyzed from 94 unrelated patients with β-thal major (β-TM) using reverse dot-blot and multiplex amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). The most frequent mutation was IVS-I-110 (G>A) (57%). The IVS-I-110, IVS-I-6 (T>C) and IVS-I-1 (G>A) mutations accounted for 87% of the β-thal anomalies. The codon 39 (C>T) and frameshift codon (FSC) 6 (-A) (GAG>-GG) mutations were only detected in Al-Minya and Qina, respectively. We did not observe the IVS-II-745 (C>G) or -101 (C>T) mutations. Forty-three percent of Upper Egyptians were homozygotes. Our efforts were an important step to complete the mutation map of β-thal in Egypt restricted to Cairo and the Nile Delta regions. This study will help to develop preventative programs for Upper Egyptians. It addressed the genetic drift of the β-thal gene mutations in Africa, Asia, and Europe.

Molecular basis of beta-thalassemia in Morocco: possible origins of the molecular heterogeneity

We present the molecular spectrum of beta-thalassemia in the Moroccan population obtained by the identification of molecular defects responsible for this disease, and herewith we show that the Moroccan population is genetically heterogeneous; 18 different mutations have been found in the 158 beta-globin chromosomes studied. Eight mutations [codon 39 (C --> T), FSC-8 (-AA), IVS-II-745 (C --> G), -29 (A --> G), FSC-6 (-A), IVS-I-110 (G --> A), IVS-I-2 (T --> C), and IVS-I-1 (G --> A)] out of 18 beta-thalassemia mutations identified accounted for 76% of the Moroccan beta-thalassemia chromosomes. Restriction fragment length polymorphism (RFLP) haplotype analysis showed that the observed genetic diversity originated from both new mutational events and gene flow due to migration.

Three new beta-globin gene promoter mutations identified through newborn screening

We report three new beta-globin gene promoter mutations identified in newborns with hemoglobin (Hb) profiles consistent with Hb S/beta(+)-thalassemia (thal) (Hbs FSA). All three mutations are in close proximity to the conserved ATAA sequence located at positions -31 to -28 relative to the mRNA Cap site. Two cases involved single base substitutions at positions -25 (G-->C) and -32 (C-->T). The remaining case involved the deletion of two bases (-AA) at positions -27 and -26.

Jordan: communities and community genetics

The population in Jordan mounted from half a million in 1952 to 5.3 millions in 2004 and is composed of a variety of ethnic groups, the majority being Arabs. Couples nowadays tend to have fewer children, with the total fertility rate falling from 7.4 in 1976 to 3.7 in 2004. Consanguineous marriages are traditionally favored, with the preferred marriage partner being the offspring of the father's brother. First-cousin marriages declined from 28.5% for marriages contracted between 1950 and 1979 to 19.5% for marriages contracted after 1980. In the overall population, carrier rates for beta-thalassemia, alpha-thalassemia and sickle cell anemia are in the range of 2-4%, 3.2-12% of males have glucose-6-phosphate dehydrogenase deficiency, and the prevalences for familial Mediterranean fever and cystic fibrosis were estimated at around 0.04% each. A mandatory premarital screening program for beta-thalassemia carriers commenced in June 2004. The high consanguinity rate and the large family size in Jordan have contributed to the description of a number of rare and new autosomal recessive conditions. Genetic services in Jordan are still scarce and do not cover all the country due to the major impediments of a paucity of resources and trained health professionals in the area of medical genetics. The demographic data suggest that the health system in Jordan is capable of introducing some basic community genetic services into the primary health care program through comprehensive and cost-effective programs.

Genetic Heterogeneity of Beta Thalassemia in Lebanon Reflects Historic and Recent Population Migration

Beta thalassemia is an autosomal recessive disorder characterized by reduced (beta(+)) or absent (beta(0)) beta-globin chain synthesis. In Lebanon it is the most predominant genetic defect. In this study we investigated the religious and geographic distribution of the beta-thalassemia mutations identified in Lebanon, and traced their precise origins. A total of 520 beta-globin chromosomes from patients of different religious and regional backgrounds was studied. Beta thalassemia mutations were identified using Amplification Refractory Mutation System (ARMS) PCR or direct gene sequencing. Six (IVS-I-110, IVS-I-1, IVS-I-6, IVS-II-1, cd 5 and the C > T substitution at cd 29) out of 20 beta-globin defects identified accounted for more than 86% of the total beta-thalassemia chromosomes. Sunni Muslims had the highest beta-thalassemia carrier rate and presented the greatest heterogeneity, with 16 different mutations. Shiite Muslims followed closely with 13 mutations, whereas Maronites represented 11.9% of all beta-thalassemic subjects and carried 7 different mutations. RFLP haplotype analysis showed that the observed genetic diversity originated from both new mutational events and gene flow from population migration. This study provides information about the types and distribution of beta-thalassemia mutations within each religious group and geographic region, which is essential for the implementation of screening and prevention programs.