Genetics background of β‐thalassemia (3.5 kb deletion) in Southern Thailand: Haplotype analysis using novel reverse dot blot hybridization

Tepakhan, Wanicha; Srewaradachpisal, Korntip; Kanjanaopas, Sataron; Jomoui, Wittaya

doi:10.1111/ahg.12416

Cited by 4 publications

(1 citation statement)

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“…However, it has been reported that eight common β-thalassemia mutations in Thailand (including codon 41/42 (-TTCT), codon 17 (A > T), NT-28 (A > G), IVS II-654 (C > T), codon 19 (A > G), codon 26; HbE (G > A), IVS I-1 (G > C) and IVS I-5 (G > C)) represent more than 85% of the total β-thalassemia mutations [ 3 , 4 , 5 ]. Several previous studies have reported the genetic relationship between populations, chromosome background of the gene and linkage analysis, as well as differences in clinical phenotypic expression using haplotype and phylogenetic analyses [ 6 , 7 , 8 ]. Single nucleotide polymorphisms (SNPs) within the β-globin gene cluster on chromosome 11 have been found, with seven–eight polymorphic sites commonly studied [ 9 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

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

Karnpean

Tepakhan

Suankul

et al. 2022

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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.

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Section: Introductionmentioning

confidence: 99%

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

Karnpean

Tepakhan

Suankul

et al. 2022

Genes

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Molecular Spectrum of β-Thalassemia Mutations in Central to Eastern Thailand

et al. 2021

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The comprehensive detection of hemoglobinopathy variants via long-read sequencing

Xiang,

Peng,

Sun

et al. 2024

Preprint

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BACKGROUND: The genetic complexity of hemoglobin genes, characterized by high GC content and homologous sequences, poses significant challenges for detecting hemoglobin variants in clinical settings. METHODS: A long-read indexed PCR method utilizing the novel CycloneSEQ nanopore sequencing platform was developed to detect all variant types, including single nucleotide variants (SNVs), deletions, structural variants (SVs) in HBA, HBB, HBD, and HBG genes. The method was validated using 507 clinical samples to assess its performance. RESULTS: The long-read indexed PCR system employed 13 primers targeting the hemoglobin gene clusters. This design enabled the detection of 37 types of HBA deletions, 5 SV (3 multicopies (alpha alpha alpha alpha alpha, alpha alpha alpha anti3.7, alpha alpha alpha anti4.2) and 2 fusion allele (HK alpha alpha and anti-HK alpha alpha)), 37 HBB deletions, and all SNVs in the targeted regions. Validation across 507 samples (84 with HBA variants, 60 with HBB variants, 256 with both HBA and HBB variants, and 107 with no known variants demonstrated 100.0% sensitivity and specificity. Additionally, the long-read sequencing enabled phasing of variants within hemoglobin genes, providing insights critical for clinical interpretation. CONCLUSIONS: The long-read indexed PCR method, combined with the CycloneSEQ nanopore sequencing platform, proved to be a robust and efficient solution for detecting hemoglobinopathy variants. The integration of indexed primers and barcoding enhances scalability, making this method ideal for large-scale population screening programs in the future.

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Genetics background of β‐thalassemia (3.5 kb deletion) in Southern Thailand: Haplotype analysis using novel reverse dot blot hybridization

Cited by 4 publications

References 23 publications

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

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

Molecular Spectrum of β-Thalassemia Mutations in Central to Eastern Thailand

The comprehensive detection of hemoglobinopathy variants via long-read sequencing

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