Molecular analysis of haemoglobin E in Southeast Asian populations

Alpha-globin gene cluster haplotypes and D1S80, D17S5, and TPO VNTR polymorphisms among four ethnic populations from lower northeastern Thailand

Laos, Khmer, Kui, and Yer ethnic populations had a high prevalence of α+-thalassemia, but the genetic background remains poorly understood. This study examined genetic variation at the α-globin gene cluster and three VNTR loci (D1S80, D17S5, and TPO) in these ethnic populations. For α-globin haplotype analysis, 110 subjects with normal α-globin and 232 subjects with α+-thalassemia were selected to analyze six polymorphic sites using the PCR-RFLP technique. For VNTR loci analysis, 447 subjects were examined for D1S80, D17S5, and TPO allele frequencies using a PCR-based method. The results of this study revealed that the most frequent haplotypes found in Laos, including (framework 1; + M - + - 0) linked to (-α3.7) and (framework 3; - S - + + -) related to (αCSα) were different from those found in Khmer and Kui [(framework 2; + S - + - 0) linked to (-α3.7) and (framework 1; + M - + + -) related to (αCSα)]. For the (αPSα) gene, the haplotype (+ S - + - -) of framework 2 was found in all ethnic groups, and the haplotype (- M - + + -) of framework 1 in the Yer only. The distribution of allele frequencies for the D1S80, D17S5, and TPO VNTR loci showed extensive genetic variation in the ethnic population studied. The number of alleles is higher than that of the previously reported populations. Based on D17S5 analysis, the phylogenetic tree suggested that Khmer and Kui ethnic groups had a close relationship but were distant from Laos. In addition, ethnic relationships were observed in the Yer and Kui populations. In contrast, consistent results were not obtained based on D1S80 and TPO analysis. The findings indicate genetic variation in these ethnic populations, but the conclusion remains tentative. However, this study provides useful information to better understand genetic origins and ethnic relationships in the region.

Population genomics advances in frontier ethnic minorities in China

China, with its large geographic span, possesses rich genetic diversity across vast frontier regions in addition to the Han Chinese majority. Importantly, demographic events and various natural and cultural environments in Chinese frontier regions have shaped the genomic diversity of ethnic minorities via local adaptations. Thus, insights into the genetic diversity and adaptive evolution of these under-represented ethnic groups are crucial for understanding evolutionary scenarios and biomedical implications in East Asian populations. Here, we focus on ethnic minorities in Chinese frontier regions and review research advances regarding genomic diversity, genetic structure, population history, genetic admixture, and local adaptation. We first provide an overview of the extensive genetic diversity across populations in different Chinese frontier regions. Next, we summarize research progress regarding genetic ancestry, demographic history, the adaptive process, and the archaic identification of multiple ethnic minorities in different Chinese frontier regions. Finally, we discuss the gaps and opportunities in genomic studies of Chinese populations and the need for a more comprehensive understanding of genomic diversity and the evolution of populations of East Asian ancestry in the post-genomic era.

The Validation of Whole β-Globin Gene Sequencing for Detecting β-Thalassemia Mutations Found in Thailand Using Next-Generation Sequencing (NGS)

Beta-thalassemia is an inherited disorder prevalent in Thailand and Southeast Asia. Several molecular techniques for identifying β-thalassemia mutations have been reported. Next-generation sequencing (NGS) is a type of effective molecular testing with high throughput and accuracy. Hence, this study aims to evaluate a novel barcode-tagged NGS approach based on a short-read assay. A total of 258 samples with 54 different β-thalassemia genotypes related to 32 mutations were gathered and evaluated. A library was constructed with the BTSeqTM kit and sequencing was performed on the Illumina NGS machine. The validation results showed 98.45% concordance with conventional genotypes. Less discordant results (1.55%) were limited to insertional mutations and included one case of each of the following: HBB:c.27dupG, HBB:c.85dupC, HBB:c.216dupT, and HBB:c.440_441dupAC. Five single-nucleotide polymorphisms that derived from the NGS results were also analyzed in terms of allele frequency and revealed significant differences between the wild types and other β-genotypes. Furthermore, this paper is the first to describe rare single-nucleotide polymorphisms including IVS II-109 (C/T), IVS II-258 (G/A), IVS II-613 (T-C), and IVS II-806 (G/C). Interestingly, the C allele of IVS II-806 was found to have 100% linkage with two cases of Hb Tak. The haplotype and phylogenetic analysis was also constructed based on variants and revealed three clusters in the Hb variants, which represented their evolution and genetic background. Finally, NGS with the barcode-tagged method has a high throughput, which is suitable for large population screening. Its cost effectiveness and less complicated process promote its application in further works.

Retrospective study and implementation of a low-cost LAMP-turbidimetric assay for screening α0-thalassemia (SEA deletion): preventing and controlling Hb Bart's hydrops fetalis syndrome in Thailand

Homozygous α0-thalassemia (SEA deletion) or Hb Bart's hydrops fetalis syndrome is a significant public health issue in Thailand and Southeast Asia. A prevention and control program has been implemented in this region. This study focuses on retrospective laboratory data collected between January 2021 and April 2023 at a single center. Additionally, we developed a low-cost LAMP-turbidimetric assay to propose in the screening strategy. A total of 3,623 samples underwent screening tests (MCV, MCH, and DCIP), including 1,658 couple screenings (84.25%) and 310 single pregnant screenings (15.75%). Negative screenings, which did not require further investigation, were found in 75.51% for couple screenings and 46.58% for single pregnant screenings. At hemoglobin (Hb) analysis identified 129 couples which had fetuses at risk of severe thalassemia, whereas molecular analysis during the retrospective period revealed 210 samples with different genotypes. These remaining samples were validated using the low-cost LAMP-turbidimetric assay to detect α0-thalassemia (SEA deletion). The developed LAMP turbidimetric assay demonstrated a sensitivity and specificity of 100% (36/36 × 100) and 97.7% (170/174 × 100), respectively, when compared with gap-PCR. Furthermore, we propose a strategy involving the addition of the low-cost LAMP-turbidimetric assay before performing the gold standard. This strategy represents a cost-saving of USD 2,608 based on 210 samples that required DNA analysis. Finally, the developed LAMP turbidimetric assays offer advantages such as reduced time, workload, cost savings, no need for highly developed instruments, and a straightforward interpreting process. Therefore, implementation of LAMP assays into routine settings would be improve the efficiency of prevention and control program for severe thalassemia disease in this region.

Genetic Background Studies of Eight Common Beta Thalassemia Mutations in Thailand Using β-Globin Gene Haplotype and Phylogenetic Analysis

Single nucleotide polymorphisms are informative for haplotype analysis associated with genetic background and clinical linkage studies of β-thalassemia mutations. Hence, the aim of this study was to investigate five polymorphisms (codon 2 (C/T), IVS II-16 (C/G), IVS II-74 (G/T), IVS II-81 (C/T) and the Hinf I (T/A) polymorphism) on the β-globin gene, related to eight common β-thalassemia mutations in Thailand, including NT-28 (A > G), codon 17 (A > T), codon 19 (A > G), HbE (G > A), IVS I-1 (G > C), IVS I-5 (G > C), codon 41/42 (-TTCT) and IVS II-654 (C > T). The strongest LD (100%) between the β-thalassemia mutation allele and all five SNPs was found in NT-28 (A > G), codon 17 (A > T) and codon 19 (A > G). In the haplotype analysis, we found three haplotypes (H1, H2 and H7) related to Hb E, whereas we only found two haplotypes related to codon 41/42 (-TTCT) (H1, H3) and IVS I-1 (G > C) (H3, H4). Of interest is the finding relating to a single haplotype in the remaining β-thalassemia mutations. Furthermore, phylogenetic tree analysis revealed three clusters of these common β-thalassemia mutations in the Thai population and enabled us to determine the origin of these mutations. Here, we present the results of our study, including four intragenic polymorphisms and the finding that the Hinf I polymorphism could be informative in genetic background analysis, population studies and for predicting the severity of β-thalassemia in Thailand.

Molecular Characterization and Hematological Aspects of Hb E-Myanmar [β26(B8)Glu→Lys and β65(E9)Lys→Asn, HBB: c.[79G>A;198G>C]): A Novel β-Thalassemic Hemoglobin Variant

Hb E [β26(B8)Glu→Lys, GAG>AAG, HBB: c.79G>A] is an inherited thalassemic β-globin variant that favors the Hb E-β-thalassemia (β-thal) syndrome when interacting with the β-thal gene. However, hemoglobin (Hb) variants carrying Hb E in combination with another variant on the same β gene are rare. We recently studied a 29-year-old pregnant woman, initially diagnosed as a β-thal carrier. Hemoglobin and DNA analysis were performed by high performance liquid chromatography (HPLC) and DNA sequencing. Hematological data revealed no anemia or altered red blood cell (RBC) parameters. Hemoglobin HPLC showed Hb A and Hb A₂ but no Hb E or abnormal Hb peaks, with a markedly elevated Hb A₂ level (6.4%) reaching the accepted range (4.0-10.0%) for β-thal trait. DNA analysis identified a GAG>AAG transition at codon 26 of the β-globin gene that is responsible for Hb E, and an AAG>AAC mutation at codon 65 in cis on the β-globin chain resulting in a lysine to asparagine substitution. These two mutations led to the formation of a novel variant, namely Hb E-Myanmar, β26(B8)Glu→Lys and β65(E9)Lys→Asn, HBB: c.[79G>A;198G>C]. Moreover, a heterozygous α-thalassemia-2 (α-thal-2) [-α^3.7 (rightward)] deletion was also observed. Hb E-Myanmar is a doubly substituted β-globin variant, which has not been previously described. This variant did not have any clinical or hematological abnormalities, and the genetic mechanism resulting in this variant is discussed. The new simultaneous allele-specific polymerase chain reaction (ASPCR) was developed for rapid detection of these two mutations within the same β-globin chain.

Hemoglobin E, malaria and natural selection

It is known that there has been positive natural selection for hemoglobin S and C in humans despite negative health effects, due to its role in malaria resistance. However, it is not well understood, if there has been natural selection for hemoglobin E (HbE), which is a common variant in Southeast Asia. Therefore, we reviewed previous studies and discussed the potential role of natural selection in the prevalence of HbE. Our review shows that in vitro studies, evolutionary genetics studies and epidemiologic studies largely support an involvement of natural selection in the evolution of HbE and a protective role of HbE against malaria infection. However, the evidence is inconsistent, provided from different regions, and insufficient to perform an aggregated analysis such as a meta-analysis. In addition, few candidate gene, genome-wide association or epistasis studies, which have been made possible with the use of big data in the post-genomic era, have investigated HbE. The biological pathways linking HbE and malaria infection have not yet been fully elucidated. Therefore, further research is necessary before it can be concluded that there was positive natural selection for HbE due to protection against malaria.

Lay summary: Our review shows that evidence largely supports an involvement of natural selection in the evolution of HbE and a protective role of HbE against malaria. However, the evidence is not consistent. Further research is necessary before it is concluded.

Molecular characteristics of α+-thalassemia (3.7 kb deletion) in Southeast Asia: Molecular subtypes, haplotypic heterogeneity, multiple founder effects and laboratory diagnostics

OBJECTIVE

The 3.7 kb deletion (-α^3.7) is the most common form of α⁺-thalassemia found in multiple populations which can be classified into three subtypes. In order not to mis-identify it, the molecular information within each population is required. We have addressed this in northeast Thai and Laos populations.

METHODS

Screening for α⁺-thalassemia was initially done on 1192 adult Thai subjects. In addition, 77 chromosomes of Thai newborns and 26 chromosomes of Laos with -α^3.7 α⁺-thalassemia were also examined. All subjects were screened for -α^3.7 α⁺-thalassemia and subtyped by PCR-RFLP assay. Exact deletion breakpoint of each -α^3.7 subtype was determined by DNA sequencing. α-Globin gene haplotypes were determined.

RESULTS

The proportions of -α^3.7 subtypes found in 216 Thai -α^3.7 chromosomes were 94.9% for -α^3.7I, 4.2% for α^3.7II and 0.9% for -α^3.7III. All 26 Laos -α^3.7 chromosomes were of -α^3.7I variety. At least six α-globin gene haplotypes were associated with the -α^3.7I α⁺-thalassemia.

CONCLUSION

All -α^3.7 subtypes were observed among Southeast Asian population. Haplotype analysis indicated a multiple origin of this common disorder in the region. A multiplex PCR assay has been developed for simultaneous detection of all subtypes of -α^3.7 α⁺-thalassemia as well as other α⁺-thalassemia found in the region including -α^4.2 α⁺-thalassemia, Hb Constant Spring and Hb Paksé.

Molecular characterisation of haemoglobin E-Udon Thani (HBB:c.[79G>A;92+7A>G]): a novel form of Hb E-β-thalassaemia syndrome

Interaction of βE-globin gene with an in trans β-thalassaemia gene leads to thalassaemia syndrome, known as haemoglobin (Hb) E-β-thalassaemia disease, with variable clinical and haematological severity. Here, we reported for the first time the Hb E-β-thalassaemia syndrome caused alternatively by an in cis interaction of βE and a novel IVSI#7;A>G mutation, namely the Hb E-Udon Thani (HBB:c.[79G>A;92+7 A>G]). The syndrome was found in an adult Thai man (32) who was generally healthy but had an unexplained hypochromic microcytosis. Hb analysis identified heterozygous Hb E with very low Hb E expression (3.1%) and elevated Hb A2 (5.7%). Final diagnosis was made on DNA analysis, which confirmed a double mutation in a single β-globin gene of the patient. A multiplex allele-specific PCR assay was developed for use in the screening of this novel form of Hb E-β-thalassaemia in the population.