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Zhuang J, Chen C, Fu W, Wang Y, Zhuang Q, Lu Y, Xie T, Xu R, Zeng S, Jiang Y, Xie Y, Wang G. Third-Generation Sequencing as a New Comprehensive Technology for Identifying Rare α- and β-Globin Gene Variants in Thalassemia Alleles in the Chinese Population. Arch Pathol Lab Med 2023; 147:208-214. [PMID: 35639603 DOI: 10.5858/arpa.2021-0510-oa] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2021] [Indexed: 02/05/2023]
Abstract
CONTEXT.— Identification of rare thalassemia variants requires a combination of multiple diagnostic technologies. OBJECTIVE.— To investigate a new approach of comprehensive analysis of thalassemia alleles based on third-generation sequencing (TGS) for identification of α- and β-globin gene variants. DESIGN.— Enrolled in this study were 70 suspected carriers of rare thalassemia variants. Routine gap-polymerase chain reaction and DNA sequencing were used to detect rare thalassemia variants, and TGS technology was performed to identify α- and β-globin gene variants. RESULTS.— Twenty-three cases that carried rare variants in α- and β-globin genes were identified by the routine detection methods. TGS technology yielded a 7.14% (5 of 70) increment of rare α- and β-globin gene variants as compared with the routine methods. Among them, the rare deletional genotype of -THAI was the most common variant. In addition, rare variants of CD15 (G>A) (HBA2:c.46G>A), CD117/118(+TCA) (HBA1:c.354_355insTCA), and β-thalassemia 3.5-kilobase gene deletion were first identified in Fujian Province, China; to the best of our knowledge, this is the second report in the Chinese population. Moreover, HBA1:c.-24C>G, IVS-II-55 (G>T) (HBA1:c.300+55G>T) and hemoglobin (Hb) Maranon (HBA2:c.94A>G) were first identified in the Chinese population. We also identified rare Hb variants of HbC, HbG-Honolulu, Hb Miyashiro, and HbG-Coushatta in this study. CONCLUSIONS.— TGS technology can effectively and accurately detect deletional and nondeletional thalassemia variants simultaneously in one experiment. Our study also demonstrated the application value of TGS-based comprehensive analysis of thalassemia alleles in the detection of rare thalassemia gene variants.
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Affiliation(s)
- Jianlong Zhuang
- From the Prenatal Diagnosis Center (J. Zhuang, Fu, Y. Wang, Q. Zhuang, Zeng, Jiang), Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China
| | - Chunnuan Chen
- From the Department of Neurology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China (Chen)
| | - Wanyu Fu
- From the Prenatal Diagnosis Center (J. Zhuang, Fu, Y. Wang, Q. Zhuang, Zeng, Jiang), Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China
| | - Yuanbai Wang
- From the Prenatal Diagnosis Center (J. Zhuang, Fu, Y. Wang, Q. Zhuang, Zeng, Jiang), Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China
| | - Qianmei Zhuang
- From the Prenatal Diagnosis Center (J. Zhuang, Fu, Y. Wang, Q. Zhuang, Zeng, Jiang), Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China
| | - Yulin Lu
- From the Third-Generation Sequencing Business Unit, Berry Genomics Corporation, Beijing, China (Lu, T. Xie, Xu)
| | - Tiantian Xie
- From the Third-Generation Sequencing Business Unit, Berry Genomics Corporation, Beijing, China (Lu, T. Xie, Xu).,From the Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China (Y. Xie)
| | - Ruofan Xu
- From the Third-Generation Sequencing Business Unit, Berry Genomics Corporation, Beijing, China (Lu, T. Xie, Xu)
| | - Shuhong Zeng
- From the Prenatal Diagnosis Center (J. Zhuang, Fu, Y. Wang, Q. Zhuang, Zeng, Jiang), Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China
| | - Yuying Jiang
- From the Prenatal Diagnosis Center (J. Zhuang, Fu, Y. Wang, Q. Zhuang, Zeng, Jiang), Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China.,Authors Jiang, Y. Xie and G. Wang are co-lead authors
| | - Yingjun Xie
- From the Third-Generation Sequencing Business Unit, Berry Genomics Corporation, Beijing, China (Lu, T. Xie, Xu).,From the Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China (Y. Xie).,Authors Jiang, Y. Xie and G. Wang are co-lead authors
| | - Gaoxiong Wang
- From the Prenatal Diagnosis Center (J. Zhuang, Fu, Y. Wang, Q. Zhuang, Zeng, Jiang), Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China.,From the Department of Surgery (G. Wang), Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China.,Authors Jiang, Y. Xie and G. Wang are co-lead authors
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Soontornpanawet C, Singha K, Srivorakun H, Tepakhan W, Fucharoen G, Fucharoen S. Molecular basis of a high Hb A 2/Hb F β-thalassemia trait: a retrospective analysis, genotype-phenotype interaction, diagnostic implication, and identification of a novel interaction with α-globin gene triplication. PeerJ 2023; 11:e15308. [PMID: 37159832 PMCID: PMC10163868 DOI: 10.7717/peerj.15308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/06/2023] [Indexed: 05/11/2023] Open
Abstract
Background β 0-thalassemia deletion removing 5´β-globin promoter usually presents phenotype with high hemoglobin (Hb) A2 and Hb F levels. We report the molecular characteristics and phenotype-genotype correlation in a large cohort of the β 0-thalassemia with 3.4 kb deletion. Methods A total of 148 subjects, including 127 heterozygotes, 20 Hb E-β-thalassemia patients, and a double heterozygote with α-globin gene triplication, were recruited. Hb and DNA analysis were performed to identify thalassemia mutations and four high Hb F single nucleotide polymorphisms (SNPs) including four base pair deletion (-AGCA) at A γ-globin promoter, rs5006884 on OR51B6 gene, -158 G γ-XmnI, BCL11A binding motifs (TGGTCA) between 3´A γ-globin gene and 5´δ-globin gene. Results It was found that heterozygous β 0-thalassemia and Hb E-β 0-thalassemia with 3.4 kb deletion had significantly higher Hb, hematocrit, mean corpuscular volume, mean corpuscular hemoglobin and Hb F values as compared with those with other mutations. Co-inheritance of heterozygous β 0-thalassemia with 3.4 kb deletion and α-thalassemia was associated with even higher MCV and MCH values. The Hb E-β 0-thalassemia patients carried a non-transfusion-dependent thalassemia phenotype with an average Hb of around 10 g/dL without blood transfusion. A hitherto undescribed double heterozygous β 0-thalassemia with 3.4 kb deletion and α-globin gene triplication presented as a plain β-thalassemia trait. Most of the subjects had wild-type sequences for the four high Hb F SNPs examined. No significant difference in Hb F was observed between those of subjects with and without these SNPs. Removal of the 5´β-globin promoter may likely be responsible for this unusual phenotype. Conclusions The results indicate that β 0-thalassemia with 3.4 kb deletion is a mild β-thalassemia allele. This information should be provided at genetic counseling and prenatal thalassemia diagnosis.
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Affiliation(s)
- Chayada Soontornpanawet
- Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Muang, Khon Kaen, Thailand
| | - Kritsada Singha
- Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Muang, Khon Kaen, Thailand
- Faculty of Medicine, Mahasarakham University, Muang, Mahasarakham, Thailand
| | - Hataichanok Srivorakun
- Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Muang, Khon Kaen, Thailand
| | - Wanicha Tepakhan
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hatyai, Songkhla, Thailand
| | - Goonnapa Fucharoen
- Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Muang, Khon Kaen, Thailand
| | - Supan Fucharoen
- Centre for Research & Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Muang, Khon Kaen, Thailand
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Soontornpanawet C, Singha K, Fuchareon S. Genotype and phenotype characteristics of homozygous and compound heterozygous β-thalassemia with 3.4 kb deletion. Int J Lab Hematol 2022; 44:e230-e232. [PMID: 35644030 DOI: 10.1111/ijlh.13900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/14/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Chayada Soontornpanawet
- Centre for Research and Development of Medical Diagnostics Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Kritsada Singha
- Centre for Research and Development of Medical Diagnostics Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Faculty of Medicine, Mahasarakham University, Mahasarakham, Thailand
| | - Supan Fuchareon
- Centre for Research and Development of Medical Diagnostics Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
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Tepakhan W, Srewaradachpisal K, Kanjanaopas S, Jomoui W. Genetics background of β-thalassemia (3.5 kb deletion) in Southern Thailand: Haplotype analysis using novel reverse dot blot hybridization. Ann Hum Genet 2021; 85:115-124. [PMID: 33559179 DOI: 10.1111/ahg.12416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/20/2021] [Accepted: 01/26/2021] [Indexed: 11/30/2022]
Abstract
β-thalassemia (β-thal) (3.5 kb deletion or NC_000011.10:g.5224302-5227791del3490bp) is a common mutation in southern Thailand. This study aimed to determine genetic diversity in subjects with β-thal (3.5 kb deletion) alleles and to ascertain the origin of this mutation using haplotype and phylogenetic analysis. The study was carried out on members of the southern Thai population, including 45 normal individuals, 116 heterozygous β-thal (3.5 kb deletion) and one homozygous β-thal (3.5 kb deletion). The 5'-haplotype in β-globin gene cluster was examined using newly developed reverse dot blot hybridization (RDB) and compared with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The results showed 100% concordance between the haplotype patterns of these two methods. From a total of 324 chromosomes, nine haplotypes were segregated. Haplotype H2 (+ - - - -) was the predominant haplotype observed in all 118 β-thal (3.5 kb deletion) chromosomes, which revealed a single origin. The phylogenetic tree demonstrated that β-thal (3.5 kb deletion) has an older genetic defect in this region. Moreover, the developed RDB is simple, less time-consuming, inexpensive, and does not restriction enzyme digestion.
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Affiliation(s)
- Wanicha Tepakhan
- Faculty of Medicine, Department of Pathology, Prince of Songkla University, Songkhla, Thailand
| | | | - Sataron Kanjanaopas
- Faculty of Medicine, Department of Pathology, Prince of Songkla University, Songkhla, Thailand
| | - Wittaya Jomoui
- Faculty of Medicine, Department of Pathology, Maha Chakri Sirindhorn Medical Center, Srinakharinwirot University, Nakhon Nayok, Thailand
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Nuinoon M, Horpet D. Simultaneous Characterization of Deletional and Nondeletional Globin Gene Mutations by Multiplex Real-Time-Polymerase Chain Reaction and High-Resolution Melting Curve Analysis. Hemoglobin 2020; 44:311-318. [PMID: 32783482 DOI: 10.1080/03630269.2020.1799819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Both deletional and nondeletional globin gene mutations are common in Southeast Asians. Normally, deletional gene mutations are characterized separately from nondeletional gene mutations. Therefore, we developed a new approach of multiplex real-time polymerase chain reaction (qPCR) followed by high-resolution melting (HRM) analysis without a fluorescently-labeled probe for the simultaneous detection of deletional and nondeletional gene mutations in a single tube. Three sets of primer pairs were used to establish the qPCR-HRM method that was used to genotype more than 20 different globin genotypes. Twenty known genotypes were used to optimize the qPCR and HRM conditions. Eight genotypes were used to determine the reproducibility of the method. A total of 351 blinded known DNA samples were used for the validation study in three separate reactions and revealed 16 distinct patterns of fragments and/or HRM. The melting temperatures (Tm) of the 3.5 kb, - -THAI, HBB-FR2 (exon 1 of the HBB gene), - -SEA (Southeast Asian), α2 and 3'-ψζ1 fragments were 79.44, 81.01, 86.47, 87.89, 90.54 and 94.15 °C, respectively. The HRM analysis was performed with the HBB-FR2 fragment to differentiate several alleles. We report a rapid and high-throughput technique that showed 100.0% concordance and low variability for each run. Our developed technique is one of the alternative techniques recommended for screening samples with both deletional and nondeletional globin gene mutations.
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Affiliation(s)
- Manit Nuinoon
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
| | - Dararat Horpet
- Center for Scientific and Technological Equipment, Walailak University, Nakhon Si Thammarat, Thailand
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