Genetic heterogeneity of the β-globin gene in various geographic populations of Yunnan in southwestern China

Malaria resistance-related biological adaptation and complex evolutionary footprints inferred from one integrative Tai-Kadai-related genomic resource

Pathogen‒host adaptative interactions and complex population demographical processes, including admixture, drift, and Darwen selection, have considerably shaped the Neolithic-to-Modern Western Eurasian population structure and genetic susceptibility to modern human diseases. However, the genetic footprints of evolutionary events in East Asia remain unknown due to the underrepresentation of genomic diversity and the design of large-scale population studies. We reported one aggregated database of genome-wide SNP variations from 796 Tai-Kadai (TK) genomes, including that of Bouyei first reported here, to explore the genetic history, population structure, and biological adaptative features of TK people from southern China and Southeast Asia. We found geography-related population substructure among TK people using the state-of-the-art population genetic structure reconstruction techniques based on the allele frequency spectrum and haplotype-resolved phased fragments. We found that the northern TK people from Guizhou harbored one TK-dominant ancestry maximized in the Bouyei people, and the southern TK people from Thailand were more influenced by Southeast Asians and indigenous people. We reconstructed fitted admixture models and demographic graphs, which showed that TK people received gene flow from ancient southern rice farmer-related lineages related to the Hmong-Mien and Austroasiatic people and from northern millet farmers associated with the Sino-Tibetan people. Biological adaptation focused on our identified unique TK lineages related to Bouyei, which showed many adaptive signatures conferring Malaria resistance and low-rate lipid metabolism. Further gene enrichment, the allele frequency distribution of derived alleles, and their correlation with the incidence of Malaria further confirmed that CR1 played an essential role in the resistance of Malaria in the ancient "Baiyue" tribes.

Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan

BACKGROUND

Yunnan is located in Southwest China and consists of great cultural, linguistic, and genetic diversity. However, the genomic diversity of ethnic minorities in Yunnan is largely under-investigated. To gain insights into population history and local adaptation of Yunnan minorities, we analyzed 242 whole-exome sequencing data with high coverage (~ 100-150 ×) of Yunnan minorities representing Achang, Jingpo, Dai, and Deang, who were linguistically assumed to be derived from three ancient lineages (the tri-genealogy hypothesis), i.e., Di-Qiang, Bai-Yue, and Bai-Pu.

RESULTS

Yunnan minorities show considerable genetic differences. Di-Qiang populations likely migrated from the Tibetan area about 6700 years ago. Genetic divergence between Bai-Yue and Di-Qiang was estimated to be 7000 years, and that between Bai-Yue and Bai-Pu was estimated to be 5500 years. Bai-Pu is relatively isolated, but gene flow from surrounding Di-Qiang and Bai-Yue populations was also found. Furthermore, we identified genetic variants that are differentiated within Yunnan minorities possibly due to the living circumstances and habits. Notably, we found that adaptive variants related to malaria and glucose metabolism suggest the adaptation to thalassemia and G6PD deficiency resulting from malaria resistance in the Dai population.

CONCLUSIONS

We provided genetic evidence of the tri-genealogy hypothesis as well as new insights into the genetic history and local adaptation of the Yunnan minorities.

Five novel globin gene mutations identified in five Chinese families by next-generation sequencing

Background

Thalassemia is one of the most common inherited diseases worldwide. This report presents three novel cases of α‐thalassemia and two novel cases of β‐thalassemia caused by five different mutations in the globin gene.

Methods

Next‐generation sequencing (NGS) was used to identify novel α‐ and β‐thalassemia in five individuals, which was confirmed by Sanger sequencing of the globin gene. Hematological parameters were determined by an automated cell counter, and hemoglobin electrophoresis was carried out by a capillary electrophoresis system, respectively. The isoelectric point (pI), molecular weight, and conservation for the mutations were described by the Internet software programs. The pathogenicity for globin mutations was analyzed by bioinformatics analysis and relative quantitative analysis.

Results

NGS revealed five novel cases of α‐ and β‐thalassemia: HBA2:c.245C>T, HBA2:c.95+11_95+34delCTCCCCTGCTCCGACCCGGGCTCC, HBA2:c.54delC, HBB:c.373C>A, and HBB:c.40G>A. The clinical implications of these mutations were described. Computational predictions were made for pI, amino acid conservation, and pathogenicity of the missense mutation. Relative quantitative data of the α‐globin mRNA were analyzed.

Conclusion

Five novel globin mutations were identified in the populations of China, and those mutations were analyzed to provide a mechanistic view for their pathogenicity. These analyzed results improve genetic diagnostics for thalassemia, which can improve screening programs for thalassemia and prenatal diagnosis for Chinese population.

[Rare thalassemia caused by novel nucleotide variants in the globin gene: four case reports and literature review]

Objective: To analyze the DNA sequences and clinical phenotypes of four cases with rare thalassemia to improve its recognition and accurate diagnosis. Methods: The DNA sequence characteristics of four cases with rare thalassemia diagnosed from May 2014 to December 2019 were retrospectively analyzed, and related literature was reviewed. Results: The results of the routine gene test for thalassemia indicated that the common three type of deletion and three point mutations in hemoglobin alpha 1/2 (HBA1/A2) , and 16 point mutations in hemoglobin beta (HBB) gene were unable to be detected in cases 1-3, and case 4 was--SEA. However, the results of HBA1/A2 and HBB whole-genome sequencing revealed that the four cases had a point mutation of HBB:c.347C>A, HBB:c.1A>G, HBB:c.393T>G, and HBA2: c.301-1G>A (IVS II-142 G>A) , respectively. Meanwhile, the father, aunt, and grandfather of case 2 carried the HBB:c.1 A>G heterozygous point mutation. Conclusion: The novel mutations in HBB and HBA2 genes, resulting in a rare thalassemia, were revealed. Among them, the HBB:c.347C>A, HBB:c.1A>G, and HBA2:c.301-1G>A (IVS II-142 G>A) mutations were first reported in Chinese patients with thalassemia. Contrarily, HBB:c.393T>G mutation has not yet been recorded in the databases of human hemoglobin variants and thalassemia. The discovery of these novel nucleotide variants in this study would enrich the DNA mutation gene database of thalassemia.

A Cross-Sectional Study of Detection of Beta Globin (HBB) Haplotypes Among Beta Thalassemia Patients

Introduction

Beta-thalassemia is among the most common monogenic disorders in the Arabian Peninsula. This study aimed to investigate the β-globin (HBB) haplotypes among β-thalassemia patients in Saudi cohort which have potential implications in understanding the clinical care of patients and population genetic factors associated with β-thalassemia.

Methods

We analyzed 60 β-thalassemia patients. Male/female distribution for β-thalassemia was 58.33%/41.66%. Results of hematological parameters and indices were obtained from the database. HBB haplotyping assay was performed for four specific loci of the HBB gene cluster using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique.

Results

HBB haplotyping assay identified three novel patterns namely haplotype 1, haplotype 2, and haplotype 3 and three common African haplotypes including Benin, Senegal, and Cameron. The frequency of haplotype 1 was the highest among the studied samples (62%, n = 37) with 56.76% (n = 21) observed in males compared to 43.24% (n = 16) in females. This was followed by Senegal, haplotype 2, Benin and haplotype 3 with similar percentage, and Cameron haplotype with 18%, 12%, 3% and 2%, respectively. The relationship between these haplotypes and various hematological parameters was calculated and our study found no significant relationship (p-value >0.05).

Conclusion

Our study indicated the importance of finding out types of β-globin haplotypes as novel types being discovered. Though no statistically significant association was identified among all the haplotypes in terms of hematological parameters, Cameroon or Benin haplotypes had the mildest form because they have the highest means among all parameters. Further studies need to be carried out on a larger population to detect the frequency of each specific mutation in each haplotype among β-thalassemia patients. This would help to re-address the question of the origin(s) of the β-thalassemia.

Development of the Next Generation Sequencing-Based Diagnostic Test for β-Thalassemia and its Validation in a Pashtun Family

β-Thalassemia (β-thal) is a common monogenic disease with ethnic-specific mutations on the HBB gene throughout the world. The reported mutations either reduce the expression or completely inactivate the HBB gene. In Pakistan, the prevalence of β-thal is high due to consanguineous marriages. Accurate identification of mutations in carriers is imperative for prevention of β-thal in subsequent generations. To overcome the limitations of traditional testing methods for β-thal, a next-generation sequencing (NGS)-based diagnostic test was designed and validated by sequencing the entire HBB gene. The primer set covering the entire HBB gene was designed and validated in a Pashtun β-thalassemic family. The polymerase chain reaction (PCR) product was sequenced using an Illumina MiSeq platform. A homozygous pathogenic insertion of A>AC/AC (rs35699606) was detected in an affected member of the family, while unaffected members were heterozygous for it. In addition, all family members were homozygous for the synonymous variant, A>G/G (rs713040), except the father who was heterozygous for it. We sequenced the entire HBB gene using the NGS-based test, which is highly sensitive, robust and specific for the diagnosis and screening of β-thal in Pakistan, especially for families practicing consanguineous marriages.

Characterization of a Novel 71.8 kb α0-Thalassemia Deletion and Subsequent Summary of a Practical Procedure for Thalassemia Molecular Diagnosis

Thalassemia is the most common monogenic disorder around the world. Based on the principle of genotype-phenotype correlation, identification of thalassemia mutations is the essential prerequisite for clinical diagnosis and management. Because only common mutations are routinely detected, the identification of rare or undetermined mutations is a challenge for clinical laboratories. Herein, a proband presenting with inconsistent phenotype-genotype correlation after routine molecular screening was investigated by multiplex ligation-dependent probe amplification (MLPA), targeted-next generation sequencing (targeted-NGS), gap-polymerase chain reaction (gap-PCR) and Sanger sequencing. Eventually, a novel 71.8 kb deletion (- -^71.8) was identified and characterized, which included HBZ (ζ), HBA2 (α2), and HBA1 (α1) genes and was causing α⁰-thalassemia (α⁰-thal). Furthermore, we summarized a practical procedure based on accumulated experience in studies and clinical practice, which can be a guide for molecular screening and clinical diagnosis of thalassemia, especially for identification of undetermined or novel mutations.

Thalassemia and Hemoglobinopathies in an Ethnic Minority Group in Northern Vietnam

This study assessed thalassemia and hemoglobinopathies in a group of the Tay ethnic minority. Participants included 289 women of reproductive-age who enrolled in a pilot screening program for thalassemia conducted at six communities of Thai Nguyen Province, northern Vietnam. Standard procedures including complete blood count (CBC), hemoglobin (Hb) and DNA analyses were performed for all samples. The prevalence of thalassemia in 289 Tay women was 15.6% (gene frequency 0.078) for α⁰-thalassemia (α⁰-thal), 10.0% (gene frequency 0.050) for α⁺-thal, 7.3% (gene frequency 0.036) for β-thalassemia (β-thal), 2.4% (gene frequency 0.012) for Hb Constant Spring [Hb CS; α142, Term→Gln, TAA>CAA (α2), HBA2: c.427T>C] and 1.7% (gene frequency 0.009) for Hb E [β26(B8)Glu→Lys, GAG>AAG; HBB: c.79G>A]. Further analysis of β-globin gene abnormalities identified four mutations including codons 41/42 (-TCTT) (HBB: c.126_129delCTTT), codon 17 (A>T) (HBB: c.52A>T), codons 71/72 (+A) (HBB: c.216_217insA), and -28 (A>G) (HBB: c.78A>G). The results hint at the remarkably high frequencies of severe forms of thalassemia that indicate a serious public health problem requiring further exploration, and most probably, also intervention within the country.

Molecular epidemiology, pathogenicity, and structural analysis of haemoglobin variants in the Yunnan province population of Southwestern China

Abnormal haemoglobin (Hb) variants result in the most commonly inherited disorders in humans worldwide. In this study, we investigated the molecular epidemiology characteristics of Hb variants, along with associated structural and functional predictions in the Yunnan province population of Southwestern China. A total of 41,933 subjects who sought haemoglobinopathy screening were included. Based on bioinformatics and structural analysis, as well as protein modeling, the pathogenesis and type of Hb genetic mutations were characterized. Among all individuals studied, 328 cases (0.78%) were confirmed as carriers of Hb variants, with 13 cases (0.03%) presenting α-globin variants, 313 (0.75%) β-globin variants, and two δ-globin variants. A total of 19 different mutations were identified, including three novel mutations. In addition, 48 cases of αα^CS mutations and 14 cases of Hb H or Hb Bart’s were found. The isoelectric point, evolutionary conservation, and genotype-phenotype correlation for these mutations were predicted. Additionally, secondary and tertiary protein structure modeling were performed for three selected mutations. In conclusion, the prevalence of Hb variants in the Yunnan population is much higher than other regions of China. Complete characterization of these Hb variants is essential for generating a rational strategy to control the haemoglobinopathies in this region.

Analysis of deletional hereditary persistence of fetal hemoglobin/δβ-thalassemia and δ-globin gene mutations in Southerwestern China

Background

Deletional hereditary persistence of fetal hemoglobin (HPFH)/δβ‐thalassemia and δ‐thalassemia are rare inherited disorders which may complicate the diagnosis of β‐thalassemia. The aim of this study was to reveal the frequency of these two disorders in Southwestern China.

Methods

A total of 33,596 subjects were enrolled for deletional HPFH/δβ‐thalassemia, and positive individuals with high fetal hemoglobin (Hb F) level were diagnosed by multiplex ligation‐dependent probe amplification (MLPA). A total of 17,834 subjects were analyzed for mutations in the δ‐globin gene. Positive samples with low Hb A₂ levels were confirmed by δ‐globin gene sequencing. Furthermore, the pathogenicity and construction of a selected δ‐globin mutation were analyzed.

Results

A total of 92 suspected cases with Hb F ≥5.0% were further characterized by MLPA. Eight different deletional HPFH/δβ‐thalassemia were observed at a frequency of 0.024%. In addition, 195 cases suspected to have a δ‐globin gene mutation (Hb A₂ ≤2.0%) were characterized by molecular analysis. δ‐Globin gene mutation was found at a frequency of 0.49% in Yunnan. The pathogenicity and construction for a selected δ‐globin mutation was predicted.

Conclusion

Screening of these two disorders was analyzed in Southwestern China, which could define the molecular basis of these conditions in this population.

Analysis of Common β-Thalassemia Mutations in North Vietnam

Available and flexible choice of methods for screening and detecting β-thalassemia (β-thal) can promote control of thalassemia in developing countries. In this study, two methods, the amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) and reverse dot-blot hybridization assays were developed to detect common β-thal mutations in 244 thalassemia patients and 152 healthy people in North Vietnam. The most common mutation was codon 26 (G>A), also known as Hb E (HBB: c.79G>A), accounting for 26.4% of the total studied chromosomes, followed by codons 41/42 (-TCTT) (HBB: c.126_129delCTTT) and codon 17 (A>T) (HBB: c.c.52A>T), accounting for 19.4 and 16.4%, respectively. In addition, codon 95 (+A) (HBB: c.c.287_288insA) that is known as the Vietnamese mutation, accounted for 0.6%. Moreover, the heterozygous state of the four mutations was also found in healthy people, of which Hb E was again the most common mutation with a frequency 3.0%. The results of this study provide available methods and indicative data for preventive and control strategies concerning the genetic diagnosis of thalassemia.

β‑thalassemia caused by compound heterozygous mutations and cured by bone marrow transplantation: A case report

In the present study, a rare familial case of severe thalassemia with compound spontaneous mutations is reported. A 2.5-year-old boy, who suffered from severe anemia with yellowish skin, enlarged liver and spleen, was provided with a blood transfusion every 20 days to maintain hemoglobin levels between 90 and 100 g/l. Sanger sequencing combined with reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and Gap-PCR revealed that the proband was a carrier of 4 compound heterozygous mutations: Hemoglobin subunit β (HBB):IVS-II-654(C>T)β⁺; Southeast Asian-type-hereditary persistence of fetal hemoglobin (SEA-HPFH); HBB:c316-148G>T; hemoglobin subunit α2 (HBA2):c.46G>A. The father of the proband was identified as a carrier of the heterozygous SEA-HPFH mutation, the mother was a carrier of compound heterozygous mutations of HBB:IVS-II-654(C>T) and HBA2:c.46G>A, and the elder sister was heterozygous for HBB:IVS-II-654(C>T)β⁺. Based on these genetic results, it was determined that the proband had both of heavy β-thalassemia and α-thalassemia. Upon human leukocyte antigen matching, bone marrow transplantation (BMT) was successfully performed on the proband by selecting his HLA-compatible sister as a donor. Following treatment, the proband was revealed to only carry the IVS-II-654(C>T)β⁺ heterozygous mutation, and further regular blood transfusions have been avoided; BMT results remained normal at six months follow-up.

Identification of a novel hypertrophic cardiomyopathy-associated mutation using targeted next-generation sequencing

Hypertrophic cardiomyopathy (HCM), one of the most common forms of myocardial diseases, is the major cause of sudden cardiac death in young adults and competitive athletes. Analyses of gene mutations associated with HCM are valuable for its molecular diagnosis, genetic counseling, and management of familial HCM. To dissect the relationship between the clinical presentation and gene mutations of HCM, the genetic characterizations of 19 HCM-related genes in 18 patients (8 cases from 6 pedigrees with familial HCM and 10 cases without familial HCM) were detected using next-generation sequencing (NGS). As a result, 12 disease-related mutations were identified in the 18 subjects, including 6 single mutations and 3 double mutations [MYBPC3 (p.Gln998Glu) plus TNNI3 (p.Arg145Gly), PRKAG2 (p.Gly100Ser) plus MYBPC3 (p.Lys1209Serfs*28) and TNNI3 (p.Glu124Gln) plus GLA (p.Trp47*)]. The 3 heterozygous double mutations were discovered for the first time in the malignant familial HCM patients. Of the 6 single mutations, a novel mutation was found in tafazzin (TAZ, p.Ile208Val), and a mutation in β-myosin heavy chain gene (MYH7, p.Arg54Gln), which was reported as rare in the general population, was firstly found in one HCM patient. Identification of novel and rare mutations in HCM patients have added new data to the spectrum of gene mutations associated with this disease. These findings provide an essential basis for the molecular diagnosis and better management of family members at risk of familial HCM.

β-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.

Haematological and electrophoretic characterisation of β-thalassaemia in Yunnan province of Southwestern China

OBJECTIVES

β-Thalassaemia is widely found in Southwestern China. Characterisation of β-thalassaemia can improve screening and prenatal diagnosis for at-risk populations.

DESIGN

A retrospective study.

METHODS

In this study, the levels of haemoglobin alpha 2 (HbA₂) and haemoglobin alpha (HbA) were analysed by gender for a total of 15 067 subjects screened by capillary electrophoresis. The cut-off value with the highest accuracy was established to identify β-thalassaemia in 723 patients suspected to have this disease. Haematological and electrophoretic characterisation of eight common types of β-thalassaemia were analysed in 486 β-thalassaemia subjects.

RESULTS

HbA levels were significantly higher in men than in women, but there was no significant difference on HbA₂ levels. A new cut-off value for the diagnosis of β-thalassaemia (HbA₂≥4.0%) with the highest accuracy was proposed for the studied populations. Haemoglobin (Hb) was significantly higher in men compared with women (p<0.05), whereas no statistically significant differences were found for mean cell volume (MCV), mean cell haemoglobin (MCH), HbA and HbA₂. The haemoglobin E (HbE) group showed comparatively higher values for haematological indices (Hb, MCV and MCH) than the other genotypes in heterozygous β-thalassaemia groups (p<0.05), and -28 (A>G) (HBB (β-globin):c.-78A>C) had significantly higher HbA₂ values compared with other β-thalassaemia.

CONCLUSIONS

Ethnic groups have diversified β-globin gene mutations and considerable haematological variations. Our study will lay the foundation for screening programmes and clinical management of thalassaemia in Southwestern China.

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

OBJECTIVE

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.

METHODS

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.

RESULTS

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 β^E -globin genes in Yunnan were mostly associated with three haplotypes [-+++++-], [+----+-], and [-+-+++-] on chromosomes with gene framework 2. Interestingly, the predominant β^E 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.

CONCLUSIONS

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 β^E -globin gene in populations from Yunnan and Southeast Asia. Am. J. Hum. Biol. 28:927-931, 2016. © 2016Wiley Periodicals, Inc.

Mutation screening for thalassaemia in the Jino ethnic minority population of Yunnan Province, Southwest China

OBJECTIVES

This study aimed to detect α- and β-thalassaemia mutations in the Jino ethnic minority population of Yunnan Province, Southwest China.

DESIGN

A total of 1613 Jino adults were continuously recruited from February 2012 to April 2012. Fasting venous blood samples were obtained to determine haematological variables. Haemoglobin analysis was conducted using high-performance liquid chromatography. Participants with hypochromic microcytic anaemia or positive haemoglobin analysis profiles were confirmed by α- and β-globin genetic testing, including DNA microarray analysis, direct sequencing methods and multiplex gap-PCR assays.

SETTING

Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University Affiliated Sixth People's Hospital.

RESULTS

We found 363 suspected cases by primary screening of haematological variables and haemoglobin analysis. After further genetic testing, four types of α- and β-thalassaemia mutation were detected in 203 out of 363 individuals. Both α(0)- and α(+)-thalassaemia mutations, --(SEA) and -α(3.7), were identified. β-Thalassaemia mutations included CD17 (HBB:c.52A>T) and CD26 (HbE or HBB:c.79G>A). In addition, 13 HbE carriers had coexisting α(0)- or α(+)-thalassaemia deletions. Clinical haematological variables indicated that, in this study, carriers of all thalassaemic genotypes had more severe hypochromic microcytic anaemia than non-thalassaemic individuals.

CONCLUSIONS

Our results provide information on the Jino ethnic minority that may be useful for further genetic counselling, prenatal screening and clinical diagnosis of thalassaemia in this region.