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Jiang F, Zhou J, Zuo L, Tang X, Li J, Li F, Yang T, Qu Y, Wan J, Liao C, Li D. Utilization of multiple genetic methods for prenatal diagnosis of rare thalassemia variants. Front Genet 2023; 14:1208102. [PMID: 37529778 PMCID: PMC10387553 DOI: 10.3389/fgene.2023.1208102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
Background: Thalassemia is the most prevalent monogenic disorder caused by an imbalance between the α- and β-globin chains as a result of pathogenic variants in the α- or β-globin genes. Novel or complex structural changes in globin genes are major hurdles for genetic consulting and prenatal diagnosis. Methods: From 2020 to 2022, genetic analysis was performed on 1,316 families suspected of having children with thalassemia major, including 42 pregnant couples suspected of being thalassemia carriers with rare variants. Multiple techniques including multiplex ligation-dependent probe amplification (MLPA), Sanger sequencing, targeted next-generation sequencing, and single-molecule real-time (SMRT) sequencing were used to diagnose rare thalassemia. Results: The rate of prenatal diagnosis for rare thalassemia variants was 3.19% (42/1,316). The most prevalent alleles of α- and β-thalassemia are Chinese Gγ(Aγδβ)0and -- THAI deletion. In addition, ten rare complex genotypes include one Chinese Gγ(Aγδβ)0 deletion combined with HBG1-HBG2 fusion, two rare deletions at HBB gene (hg38, Chr11: 5224211-5232470, hg38, Chr11: 5224303-5227790), one complete 7,412 bp fusion gene for anti-Lepore Hong Kong, two complex rearrangements of the α-globin gene cluster, two novel duplications, and two rare large deletions in the α-globin gene cluster. Conclusion: Accurate gene diagnosis for probands with combined molecular biology techniques is the key to prenatal diagnosis of rare thalassemia.
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Affiliation(s)
- Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jianying Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Liandong Zuo
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xuewei Tang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jian Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fatao Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Tianhe Yang
- Xiangya School of Nursing, Central South University, Changsha, Hunan, China
| | - Yanxia Qu
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Junhui Wan
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Can Liao
- *Correspondence: Can Liao, ; Dongzhi Li,
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
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Identification of novel mutations in β-thalassemia patients in Maysan Governorate, Iraq. Mol Biol Rep 2023; 50:3053-3062. [PMID: 36683082 DOI: 10.1007/s11033-023-08271-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/10/2023] [Indexed: 01/23/2023]
Abstract
BACKGROUND In homozygous β-thalassemia, the primary genetic modifiers affecting the clinical severity of β-thalassemia are genetic variants and the ability to reduce globin chain imbalance, thus resulting in a milder form of thalassemia. However, there are few reports on the molecular genetics of β-thalassemia in Iraq. METHODS We performed PCR and DNA sequencing on 40 Iraqi patients who were clinically suspected of having β-thalassemia. RESULTS The first genetic sequencing study was conducted in Maysan Governate, Iraq, using patients from various locations to identify novel mutations. There were five novel mutations: 294.T>C 12% (city center and Almajar district), 205. C>T 25% (city center, Alsalam, and Almashrah districts), 289.G>A 38% (Almaymuna and Gleat Salih districts), 49.T>C 32% (city center), and 624.C>A 32% (city center). These mutations were identified among β-thalassemia patients by two regions of HBB gene 696 bp and 861 bp. CONCLUSIONS The discovery of new genetic variants helps predict the severity of β-thalassemia disease. There are relatively few studies in molecular genetics of β-thalassemia in Iraq, and the new mutations reported here will provide valuable data for the prevention and control of β-thalassemia in Maysan Governate, Iraq. The results can lead to new genetic sequencing investigations for other Iraqi regions.
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Hassan S, Bahar R, Johan MF, Mohamed Hashim EK, Abdullah WZ, Esa E, Abdul Hamid FS, Zulkafli Z. Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) for the Diagnosis of Thalassemia. Diagnostics (Basel) 2023; 13:diagnostics13030373. [PMID: 36766477 PMCID: PMC9914462 DOI: 10.3390/diagnostics13030373] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Thalassemia is one of the most heterogeneous diseases, with more than a thousand mutation types recorded worldwide. Molecular diagnosis of thalassemia by conventional PCR-based DNA analysis is time- and resource-consuming owing to the phenotype variability, disease complexity, and molecular diagnostic test limitations. Moreover, genetic counseling must be backed-up by an extensive diagnosis of the thalassemia-causing phenotype and the possible genetic modifiers. Data coming from advanced molecular techniques such as targeted sequencing by next-generation sequencing (NGS) and third-generation sequencing (TGS) are more appropriate and valuable for DNA analysis of thalassemia. While NGS is superior at variant calling to TGS thanks to its lower error rates, the longer reads nature of the TGS permits haplotype-phasing that is superior for variant discovery on the homologous genes and CNV calling. The emergence of many cutting-edge machine learning-based bioinformatics tools has improved the accuracy of variant and CNV calling. Constant improvement of these sequencing and bioinformatics will enable precise thalassemia detections, especially for the CNV and the homologous HBA and HBG genes. In conclusion, laboratory transiting from conventional DNA analysis to NGS or TGS and following the guidelines towards a single assay will contribute to a better diagnostics approach of thalassemia.
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Affiliation(s)
- Syahzuwan Hassan
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Institute for Medical Research, Shah Alam 40170, Malaysia
| | - Rosnah Bahar
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Muhammad Farid Johan
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | | | - Wan Zaidah Abdullah
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ezalia Esa
- Institute for Medical Research, Shah Alam 40170, Malaysia
| | | | - Zefarina Zulkafli
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Correspondence:
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Ren ZM, Xing ZH, Chen SL, Fu XY, Chen YS, Li DF. Identification of a Novel Hb H Disease with Glucose-6-Phosphate Dehydrogenase Deficiency Using Whole Genome Sequencing. Hemoglobin 2022; 46:160-163. [PMID: 35582759 DOI: 10.1080/03630269.2022.2070072] [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: 11/04/2022]
Abstract
With the development of sequencing technology, more and more rare thalassemia types have been found. In this article, we found a novel Hb H disease combined with glucose-6-phosphate dehydrogenase (G6PD) deficiency through whole genome sequencing (WGS), which was verified by Sanger sequencing and polymerase chain reaction (PCR)-reverse dot-blot hybridization, respectively.
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Affiliation(s)
- Zhen-Min Ren
- Department of Laboratory Medicine, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, People's Republic of China
| | - Zhi-Hao Xing
- Department of Laboratory Medicine, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, People's Republic of China
| | - Shi-Lin Chen
- Aegicare Technology Co. Ltd., Shenzhen, Guangdong Province, People's Republic of China
| | - Xiao-Ying Fu
- Department of Laboratory Medicine, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, People's Republic of China
| | - Yun-Sheng Chen
- Department of Laboratory Medicine, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, People's Republic of China
| | - De-Fa Li
- Department of Laboratory Medicine, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, People's Republic of China
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Long J, Sun L, Gong F, Zhang C, Mao A, Lu Y, Li J, Liu E. Third-generation sequencing: A novel tool detects complex variants in the α-thalassemia gene. Gene 2022; 822:146332. [PMID: 35181504 DOI: 10.1016/j.gene.2022.146332] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/23/2022] [Accepted: 02/11/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Thalassemia is a monogenic disorder with a high carrier rate in the southern region of China. Most laboratories currently follow the protocol of testing hematologic indicators in individuals with positive hematologic indicators and then using the hot-spot mutation test kit. A novel thalassemia gene test is performed if there is a mismatch between the hematology and hot-spot mutation test results. However, due to the large population in southern China, some individuals carry complex α-globin gene cluster (CAGC) variants in NG_000006.1, which are difficult to detect using conventional thalassemia genetic analysis protocols, leading to missed or false genetic test results for individuals carrying these complex α-globin gene cluster variants. When an individual carries a complex α-thalassemia gene variant, and an individual carries a β- thalassemia gene variant, there may be clinical symptoms that might complicate clinical consultation and prenatal diagnosis if not accurately detected. Third-generation sequencing (TGS) enables long-read single-molecule sequencing with high detection accuracy, and long-length DNA chain reads in high-fidelity reads mode. TGS can be used to analyze high homology and rich GC DNA sequences. RESULTS Four samples that showed abnormalities in the thalassemia genetic test were studied using TGS, revealing that they carried genotypes with complex α-globin gene cluster variants, one of which was a complex variant αα anti3.7 α anti3.7 α 17.2. CONCLUSIONS TGS detects complex α-globin gene cluster variants. This study may provide a reference protocol for the use of TGS for the detection of complex α-globin gene cluster variants. TGS can reveal individuals with complex α-thalassemia genotypes in the population and improve the accuracy of genetic counseling and prenatal diagnosis.
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Affiliation(s)
- Ju Long
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China.
| | - Lei Sun
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China
| | - Feifei Gong
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China
| | - Chenghong Zhang
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China
| | - Aiping Mao
- Third-Generation Sequencing BU, Berry Genomics Corporation, Beijing 102200, China
| | - Yulin Lu
- Third-Generation Sequencing BU, Berry Genomics Corporation, Beijing 102200, China
| | - Jiaqi Li
- Third-Generation Sequencing BU, Berry Genomics Corporation, Beijing 102200, China
| | - Enqi Liu
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China.
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Wu S, Yuan Z, Sun Z, Zhu T, Wei X, Zou X, Sui R. A novel tandem duplication of PRDM13 in a Chinese family with North Carolina macular dystrophy. Graefes Arch Clin Exp Ophthalmol 2022; 260:645-653. [PMID: 34427740 DOI: 10.1007/s00417-021-05376-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/29/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022] Open
Abstract
PURPOSES North Carolina macular dystrophy (NCMD) is a rare autosomal dominant inherited disorder characterized by macular impairment with a variety of phenotypic manifestations. The aims of this study were to assess the clinical features of a Chinese family with NCMD and to identify the underlying genetic cause of the disease. METHODS Three patients from a Chinese family were included in this study. Detailed ophthalmological examinations were performed, including best corrected visual acuity (BCVA), slit lamp, dilated indirect ophthalmoscopy, fundus photography, optical coherence tomography (OCT), fundus autofluorescence, full-field electroretinography (ERG), and electrooculography (EOG). Genomic DNA was extracted from peripheral blood samples. Whole-genome sequencing and long-read genome sequencing were applied to detect the pathogenic variants. Sanger sequencing was performed to confirm the breakpoints. RESULTS All three patients had macular involvement ranging from patchy yellowish-white lesions to big-area thinning, which are typical for NCMD. The BCVA ranged from 20/50 to 20/20. OCT revealed varying degrees of macular structure disorganization. The ERG responses were normal, and the Arden ration of the EOG was reduced. A novel 134.6 kb (g.99932464-100067110dup) tandem duplication on chromosome 6 (NC_000006.11) encompassing the entire CCNC and PRDM13 genes and a DNase 1 hypersensitivity site in the MCDR1 locus was identified. CONCLUSION A novel large tandem duplication in MCDR1 locus was confirmed in a Chinese family with NCMD with a variety of macular phenotypes.
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Affiliation(s)
- Shijing Wu
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhisheng Yuan
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zixi Sun
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Tian Zhu
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xing Wei
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xuan Zou
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Ruifang Sui
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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Jiang F, Xu LL, Tang XW, Li DZ. A novel deletion of the major regulatory element flanking the α-globin gene cluster as a cause of α 0 -thalassemia. Int J Lab Hematol 2021; 43:O190-O192. [PMID: 33687151 DOI: 10.1111/ijlh.13505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/09/2021] [Accepted: 02/14/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center Affiliated to Guangzhou Medical University, Guangzhou, China
| | - Li-Li Xu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center Affiliated to Guangzhou Medical University, Guangzhou, China
| | - Xue-Wei Tang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center Affiliated to Guangzhou Medical University, Guangzhou, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center Affiliated to Guangzhou Medical University, Guangzhou, China
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