The molecular characterization of Beta globin gene in thalassemia patients reveals rare and a novel mutations in Pakistani population

Mutation Spectrum of β-Globin Gene in Patients with β-Thalassemia at Tidar Hospital, Magelang, Central Java, Indonesia

β-Thalassemia is genetic disorder characterized by β-globin chain deficiency resulting from mutations in the β-globin coding gene. Both the quantity and quality of blood produced will be impacted by this condition. The distribution of mutation causing thalassemia is vary across ethnic and different regions in Indonesia. This study aims to identify the variant mutation in patients with β-thalassemia at Tidar Hospital as representative samples of Javanese population, the largest ethnicity in Indonesia. Sixty-one blood samples were obtained from blood transfusion-dependent patients with β-thalassemia. Mutation was identified using ARMS and RFLP PCR-based methods, and inconclusive samples were subjected to DNA sequencing. Results showed that the mutation variants were Cd 26/IVSI-5 (G > C) 47.54%, Cd 26/Cd 35 16.30%, Cd 26/IVSI-1 (G > T) 11.47%, Cd 26/IVSI-2 4.91%, IVSI-5 (G > C)/Cd 40 3.27%; 1.63%; IVSI-5 (G > C)/IVSI-1 (G > A) 1.63%; IVSI-5 (G > C)/Cap + 1 1.63%; Cd 26/Cd 15 1.63%; Cd 26/Cd 30 1.63%. We also found three homozygous of IVSI-1 (G > T), IVSI-5 (G > C) 6.55%, and Cd 35 1.63%. The most prevalent alleles would be recommended to be used as part of screening for β-thalassemia in the Javanese ethnicity in Central Java, especially for families affected by thalassemia.

Mutational analysis of hemoglobin genes and functional characterization of detected variants, through in-silico analysis, in Pakistani beta-thalassemia major patients

Thalassemia is one of the most prevalent genetic disorders worldwide. The present study aimed to explore the mutational spectrum of all hemoglobin (HB) encoding genes and to identify the potentially damaging and pathogenic variants in the beta (β)-thalassemia major patients and thalassemia minor carriers of Southern Punjab, Pakistan. A total of 49 β-thalassemia major patients and 49 carrier samples were screened for the identification of HBA1, HBA2, HBB, HBD, HBE1, HBG1 and HBG2 variants by NGS. PCR was performed for the amplification of HB encoding genes and the amplified product of 13 patients and 7 carrier samples were processed for the Sanger sequencing. Various bioinformatics tools and databases were employed to reveal the functional impact and pathogenicity potential of the observed variants. Results depicted a total of 20 variants of HB-related genes by NGS and 5 by Sanger sequencing in thalassemia patients. While 20 variants by NGS and 3 by Sanger were detected in carriers. Few known genetic variants of HB-encoding genes are being reported for the first time in Pakistani thalassemia patients and carriers. However, two novel HBB variants c.375A>C (p.P125P) and c.*61T>G and a novel variant of HBE1 (c.37A>T (p.T13S)) were also documented. Pathogenicity analysis predicted the pathogenic potential of HBB variants (c.47G>A (p.W16*), c.27-28insG (p. S10fs), and c.92+5G>C) for β thalassemia. The study of functional impact indicated that these HBB variants result in the premature termination of translation leading to the loss of functional β-globin protein. It is therefore suggested that the pathogenic HBB variants, identified during present study, can be employed for the diagnosis, carrier screening, and planning therapy of thalassemia.

Rare and New Mutations of B-Globin in Azari Population of Iran, a Considerable Diversity

Background

Thalassemia, as the most common single-gene genetic disorder, is related to a defect in the synthesis of one or more hemoglobin chains. More than 200 mutations have been identified in the β-globin gene. Globally, every susceptible racial group has its own specific spectrum of the common mutations that are well-known to a particular geographic region. On the other hand, varying numbers of diverse rare mutations may occur.

Materials and Methods

The subjects of the study included 2113 heterozygote or homozygote β-thalassemia cases selected among couples who participated in the Iranian national thalassemia screening program from January 2011 to November 2019. Molecular characterization of the β-thalassemia mutation was initially carried out by the amplification-refractory mutation system-polymerase chain reaction (ARMS-PCR) technique for common mutations, followed by sequencing, Gap PCR, and Multiple ligation-dependent probe amplification (MLPA) methods - in cases not detected by the ARMS-PCR.

Results

The existence of 39 rare and new point mutations and 4 large deletions were described in our cohort. Sicilian (-13,337bp) deletion, CD36/37 (-T), and CD15 TGG>TGA were encountered more often than the others in a decreasing order, in terms of frequency. The least frequent mutations/deletions were deletion from HBD exon 1 to HBB promoter, 619 bp deletion, Deletion from up HBBP1-Exon3 HBBP1 and up HBB-0.5Kb down HBB, CAP+8 C>A, CD37 (G>A), CD6 (-A), IVSI-2 (T>C), IVSII-705 T>G, and IVSII-772 (G>A). Each occurred once. Five mutations/variants were also determined which have not been reported previously in Iran.

Conclusion

According to the findings of the study, the Northwestern Iranian population displayed a wide variety of thalassemia allelic distributions. Identification of rare and new mutations in the β-thalassemia in the national population is beneficial for screening programs, genetic counseling, and prenatal diagnosis.

α- and β-Globin Gene Mutations in Individuals with Hemoglobinopathies in the Chattogram and Sylhet Regions of Bangladesh

Hemoglobinopathies, including α- and β-thalassemias and sickle cell disease, are among the most widely disseminated hereditary blood disorders worldwide. Bangladesh is considered a hotspot for hemoglobinopathies, and these diseases cause a significant health concern in the country. However, the country has a dearth of knowledge on the molecular etiology and carrier frequency of thalassemias, primarily due to a lack of diagnostic facilities, limited access to information, and the absence of efficient screening programs. This study sought to investigate the spectrum of mutations underlying hemoglobinopathies in Bangladesh. We developed a set of polymerase chain reaction (PCR)-based techniques to detect mutations in α- and β-globin genes. We recruited 63 index subjects with previously diagnosed thalassemia. Along with age- and sex-matched control subjects, we assessed several hematological and serum indices and genotyped them using our PCR-based methods. We identified that parental consanguinity was associated with the occurrence of these hemoglobinopathies. Our PCR-based genotyping assays identified 23 HBB genotypes, with the codons 41/42 (-TTCT) (HBB: c.126_129delCTTT) mutation leading the spectrum. We also observed the presence of cooccurring HBA conditions, of which the participants were not aware. All index participants in this study were on iron chelation therapies, yet we found they had very high serum ferritin (SF) levels, indicating inefficient management of the individuals undergoing such treatments. Overall, this study provides essential information on the hemoglobinopathy mutation spectrum in Bangladesh and highlights the need for nationwide screening programs and an integrated policy for diagnosing and managing individuals with hemoglobinopathies.

Spectrum of HBB gene mutations among 696 β-thalassemia patients and carriers in Southern Vietnam

BACKGROUND

Thalassemias are common inherited blood disorders that have been extensively studied in Asia. Thus far, data on mutations of the HBB gene in Vietnamese patients with β-thalassemia are limited to small studies.

METHODS

We recruited 696 β-thalassemia patients and carriers in southern Vietnam and analyzed for the HBB gene mutations using Sanger sequencing technology.

RESULTS

We documented 27 types of known mutations and 10 types of novel variants on 737 alleles out of 1392 surveyed alleles. The three most common mutations, which account for more than ¾ of all mutant alleles, were c.79G > A (HbE), c.124_127delTTCT, and c.52A > T. The novel variants were mainly located in 5' untranslated region (c.-92delC and c.-67A > G) and 3' untranslated region (c.*4C > T, c.*116_*117insA, c.*142 T > C, c.*156G > C, c.*176_*177insA, and c.*247 T > C), except for one in intron 2 (c.316-99 T > G) and one in exon 3 (c.385delG).

CONCLUSION

We provide here a comprehensive mutation spectrum of the HBB gene in Southern Vietnam, which is crucial for carrier screening and prenatal diagnosis in the future.

Genetic variation patterns of β-thalassemia in Western Andalusia (Spain) reveal a structure of specific mutations within the Iberian Peninsula

BACKGROUND

Analyses of the genomic variation in the western Mediterranean population are being used to reveal its evolutionary history and to understand the molecular basis of particular diseases.

AIM

To observe the β-thalassemia mutational spectrum in western Andalusia, Spain, in the context of the Mediterranean. In addition, associations between disease and neutral gene variants within the β-globin gene (HBB) were also evaluated.

SUBJECTS AND METHODS

This study included 63 unrelated individuals diagnosed with β-thalassemia. In addition, 97 unrelated, healthy subjects of the same territory were also analysed as proxies of the normal genetic background. Allele associations and population genetic structure analyses were performed using different methodologies.

RESULTS

Data have revealed a rather restricted spectrum of β-thalassemia mutations in the analysed sample. Although the detected variants fit well with the Mediterranean pattern, certain singularities support a structure of some specific β-thalassemia alleles. The IVSI-1 (G > A) shows a strong regionalisation. The spatial correlogram revealed a typically narrow wave structure, presumably linked to genetic isolation and genetic drift.

CONCLUSIONS

The long history of endemic malaria in the study territory, the rather high consanguinity rates among its autochthonous population, and other demographic features have been used here to understand the western Andalusian β-thalassemia molecular portrait.

Machine learning assistive rapid, label-free molecular phenotyping of blood with two-dimensional NMR correlational spectroscopy

Translation of the findings in basic science and clinical research into routine practice is hampered by large variations in human phenotype. Developments in genotyping and phenotyping, such as proteomics and lipidomics, are beginning to address these limitations. In this work, we developed a new methodology for rapid, label-free molecular phenotyping of biological fluids (e.g., blood) by exploiting the recent advances in fast and highly efficient multidimensional inverse Laplace decomposition technique. We demonstrated that using two-dimensional T1-T2 correlational spectroscopy on a single drop of blood (<5 μL), a highly time- and patient-specific 'molecular fingerprint' can be obtained in minutes. Machine learning techniques were introduced to transform the NMR correlational map into user-friendly information for point-of-care disease diagnostic and monitoring. The clinical utilities of this technique were demonstrated through the direct analysis of human whole blood in various physiological (e.g., oxygenated/deoxygenated states) and pathological (e.g., blood oxidation, hemoglobinopathies) conditions.

Enabling routine β-thalassemia Prevention and Patient Management by scalable, combined Thalassemia and Hemochromatosis Mutation Analysis

BACKGROUND

Beta (β)-thalassemia is one of the most common inherited disorders worldwide, with high prevalence in the Mediterranean, the Middle East and South Asia. Over the past 40 years, awareness and prevention campaigns in many countries have greatly reduced the incidence of affected child births. In contrast, much remains to be done in South-Asia. Thus, for Pakistan, an estimated ~ 7000 children annually are born with thalassemia, with no sign of improvement. Although there is good agreement that intermarriage of carriers significantly contributes to the high prevalence of the disorder, effective tools for molecular screening and diagnosis on which to base prevention programs are not readily available.

METHODS

Here, we present results for a novel LeanSequencing™ process to identify a combination of 18 β-thalassemia mutations (including the sickle cell anemia mutation, HbS, and structural variants HbC and HbE) and 2 hemochromatosis mutations in a multi-ethnic population of 274 pediatric and adolescent patients treated at Afzaal Memorial Thalassemia Foundation in Karachi, Pakistan.

RESULTS

We found substantial differences in the predominance of disease-causing mutations among the principal ethnic groups in our cohort. We also found the hemochromatosis mutation H63D C > G in 61 (or 22.1%) of our patients including 6 (or 2.2%) homozygotes.

CONCLUSIONS

To our knowledge, this is the first screen combining a large set of β-thalassemia and hemochromatosis mutations, so as to facilitate the early identification of patients who may be at increased potential risk for complications from iron overload and thereby to improve the prospective management of thalassemia patients.

Epidemiology and risk factors of transfusion transmitted infections in thalassemia major: a multicenter study in Pakistan

Background

Blood transfusion-transmitted infections in individuals suffering from beta-thalassemia have been reported in Pakistan, but the information on their sociodemographic and clinical determinants is lacking. This study aims to describe the prevalence, as well as the factors, contributing in blood transfusion-transmitted infections.

Method

Between December 2011 and December 2013, in a non-probable sampling, 350 thalassemia patients were recruited in Lahore, Multan, Karachi and Peshawar, Pakistan. Subjects were screened for transfusion-transmitted infections.

Results

A seropositive rate of 36.5% was observed; males (94, 73.4%) and females (34, 26.6%). Among several risk factors associated with transfusion-transmitted infections, province (p = 0.001), gender (p = 0.003), age (p < 0.03), education (p < 0.00), degree of consanguinity (p = 0.05), age at fetal blood test (p = 0.005), fetal hemoglobin levels (p = 0.005), death due to thalassemia (p = 0.001) and iron-related complications (p = 0.04) showed significant correlation. Participants with an age >10 years were significantly more prone to seropositivity than those aged ≤10 years. Moreover, the ferritin level was also significantly higher in those aged >10 years than in those ≤10 years. It was observed that males had a higher seroprevalence rate (94, 73.4%) than females (34, 26.6%). The most prevalent transfusion-transmitted infections was the hepatitis C virus, with 115 cases (89.8%).

Conclusion

A high prevalence rate of HCV in subjects with transfusion-dependent thalassemia is linked with insufficient facilities, poor management and compromised socioeconomic status. Therefore, more multicenter studies covering cities from different regions of the country are needed in order to develop preventive measurements at the regional and national level.

A Novel Mutation at HBB: c.91delA (Codon 30, -A) Causing β-Thalassemia in a Chinese Family

β-Thalassemia is a genetic disease characterized by the defective synthesis of the hemoglobin tetramer β-globin chains. So far, a number of mutations have been identified and associated with this genetic disease. A high incidence of thalassemia has been found in Guangxi (China). Herein, we report a case of a patient with slightly increased HbA2 levels (4.6%). Based on the clinical data and laboratory findings, the patient was diagnosed with β-thalassemia. Routine genetic screening tests were negative. Sequencing revealed an A deletion at codon 30 (HBB: c.91delA) and the genotype of this patient was βCD30M/β. This mutation changes the splice receptor site of intron 1 from AG to GG, which likely abolishes splicing at the normal 5' splicing site and may cause β0-thalassemia. Based on hematological and clinical evaluations, this novel mutation was regarded as a β0-thalassemia allele. A homozygosity or compound heterozygosity of this mutation and other β0-thalassemia alleles can lead to severe thalassemia disease.

Reflection of treatment proficiency of hydroxyurea treated β-thalassemia serum samples through nuclear magnetic resonance based metabonomics

β-Thalassemia is a widespread autosomal recessive blood disorder found in most parts of the world. Fetal hemoglobin (HbF), a form of hemoglobin is found in infants, replaced by adult hemoglobin (HbA) after birth. Hydroxyurea (HU) is one of the most effective HbF inducer used for the treatment of anemic diseases. We aimed to improve the understanding of HU therapy in β-thalassemia by metabonomics approach using ¹H NMR spectroscopy. This study includes 40 cases of β-thalassemia before and after HU therapy along with 40 healthy as controls. Carr-Purcell-Meiboom-Gill (CPMG) sequence was used to identify forty-one putative metabolites. Generation of models like partial least square discriminant analysis (PLS-DA) and orthogonal projections to latent structures discriminant analysis (OPLS-DA) based on different metabolites including lipids, amino acids, glucose, fucose, isobutyrate, and glycerol revealed satisfactory outcomes with 85.2% and 91.1% classification rates, respectively. The concentration of these metabolites was altered in β-thalassemia samples. However, after HU treatment metabolic profile of same patients showed closeness towards healthy. Deviant metabolic pathways counting lipoprotein changes, glycolysis, TCA cycle, fatty acid and choline metabolisms were identified as having significant differences among study groups. Findings of this study may open a better way to monitor HU treatment effectiveness in β-thalassemia patients, as the results suggested that metabolic profile of β-thalassemia patients shows similarity towards normal profile after this therapy.

Hydroxyurea Treated β-Thalassemia Children Demonstrate a Shift in Metabolism Towards Healthy Pattern

Augmentation of fetal hemoglobin (HbF) production has been an enduring therapeutic objective in β-thalassemia patients for which hydroxyurea (HU) has largely been the drug of choice and the most cost-effective approach. A serum metabolomics study on 40 patients with β-thalassemia prior to and after administration of HU was done along with healthy controls. Treated patients were divided further into non-responders (NR), partial (PR) and good (GR) per their response. 25 metabolites that were altered before HU therapy at p ≤ 0.05 and fold change >2.0 in β-thalassemia patients; started reverting towards healthy group after HU treatment. A prediction model based on another set of 70 HU treated patients showed a good separation of GR from untreated β-thalassemia patients with an overall accuracy of 76.37%. Metabolic pathway analysis revealed that various important pathways that were disturbed in β-thalassemia were reverted after treatment with HU and among them linoleic acid pathway was most impactfully improved in HU treated patients which is a precursor of important signaling molecules. In conclusion, this study indicates that HU is a good treatment option for β-thalassemia patients because in addition to reducing blood transfusion burden it also ameliorates disease complications by shifting body metabolism towards normal.

New Bioinformatics-Based Discrimination Formulas for Differentiation of Thalassemia Traits From Iron Deficiency Anemia

Thalassemia traits (TTs) and iron deficiency anemia (IDA) are the most common disorders of hypochromic microcytic anemia (HMA). The present study aimed to differentiate TTs from IDA by analyzing discrimination formulas and provides comprehensive data of hemoglobin disorders prevalent in Pakistan. Among 12 published discrimination formulas, 6 formulas-MI, EF, G&K, RDWI, R, and HHI-were the most reliable to discriminate TTs from IDA. The failure cutoff values were improved by the random forest (RF) decision-tree approach. Moreover, the Shine and Lal (S&L) formula, which completely failed to discriminate IDA from TTs with original cutoff value (<1530), improved with the use of new proposed cutoff value (<1016) and was found to successfully discriminate all cases of TTs from those with IDA. In addition, 2 newly proposed formulas discriminated TTs from IDA more reliably than the original 12 formulas assessed. The proposed formulas could play a crucial role for clinicians to discriminate between TTs and IDA.

[Identification of a new 3.8kb deletional α thalassemia and detection of the deletion fragment]

OBJECTIVE

To report the identification of a novel 3.8-kb deletion that caused α thalassemia and establish the method for detecting the deletion fragment.

METHODS

Peripheral blood samples were collected from the proband and his mother for analysis of the hematological parameters and routine test for thalassemia genes. For the sample with an inconsistency between the genotyping results and phenotypic analysis results, a specific gap-PCR was employed to identify the rare or novel mutations.

RESULTS

A novel 3814-bp deletion causing α thalassemia was found in the proband and his mother, who had genotypes of -α4.2/-α3.8 and αα/-α3.8, respectively.

CONCLUSION

We identified a 3.8-kb deletion in the α-globin gene cluster that caused α thalassemia, and this finding enriches the α thalassemia gene mutation spectrum. Specific gap-PCR offers a convenient and efficient means for for detecting this deletion fragment.