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Wei X, Wang X, Xiong F, Zhang X, Liu D, Zhou W, He F, Shang X. SNPscan Combined With CNVplex as a High-Performance Diagnostic Method for Thalassemia. Prenat Diagn 2024. [PMID: 39256948 DOI: 10.1002/pd.6661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/20/2024] [Accepted: 08/25/2024] [Indexed: 09/12/2024]
Abstract
OBJECTIVE Thalassemia is a Mendelian-inherited blood disorder with severe consequences, including disability and mortality, making it a significant public health concern. Therefore, there is an urgent need for precise diagnostic technologies. We introduce two innovative diagnostic techniques for thalassemia, SNPscan and CNVplex, designed to enhance molecular diagnostics of thalassemia. METHODS The SNPscan and CNVplex assays utilize variations in PCR product length and fluorescence to identify multiple mutations. In the SNPscan method, we designed three probes per locus: two 5' and one 3', and incorporated allele identification link sequences into one of the 5' probes to distinguish the alleles. The detection system was designed for 67 previously reported loci in the Chinese population for a specific genetic condition. CNVplex identifies deletion types by analyzing the specific positions of probes within the globin gene. This innovative approach enables the detection of six distinct deletional mutations, enhancing the precision of thalassemia diagnostics. We evaluated and refined the methodologies in a training cohort of 100 individuals with confirmed HBA and HBB genotypes. The validation cohort, consisting of 1647 thalassemia patients and 100 healthy controls, underwent a double-blind study. Traditional diagnostic techniques served as the control methods. RESULTS In the training set of 100 samples, 10 mutations (Hb QS, Hb CS, Hb Westmead, CD17, CD26, CD41-42, IVS-II-654, --SEA, -α3.7 and -α4.2) were identified, consistent with those identified by traditional methods. The validation study showed that SNPscan/CNVplex offered superior molecular diagnostic capabilities for thalassemia, with 100% accuracy compared to 99.43% for traditional methods. Notably, the assay identified three previously undetected mutations in 10 cases, including two deletion mutations (Chinese Gγ(Aγδβ)0 del and SEA-HPFH), and one non-deletion mutation (Hb Q-Thailand). CONCLUSIONS The SNPscan/CNVplex assay is a cost-effective and user-friendly tool for diagnosing thalassemia, demonstrating high accuracy and reliability, and showing great potential as a primary diagnostic method in clinical practice.
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Affiliation(s)
- Xiaofeng Wei
- Department of Medical Genetics, School of Basic Medicine Science, Southern Medical University, Guangdong, China
- Experimental Education and Administration Center, School of Basic Medical Science, Southern Medical University, Guangdong, China
| | - Xingmin Wang
- Department of Medical Genetics, School of Basic Medicine Science, Southern Medical University, Guangdong, China
| | - Fu Xiong
- Department of Medical Genetics, School of Basic Medicine Science, Southern Medical University, Guangdong, China
- Experimental Education and Administration Center, School of Basic Medical Science, Southern Medical University, Guangdong, China
| | - Xinhua Zhang
- Department of Hematology, 923rd Hospital of the People's Liberation Army, Guangxi, China
| | - Dun Liu
- Reproductive Medical Center, Guangdong Women and Children Hospital, Guangdong, China
| | - Wanjun Zhou
- Department of Medical Genetics, School of Basic Medicine Science, Southern Medical University, Guangdong, China
- Experimental Education and Administration Center, School of Basic Medical Science, Southern Medical University, Guangdong, China
| | - Fei He
- Department of Medical Genetics, School of Basic Medicine Science, Southern Medical University, Guangdong, China
- Experimental Education and Administration Center, School of Basic Medical Science, Southern Medical University, Guangdong, China
| | - Xuan Shang
- Department of Medical Genetics, School of Basic Medicine Science, Southern Medical University, Guangdong, China
- Experimental Education and Administration Center, School of Basic Medical Science, Southern Medical University, Guangdong, China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangdong, China
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Halim-Fikri H, Zulkipli NN, Alauddin H, Bento C, Lederer CW, Kountouris P, Kleanthous M, Hernaningsih Y, Thong MK, Mahmood MH, Mohd Yasin N, Esa E, Elion J, Coviello D, Raja-Sabudin RZA, El-Kamah G, Burn J, Mohd Yusoff N, Ramesar R, Zilfalil BA. Global Globin Network and adopting genomic variant database requirements for thalassemia. Database (Oxford) 2024; 2024:baae080. [PMID: 39231257 PMCID: PMC11373567 DOI: 10.1093/database/baae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 07/24/2024] [Accepted: 08/02/2024] [Indexed: 09/06/2024]
Abstract
Thalassemia is one of the most prevalent monogenic disorders in low- and middle-income countries (LMICs). There are an estimated 270 million carriers of hemoglobinopathies (abnormal hemoglobins and/or thalassemia) worldwide, necessitating global methods and solutions for effective and optimal therapy. LMICs are disproportionately impacted by thalassemia, and due to disparities in genomics awareness and diagnostic resources, certain LMICs lag behind high-income countries (HICs). This spurred the establishment of the Global Globin Network (GGN) in 2015 at UNESCO, Paris, as a project-wide endeavor within the Human Variome Project (HVP). Primarily aimed at enhancing thalassemia clinical services, research, and genomic diagnostic capabilities with a focus on LMIC needs, GGN aims to foster data collection in a shared database by all affected nations, thus improving data sharing and thalassemia management. In this paper, we propose a minimum requirement for establishing a genomic database in thalassemia based on the HVP database guidelines. We suggest using an existing platform recommended by HVP, the Leiden Open Variation Database (LOVD) (https://www.lovd.nl/). Adoption of our proposed criteria will assist in improving or supplementing the existing databases, allowing for better-quality services for individuals with thalassemia. Database URL: https://www.lovd.nl/.
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Grants
- 305.PPSP.6114202 the International Collaboration Fund (IFC), Ministry of Science, Technology and Innovation (MOSTI), Malaysia
- EXCELLENCE/1216/92, EXCELLENCE/1216/256 the European Regional Development Fund and the Republic of Cyprus through the Research and Innovation Foundation
- 304.PPSP.6150166.K151 Ministry of International Trade and Industry (MITI), Malaysia
- COST Action CA22119 (HELIOS) COST (European Cooperation in Science and Technology)
- 305.PPSP.6114202 the International Collaboration Fund (IFC), Ministry of Science, Technology and Innovation (MOSTI), Malaysia
- EXCELLENCE/1216/92, EXCELLENCE/1216/256 the European Regional Development Fund and the Republic of Cyprus through the Research and Innovation Foundation
- 304.PPSP.6150166.K151 Ministry of International Trade and Industry (MITI), Malaysia
- COST Action CA22119 (HELIOS) COST (European Cooperation in Science and Technology)
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Affiliation(s)
- Hashim Halim-Fikri
- School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Jalan Raja Perempuan Zainab II, Kubang Kerian, Kelantan 16150, Malaysia
| | - Ninie Nadia Zulkipli
- School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Jalan Raja Perempuan Zainab II, Kubang Kerian, Kelantan 16150, Malaysia
- School of Biomedicine, Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Gong Badak Campus, Kuala Nerus, Terengganu 21300, Malaysia
| | - Hafiza Alauddin
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia
| | - Celeste Bento
- Department of Hematology, Hospital Pediátrico de Coimbra, Avenida Afonso Romão, Coimbra 3000-602, Portugal
| | - Carsten W Lederer
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Ayios Dometios, Nicosia 2371, Cyprus
| | - Petros Kountouris
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Ayios Dometios, Nicosia 2371, Cyprus
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Ayios Dometios, Nicosia 2371, Cyprus
| | - Yetti Hernaningsih
- Department of Clinical Pathology, Faculty of Medicine Universitas Airlangga, Dr. Soetomo Academic General Hospital, Surabaya, East Java 60132, Indonesia
| | - Meow-Keong Thong
- Department of Paediatrics, Faculty of Medicine, Universiti Malaya, Lembah Pantai, Kuala Lumpur 50603, Malaysia
| | - Muhammad Hamdi Mahmood
- Department of Basic Medical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak 94300, Malaysia
| | - Norafiza Mohd Yasin
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, No. 1, Jalan Setia Murni U13/52, Seksyen U13, Bandar Setia Alam, Shah Alam, Selangor Darul Ehsan 40170, Malaysia
| | - Ezalia Esa
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, No. 1, Jalan Setia Murni U13/52, Seksyen U13, Bandar Setia Alam, Shah Alam, Selangor Darul Ehsan 40170, Malaysia
| | - Jacques Elion
- Medical School, Université Paris Diderot, Paris 75018, France
| | - Domenico Coviello
- Laboratorio di Genetica Umana, IRCCS Istituto Giannina Gaslini, Largo Gerolamo Gaslini 5, Genova 16147, Italy
| | - Raja-Zahratul-Azma Raja-Sabudin
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, Kuala Lumpur 56000, Malaysia
| | - Ghada El-Kamah
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo 12622, Egypt
| | - John Burn
- Translational and Clinical Research Institute, Newcastle University, International Centre for Life, Times Square, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Narazah Mohd Yusoff
- Molecular Genetics Section, Clinical Diagnostic Laboratory, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas, Pulau Pinang 13200, Malaysia
| | - Raj Ramesar
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
| | - Bin Alwi Zilfalil
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Jalan Raja Perempuan Zainab II, Kubang Kerian, Kelantan 16150, Malaysia
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Guo X, Zhang X, Li M, Peng Y, Wang Z, Liu J. Preliminary screening of biomarkers and drug candidates in a mouse model of β-thalassemia based on quasi-targeted metabolomics. Front Physiol 2024; 15:1452558. [PMID: 39247159 PMCID: PMC11377281 DOI: 10.3389/fphys.2024.1452558] [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: 06/21/2024] [Accepted: 08/06/2024] [Indexed: 09/10/2024] Open
Abstract
Background β-thalassemia (β-TH) is a hereditary hemolytic anemia that results in deficient hemoglobin (Hb) synthesis. It is characterized by ineffective erythropoiesis, anemia, splenomegaly, and systemic iron overload. Exploration new potential biomarkers and drug candidates is important to facilitate the prevention and treatment of β-TH. Methods We applied quasi-targeted metabolomics between wild type (Wt) and heterozygous β-TH mice (Th3/+), a model of non-transfusion-dependent β-TH intermedia, in plasma and peripheral blood (PB) cells. Futher data was deeply mined by Kyoto Encyclopedia of Genomes (KEGG) and machine algorithms methods. Results Using KEGG enrichment analysis, we found that taurine and hypotaurine metabolism disorders in plasma and alanine, aspartate and glutamate metabolism disorders in PB cells. After systematically anatomize the metabolites by machine algorithms, we confirmed that alpha-muricholic acidUP and N-acetyl-DL-phenylalanineUP in plasma and Dl-3-hydroxynorvalineUP, O-acetyl-L-serineUP, H-abu-OHUP, S-(Methyl) glutathioneUP, sepiapterinDOWN, and imidazoleacetic acidDOWN in PB cells play key roles in predicting the occurrence of β-TH. Furthermore, Sepiapterin, Imidazoleacetic acid, Methyl alpha-D-glucopyranoside and alpha-ketoglutaric acid have a good binding capacity to hemoglobin E through molecular docking and are considered to be potential drug candidates for β-TH. Conclusion Those results may help in identify useful molecular targets in the diagnosis and treatment of β-TH and lays a strong foundation for further research.
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Affiliation(s)
- Xianfeng Guo
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha, China
| | - Xuchao Zhang
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha, China
| | - Min Li
- Department of medical laboratory college, Changsha Medical University, Changsha, China
| | - Yuanliang Peng
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha, China
| | - Zi Wang
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha, China
| | - Jing Liu
- Department of Hematology, The Second Xiangya Hospital, Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University, Changsha, China
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Huang R, Liu Y, Xu J, Lin D, Mao A, Yang L, Zhong G, Wang H, Xu R, Chen Y, Zhou Q. Back-to-Back Comparison of Third-Generation Sequencing and Next-Generation Sequencing in Carrier Screening of Thalassemia. Arch Pathol Lab Med 2024; 148:797-804. [PMID: 36630651 DOI: 10.5858/arpa.2022-0168-oa] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2022] [Indexed: 01/13/2023]
Abstract
CONTEXT.— Recently, new technologies, such as next-generation sequencing and third-generation sequencing, have been used in carrier screening of thalassemia. However, there is no direct comparison between the 2 methods in carrier screening of thalassemia. OBJECTIVE.— To compare the clinical performance of third-generation sequencing with next-generation sequencing in carrier screening of thalassemia. DESIGN.— Next-generation sequencing and third-generation sequencing were simultaneously conducted for 1122 individuals in Hainan Province. RESULTS.— Among 1122 genetic results, 1105 (98.48%) were concordant and 17 (1.52%) were discordant between the 2 methods. Among the 17 discordant results, 4 were common thalassemia variants, 9 were rare thalassemia variants, and 4 were variations with unknown pathogenicity. Sanger sequencing and polymerase chain reaction for discordant samples confirmed all the results of third-generation sequencing. Among the 685 individuals with common and rare thalassemia variants detected by third-generation sequencing, 512 (74.74%) were carriers of α-thalassemia, 110 (16.06%) were carriers of β-thalassemia, and 63 (9.20%) had coinheritance of α-thalassemia and β-thalassemia. Three thalassemia variants were reported for the first time in Hainan Province, including -THAI, -α2.4, and ααααanti3.7. Eleven variants with potential pathogenicity were identified in 36 patients with positive hemoglobin test results. Among 52 individuals with negative hemoglobin test results, 17 were identified with thalassemia variants. In total, third-generation sequencing and next-generation sequencing correctly detected 763 and 746 individuals with variants, respectively. Third-generation sequencing yielded a 2.28% (17 of 746) increment compared with next-generation sequencing. CONCLUSIONS.— Third-generation sequencing was demonstrated to be a more accurate and reliable approach in carrier screening of thalassemia compared with next-generation sequencing.
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Affiliation(s)
- Renliang Huang
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Jing Xu
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Dan Lin
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Liuqing Yang
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Gaobu Zhong
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Huoniao Wang
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Ruofan Xu
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Yiwei Chen
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Qiaomiao Zhou
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
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Traisrisilp K, Zheng Y, Choy KW, Chareonkwan P. Thalassemia screening by third-generation sequencing: Pilot study in a Thai population. Obstet Med 2024; 17:101-107. [PMID: 38784187 PMCID: PMC11110746 DOI: 10.1177/1753495x231207676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/27/2023] [Indexed: 05/25/2024] Open
Abstract
Background Conventional thalassemia screening takes a stepwise approach and has limitations in comprehensively identifying all spectrums of mutations. This study aimed to investigate the performance of third-generation sequencing (TGS) compared to conventional molecular testing. Methods TGS was applied to validate all known variants detected by conventional testing and to detect missing variants in undiagnosed cases. The study was conducted at Maharaj Nakorn Chiang Mai Hospital between December 2021 and April 2022. Results In total, 19 cases were included in this study, among which 52.6% (10/19) had known thalassemia variants, while 47.7% (9/19) cases were undiagnosed by conventional methods. All 16 variants previously detected were validated by TGS, and TGS additionally detected 43.8% (7/16) thalassemia variants for 36.8% (7/19) cases. Conclusion TGS could provide additional genetic diagnoses compared with conventional methods. Further cost-effectiveness studies with a larger sample size are needed to explore the role of TGS in clinical practices.
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Affiliation(s)
- Kuntharee Traisrisilp
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Yu Zheng
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Pimlak Chareonkwan
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
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Peng L, Lidan H, Cuicui Z, Zhe Z, Sen Y, Xuan W, Ganghua L, Chao Z, Zhensheng L, Qiming W. DNA double-strand break repair capacity and its pathway gene variants predict the risk and prognosis of lung cancer. Lung Cancer 2024; 192:107831. [PMID: 38805902 DOI: 10.1016/j.lungcan.2024.107831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/19/2024] [Accepted: 05/23/2024] [Indexed: 05/30/2024]
Abstract
OBJECTIVES This study aims to investigate the association between DNA double-strand breaks (DSBs) repair capacity, variations in DSBs-related genes, and the occurrence and prognosis of lung cancer in the Chinese population. METHODS Peripheral blood mononuclear cells (PBMC) were collected from 98 lung cancer patients and 60 healthy individuals. The individual DSBs repair capacity was assessed by measuring changes in γ-H2AX levels after treatment with etoposide. Exonic sequencing of 45 DSBs-related genes was performed on PBMC DNA. Logistic regression analysis was conducted to examine the relationship between lung cancer risk and DSBs repair capacity as well as germlines gene variations. Survival analysis employed the Cox proportional hazards regression model, Kaplan-Meier method, and Log-rank test. RESULTS Lower DSBs repair capacity predicted an increased risk of developing lung cancer (OR = 0.94, 95 %CI = 0.917-0.964, P<0.001). Among lung cancer patients, higher DSBs repair capacity was associated with shorter progression-free survival (PFS) during first-line treatment (HR = 1.80, 95 %CI = 1.10-3.00, P = 0.031). Patients with BRCA1 mutations had shorter overall survival (OS) (HR = 1.92, 95 %CI = 1.12-3.28, P = 0.018). Patients with FOXO3 mutations had shorter PFS (HR = 4.23, 95 %CI = 1.44-12.36, P = 0.009). Analysis of patients treated with immune checkpoint inhibitors (ICIs) indicated that LIG4 mutations were associated with shorter PFS (HR = 2.90, 95 %CI = 1.00-8.10, P = 0.041). CONCLUSIONS This study concludes that assessing DSBs repair capacity holds promise for predicting both lung cancer risk and prognosis in the Chinese population. Further large-scale studies and functional validation of specific gene mutations related to double-strand breaks are necessary for confirmation.
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Affiliation(s)
- Li Peng
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China; Institute of Cancer Research, Henan Academy of Innovations in Medical Science, Zhengzhou 450008, China
| | - Hao Lidan
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China
| | - Zhang Cuicui
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China; Institute of Cancer Research, Henan Academy of Innovations in Medical Science, Zhengzhou 450008, China
| | - Zhang Zhe
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China; Institute of Cancer Research, Henan Academy of Innovations in Medical Science, Zhengzhou 450008, China
| | - Yang Sen
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China; Institute of Cancer Research, Henan Academy of Innovations in Medical Science, Zhengzhou 450008, China
| | - Wu Xuan
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China
| | - Li Ganghua
- Geneplus-Shenzhen, Shenzhen 518000, China
| | - Zhang Chao
- Geneplus-Shenzhen, Shenzhen 518000, China
| | - Liu Zhensheng
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China
| | - Wang Qiming
- Department of Internal Medicine, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China; Institute of Cancer Research, Henan Academy of Innovations in Medical Science, Zhengzhou 450008, China.
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Lin Z, Liang X, Wei X, Liang G, Zhu D, Xie H, Yan T, Shang X. SUPT5H mutations associated with elevation of Hb A 2 level: Identification of two novel variants and literature review. Gene 2024; 908:148294. [PMID: 38373659 DOI: 10.1016/j.gene.2024.148294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 02/21/2024]
Abstract
β-thalassemia is one of the most common monogenic disorders in areas of the tropics and subtropics, which represents a major familial and social burden to local people. The elevated Hb A2 level, generally specified as greater than 3.5 %, is commonly used as a high efficiency index for screening of β-thalassemia carriers. However, mutations in other genes such as GATA1 and KLF1, could also result in increased Hb A2 level. In this study, we identified two novel variants in the SUPT5H gene: a frameshift mutation (SUPT5H: c.3032_3033delTG, p.M1011Mfs*9) and a nonsense mutation (SUPT5H: c.397C > T, p.Arg133*) in two Chinese individuals. Utilizing a combination of phenotype analysis, bioinformatics analysis, and functional analysis, we deduced that these two variants modified the SUPT5H protein's structure, thereby impacting its function and consequently leading to the heightened Hb A2 level phenotype found in the carriers. Furthermore, through a comprehensive literature review, a mutation spectrum was consolidated for SUPT5H, an investigation into the genotype-phenotype correlation was conducted, and factors known to influence Hb A2 levels were identified. Based on this in-depth understanding, clinicians are better equipped to carry out large scale screenings in regions with high prevalence of β-thalassemia.
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Affiliation(s)
- Zezhang Lin
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiongda Liang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiaofeng Wei
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Guanxia Liang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Dina Zhu
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Hongting Xie
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Tizhen Yan
- Prenatal Diagnostic Center, Affiliated Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan, China
| | - Xuan Shang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China; Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China.
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Liang G, Lin Z, Zhang Y, Zhang Q, Zhu D, Liang X, Xie H, Wei X, Shang X. Precise diagnosis of a hereditary spherocytosis patient with complicated hematological phenotype. Mol Genet Genomics 2024; 299:57. [PMID: 38787432 DOI: 10.1007/s00438-024-02150-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Hereditary spherocytosis (HS) is one of the most common causes of hereditary hemolytic anemia. The current diagnostic guidelines for HS are mainly based on a combination of physical examination and laboratory investigation. However, some patients present with complicated clinical manifestations that cannot be explained by routine diagnostic protocols. Here, we report a rare HS case of mild anemia with extremely high indirect bilirubin levels and high expression of fetal hemoglobin. Using whole exome sequencing analysis, this patient was identified as a heterozygous carrier of a de novo SPTB nonsense mutation (c.605G > A; p.W202*) and a compound heterozygous carrier of known UGT1A1 and KLF1 mutations. This genetic analysis based on the interpretation of the patient's genomic data not only achieved precise diagnosis by an excellent explanation of the complicated phenotype but also provided valuable suggestions for subsequent appropriate approaches for treatment, surveillance and prophylaxis.
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Affiliation(s)
- Guanxia Liang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zezhang Lin
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yang Zhang
- Department of Basic medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qianqian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Dina Zhu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiongda Liang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hongting Xie
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiaofeng Wei
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xuan Shang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, China.
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
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9
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He X, Tian P, Zhong L, Peng S, Chen S, Pan L, Du Y, Zhang R. A Novel 165 Kb Duplication Involving the α-Globin Gene Cluster Is Identified by Low-Pass Whole Genome Sequencing in a Chinese Thalassemia Intermedia Patient. Hemoglobin 2024:1-6. [PMID: 38693050 DOI: 10.1080/03630269.2024.2346143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/08/2024] [Indexed: 05/03/2024]
Abstract
Copy number variations (CNVs) involving the α-globin gene cluster can lead to an imbalance in the proportion of α- and β-globin chains and consequently cause clinical symptoms of β-thalassemia. In our case, a 6-year-old boy, clinically diagnosed with β thalassemia intermedia, was admitted for further genetic diagnosis with his family. Targeted sequencing and third generation sequencing (TGS) were used to detect the possible variants of the thalassemia genes. Low-pass whole genome sequencing (lpWGS) was conducted to specify the exact location of relevant CNVs across the genome, which was then validated by multiplex ligation-dependent probe amplification.The results revealed that the patient had a heterozygous β0 mutation of Codon17 (A > T) and a full duplication of the α-globin gene cluster, inherited from his mother and father, respectively. Besides, a novel point mutation within the 5' untranslated region of β-Globin (HBB: c. -175 (G > A) was only detected in the patient. This study suggests that lpWGS seems a powerful alternative to detect large CNVs related to thalassemia with second intention for more information of the breakpoints and a simultaneous genome-scale detection of other pathogenic CNVs.
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Affiliation(s)
- Xiaohong He
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | | | - Lijuan Zhong
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Shanshan Peng
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | | | - Lei Pan
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Yutao Du
- BGI-Shenzhen, Shenzhen, China
- Hebei Medical University, Shijiazhuang, China
| | - Rui Zhang
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
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10
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Ozalp O, Anlas O. Detection of 13 Novel Variants and Investigation of Mutation Distribution by Next Generation Sequencing in Hemoglobinopathies: A Single Center Experience. Indian J Hematol Blood Transfus 2024; 40:268-280. [PMID: 38708170 PMCID: PMC11065806 DOI: 10.1007/s12288-023-01694-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 08/21/2023] [Indexed: 05/07/2024] Open
Abstract
Hemoglobinopathies are the most common monogenic disorders in the world. Traditional diagnostic algorithms generated by conventional methods for thalassemia can be labor-intensive and time-consuming due to the complexities of the genes involved and the variability in disease-causing mutations. With the advantages of next-generation sequencing (NGS) technology, molecular analysis of highly complex diseases such as hemoglobinopathies has become easier. Next-generation sequencing is a highly sensitive and effective method due to its capacity to sequence many gene regions simultaneously while allowing good read depths. In this study, single nucleotide changes, small deletions and copy number variations in HBA1, HBA2 and HBB in 914 patients with suspected hemoglobinopathy were analysed with NGS. At least one HBA1, HBA2, HBB or HBD variant was detected in 483 (52.8%) patients. Ten novel variants were detected in HBA1 and HBA2, three in HBB, and one in HBD. From these variants, c.*76T > A, c.301-24 G > A, c.301-24G > C c.-41C > G, c.-37-40C > G, c.-9G > C, c. 95 + 9C > T, c.95 + 26C > A, c.95 + 38C > T and c.*18C > G variants were located in α-globin genes, c.-25T > C, c.*103T > C and c92 + 39A > G variants were located in β-globin genes, and c.-43C > A was located in HBD. This is the first comprehensive study using NGS for the molecular diagnosis of hemoglobinopathies in Turkey. Accurate molecular diagnosis is of critical importance in hemoglobinopathies which are a public health problem due to their increased prevalence, high burden to society, and lack of curative treatment. Currently, NGS appears to be an advanced option over conventional methods to detect all variants occurring by molecular mechanisms and simultaneously analyse many genomic sequences.
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Affiliation(s)
- Ozge Ozalp
- Department of Medical Genetics, Adana City Training and Research Hospital, University of Health Sciences, 4522. Street, 01230 Adana, Turkey
| | - Ozlem Anlas
- Department of Medical Genetics, Adana City Training and Research Hospital, University of Health Sciences, 4522. Street, 01230 Adana, Turkey
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11
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Wu LS, Luo X, Tan M, Zhang LJ, Luo HF, Huang G, Huang P, Chen J, Chen Y. Prevalence of thalassemia-carrier couples and fertility risk assessment. Int J Hematol 2024; 119:374-382. [PMID: 38411864 DOI: 10.1007/s12185-024-03722-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/28/2024]
Abstract
Thalassemia is a highly prevalent hematologic disease in Guizhou, China. This study aimed to determine the epidemiological characteristics of thalassemia in couples at childbearing age and assess the neonatal risk of thalassemia in this subpopulation. A cohort of 4481 couples at childbearing age were recruited for thalassemia carrier screening by both traditional hematological tests and next-generation sequencing. Of them, 1314 (14.66%) thalassemia carriers were identified, including 857 (9.76%) α-thalassemia, 391 (4.36%) β-thalassemia, and 48 (0.54%) composite α and β-thalassemia. A total of 12 α-globin gene alterations and 16 β-globin mutations were detected, including four novel thalassemia mutations. SEA was the most common α-thalassemia genotype (26.86%), CD41-42 the most common β-thalassemia genotype (36.57%), and αα/- α3.7 + CD41-42 the most common composite α- and β-thalassemia genotype (18.75%). Ethnically, the Zhuang had the highest rate of thalassemia gene carriers among the ethnic groups. Geographically, Qiannan had the highest rate of thalassemia gene carriers. In addition, 38 of the 48 couples with composite α- and β-thalassemia were high-risk thalassemia carriers, and 4 carrying the -SEA/αα gene needed fertility guidance.
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Affiliation(s)
- Liu-Song Wu
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Xi Luo
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Mei Tan
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Li-Jun Zhang
- Department of Pediatrics, The Qian-Nan-Zhou People's Hospital of Guizhou, Guizhou, China
| | - Hong-Fang Luo
- Department of Pediatrics, The 2nd Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Ge Huang
- Clinical Laboratory, The Qian-Dong-Nan People's Hospital of Guizhou, Guizhou, China
| | - Pei Huang
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China
| | - Jindong Chen
- Exploring Health, LLC., 3 Lanyue Rd., Huangpu District, Guangzhou, 510663, China.
- Department of Urology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
| | - Yan Chen
- Department of Pediatrics, The Affiliated Hospital of Zunyi Medical University, 149 Dalian Rd., Zunyi, 56300, Guizhou, China.
- Department of Pediatrics, Guizhou Children's Hospital, Zunyi, Guizhou, China.
- Collaborative Innovation Center for Tissue Injury Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, Guizhou, China.
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12
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Zhang Q, Lin P, Mao A, Liu Y, Shang X, Wei X, Li Y, Lin B, Xu X. An unusual case of thalassemia intermedia with inheritable complex repeats detected by single-molecule optical mapping. Haematologica 2024; 109:1000-1006. [PMID: 37767576 PMCID: PMC10905065 DOI: 10.3324/haematol.2023.282902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Affiliation(s)
- Qianqian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences; Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China; Dongguan Maternal and Child Health Care Hospital, Postdoctoral Innovation Practice Base of Southern Medical University; Prenatal Diagnosis Center, Dongguan Maternal and Child Health Care Hospital, Dongguan 523001, Guangdong
| | - Peng Lin
- Department of Medical Genetics, School of Basic Medical Sciences; Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China; Dongguan Maternal and Child Health Care Hospital, Postdoctoral Innovation Practice Base of Southern Medical University; Prenatal Diagnosis Center, Dongguan Maternal and Child Health Care Hospital, Dongguan 523001, Guangdong
| | - Aiping Mao
- Department of TGS Research and Development, Berry Genomics Corporation, Beijing 102200
| | - Yongqiong Liu
- Department of Medical Genetics, School of Basic Medical Sciences; Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong
| | - Xuan Shang
- Department of Medical Genetics, School of Basic Medical Sciences; Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong
| | - Xiaofeng Wei
- Department of Medical Genetics, School of Basic Medical Sciences; Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong
| | - Yuezhen Li
- Department of TGS Research and Development, Berry Genomics Corporation, Beijing 102200
| | - Bin Lin
- Guangzhou Jiexu Gene Technology Co., Ltd., Guangzhou 510530, Guangdong
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences; Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong.
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13
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Chen Y, Zhong R, Guo X, Chen S, Wang Y, Li J, Huang L, Li Y, Wang X, Wu L, Huang M, Huang X, Fang J, Chu Z, Sun J, Peng Z, Sun Y. Carrier rate of thalassemia among 25,910 high school students in Shaoguan area, China. J Med Screen 2024; 31:53-57. [PMID: 37439030 DOI: 10.1177/09691413231188069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
OBJECTIVES As one of the most common hereditary diseases, thalassemia affects a large number of people in China. The aim of this study was to investigate the feasibility of a method based on next-generation sequencing (NGS) for screening of thalassemia carriers among high school students in the Shaoguan area. MATERIALS AND METHODS The NGS-based method was performed using 25,910 high school students recruited from 38 schools. The screening yield was systematically analyzed. Before screening, a lecture on how the disease is inherited, the symptoms of thalassemia, and how to prevent it was given to 28,780 students. RESULTS Implying successful delivery of information on the disease, 90.03% (25,910 of 28,780) of the students agreed to join this program for thalassemia screening. A thalassemia carrier rate of 15.99% (4144 of 25,910) was found. Also, 69 rare genotypes (28 of α-thalassemia and 41 of β-thalassemia) and 9 novel variants were identified. CONCLUSIONS This NGS-based method provided a feasible platform for high school population thalassemia screening. Combined with a clinical follow-up strategy, it could help eventually to prevent the births of affected children.
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Affiliation(s)
- Yajun Chen
- Shaoguan Maternal and Child Health Hospital, Shaoguan, China
| | - Rui Zhong
- Shaoguan Maternal and Child Health Hospital, Shaoguan, China
| | - Xueqin Guo
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Shiping Chen
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Yan Wang
- Shaoguan Maternal and Child Health Hospital, Shaoguan, China
| | - Jiufeng Li
- Shaoguan Maternal and Child Health Hospital, Shaoguan, China
| | - Lichan Huang
- Shaoguan Maternal and Child Health Hospital, Shaoguan, China
| | - Yi Li
- Shaoguan Maternal and Child Health Hospital, Shaoguan, China
| | - Xiaoling Wang
- Shaoguan Maternal and Child Health Hospital, Shaoguan, China
| | - Liting Wu
- Shaoguan Maternal and Child Health Hospital, Shaoguan, China
| | - Mubao Huang
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Xiaoyan Huang
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Junbin Fang
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Zhongjie Chu
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yan Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
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14
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Xu Z, Hu L, Liu Y, Peng C, Zeng G, Zeng L, Yang M, Linpeng S, Bu X, Jiang X, Xie T, Chen L, Zhou S, He J. Comparison of Third-Generation Sequencing and Routine Polymerase Chain Reaction in Genetic Analysis of Thalassemia. Arch Pathol Lab Med 2024; 148:336-344. [PMID: 37270807 DOI: 10.5858/arpa.2022-0299-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 06/06/2023]
Abstract
CONTEXT.— Thalassemia is the most widely distributed monogenic autosomal recessive disorder in the world. Accurate genetic analysis of thalassemia is crucial for thalassemia prevention. OBJECTIVE.— To compare the clinical utility of a third-generation sequencing-based approach termed comprehensive analysis of thalassemia alleles with routine polymerase chain reaction (PCR) in genetic analysis of thalassemia and explore the molecular spectrum of thalassemia in Hunan Province. DESIGN.— Subjects in Hunan Province were recruited, and hematologic testing was performed. Five hundred four subjects positive on hemoglobin testing were then used as the cohort, and third-generation sequencing and routine PCR were used for genetic analysis. RESULTS.— Of the 504 subjects, 462 (91.67%) had the same results, whereas 42 (8.33%) exhibited discordant results between the 2 methods. Sanger sequencing and PCR testing confirmed the results of third-generation sequencing. In total, third-generation sequencing correctly detected 247 subjects with variants, whereas PCR identified 205, which showed an increase in detection of 20.49%. Moreover, α triplications were identified in 1.98% (10 of 504) hemoglobin testing-positive subjects in Hunan Province. Seven hemoglobin variants with potential pathogenicity were detected in 9 hemoglobin testing-positive subjects. CONCLUSIONS.— Third-generation sequencing is a more comprehensive, reliable, and efficient approach for genetic analysis of thalassemia than PCR, and allowed for a characterization of the thalassemia spectrum in Hunan Province.
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Affiliation(s)
- Zhen Xu
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Lanping Hu
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, China (Liu, Xie, Chen)
| | - Can Peng
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Guo Zeng
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Li Zeng
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Mengyue Yang
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Siyuan Linpeng
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Xiufen Bu
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Xuanyu Jiang
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Tiantian Xie
- Berry Genomics Corporation, Beijing, China (Liu, Xie, Chen)
| | - Libao Chen
- Berry Genomics Corporation, Beijing, China (Liu, Xie, Chen)
| | - Shihao Zhou
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Jun He
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
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15
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Liu Y, Zhuang Y, Chen J, Zhong Z, Fang J, Li X, Xiao B, Li P, Lin B, Tao Z, Liang Y, Lin P, Wang X, Song M, Luo H, Qin L, Huang L, Tan J, Li H, Zhong T, Yu L, Liu Z, Tang D, Zhao Y, Zhang X, Ye Y, Xu X. Quantitative evaluation of the clinical severity of hemoglobin H disease in a cohort of 591 patients using a scoring system based on regression analysis. Haematologica 2024; 109:632-638. [PMID: 37646667 PMCID: PMC10828758 DOI: 10.3324/haematol.2023.283211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Affiliation(s)
- Yumeng Liu
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuan Zhuang
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Jianhong Chen
- Department of Medical Genetics and Prenatal Diagnosis, Huizhou First Maternal and Child Health Care Hospital, Huizhou, Guangdong, China
| | - Zeyan Zhong
- Department of Medical Genetics and Prenatal Diagnosis, Huizhou First Maternal and Child Health Care Hospital, Huizhou, Guangdong, China
| | - Jianpei Fang
- Department of Pediatric Hematology/ Oncology, Children’s Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyu Li
- Department of Pediatric Hematology/ Oncology, Children’s Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bin Xiao
- Department of Hematology, 923rd Hospital of the People’s Liberation Army, Nanning, Guangxi, China
| | - Pingping Li
- Department of Hematology, 923rd Hospital of the People’s Liberation Army, Nanning, Guangxi, China
| | - Bin Lin
- Guangzhou Huayin Healthcare Group Co. Ltd., Guangzhou, Guangdong, China
- Guangzhou Jiexu Gene Technology Co. Ltd., Guangzhou, Guangdong, China
| | - Zhenzhong Tao
- Guangzhou Huayin Healthcare Group Co. Ltd., Guangzhou, Guangdong, China
- Guangzhou Jiexu Gene Technology Co. Ltd., Guangzhou, Guangdong, China
| | - Yidan Liang
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Peng Lin
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Xingmin Wang
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Mengyang Song
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Hualei Luo
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Lang Qin
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Li Huang
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Jufang Tan
- Prenatal Diagnosis Center, Chenzhou First People’s Hospital, Chenzhou, Hunan, China
| | - Hailiang Li
- Department of Laboratory Hematology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Tianyu Zhong
- Department of Laboratory Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Lian Yu
- Department of Hematology and Rheumatology, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan, Fujian, China
| | - Zhixiang Liu
- Department of Medical Dispute, Maternal and Child Health Hospital, Heyuan China Heyuan, Guangdong, China
| | - Deguo Tang
- Maternal and Child Health Hospital of Yongzhou City, Yongzhou, Hunan, China
| | - Yongzhong Zhao
- Biologics, Gene and Cell Therapy, Frontage Laboratories, Exton, PA, USA
| | - Xinhua Zhang
- Department of Hematology, 923rd Hospital of the People’s Liberation Army, Nanning, Guangxi, China
| | - Yuhua Ye
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiangmin Xu
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
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16
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Zhang X, Chen Q, Li J, Luo X, Luo J, Li J, Zeng Z, Wu Y, Zhang H, Dong Y. The effectiveness of expanded carrier screening based on next-generation sequencing for severe monogenic genetic diseases. Hum Genomics 2024; 18:9. [PMID: 38297315 PMCID: PMC10829374 DOI: 10.1186/s40246-024-00577-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 01/24/2024] [Indexed: 02/02/2024] Open
Abstract
Expanded carrier screening (ECS) based on next-generation sequencing has been the subject of few studies to estimate the effectiveness of ECS in the Chinese population. A total of 3737 individuals from Southwest China or the general Chinese population, including 1048 pairs and 1641 individuals, were analysed by ECS for 155 monogenetic diseases. An ECS panel was used to detect 147 genes and 10,449 variants in 145 autosomal recessive and 10 X-linked recessive disorders. A total of 43.27% (1617/3737) were found to be carriers of at least one of the 155 monogenetic diseases. The average number of carriers of these recessive mutations was 0.54 and ranged from 0 to 4. Of the 1048 couples, 74.81% (n = 784) were found to have at least one partner carrying more than one disease. In addition, 5.34% of the couples at risk (n = 56) were heterozygous for the same autosomal recessive disease, and 0.37% of the women (9/2440) were carriers of X-linked diseases. Our study demonstrated the clinical significance of ECS in Chinese populations and the need for a programme of familial screening for the prevention of severe recessive monogenetic diseases.
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Affiliation(s)
- Xue Zhang
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Qian Chen
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Junnan Li
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Xin Luo
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Jianyun Luo
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Jian Li
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Ziye Zeng
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Yan Wu
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Hua Zhang
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China.
| | - Yanling Dong
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuanjiagang, Yuzhong District, Chongqing, 400016, People's Republic of China.
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Shao B, Wang Y, Zhang J, Wang Y, Tan J, Wang L, Hu P, Tan J, Xu Z. Mutation spectrum of thalassemia among pre-pregnant adults in the Jiangsu Province by capillary electrophoresis-based multiplex PCR assay. Mol Genet Genomic Med 2024; 12:e2344. [PMID: 38112059 PMCID: PMC10767610 DOI: 10.1002/mgg3.2344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 11/02/2023] [Accepted: 12/07/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Thalassemia is a common genetic disorder in southwestern China, and an increasing number of cases from eastern China have been recently reported. Here, we developed a rapid, convenient, and accurate assay to evaluate the mutation spectrum of thalassemia in eastern China. METHODS A carrier screening assay for 61 hotspot variants among HBA1/HBA2 and HBB (OMIM: 141800, 141850, and 141900) genes was developed by SNaPshot/high-throughput ligation-dependent probe amplification (HLPA) technology. We used this assay to detect the mutation spectrum of thalassemia in individuals from eastern China and compared with the data collected from literatures focused on southern and northern China for variant distribution. RESULTS Among 4276 tested individuals, 2.62% (112/4276) were α-thalassemia carriers, with 90 carrying one deletion or mutation and 22 carrying two deletions. 0.40% (17/4276) were β-thalassemia carriers, and the most common variant of β-thalassemia was c.126_129delCTTT (29.41%) followed by c.316-197C>T (23.53%). The genotype distribution in our study was similar to those from southern China populations. CONCLUSION The Chinese population from different regions presented comparable mutation spectrum of thalassemia, and the SNaPshot/HLPA technique may serve as a capable assay for a routine genetic test in clinical practice with its accurate, rapid, and inexpensive advantage.
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Affiliation(s)
- Binbin Shao
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Yuguo Wang
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Jingjing Zhang
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Yan Wang
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Juan Tan
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Lulu Wang
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Ping Hu
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Jianxin Tan
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
| | - Zhengfeng Xu
- Department of Prenatal DiagnosisWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjingPeople's Republic of China
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18
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Sani A, Idrees Khan M, Shah S, Tian Y, Zha G, Fan L, Zhang Q, Cao C. Diagnosis and screening of abnormal hemoglobins. Clin Chim Acta 2024; 552:117685. [PMID: 38030031 DOI: 10.1016/j.cca.2023.117685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023]
Abstract
Hemoglobin (Hb) abnormalities, such as thalassemia and structural Hb variants, are among the most prevalent inherited diseases and are associated with significant mortality and morbidity worldwide. However, there were not comprehensive reviews focusing on different clinical analytical techniques, research methods and artificial intelligence (AI) used in clinical screening and research on hemoglobinopathies. Hence the review offers a comprehensive summary of recent advancements and breakthroughs in the detection of aberrant Hbs, research methods and AI uses as well as the present restrictions anddifficulties in hemoglobinopathies. Recent advances in cation exchange high performance liquid chromatography (HPLC), capillary zone electrophoresis (CZE), isoelectric focusing (IEF), flow cytometry, mass spectrometry (MS) and polymerase chain reaction (PCR) etc have allowed for the definitive detection by using advanced AIand portable point of care tests (POCT) integrating with smartphone microscopic classification, machine learning (ML) model, complete blood counts (CBC), imaging-based method, speedy immunoassay, and electrochemical-, microfluidic- and sensing-related platforms. In addition, to confirm and validate unidentified and novel Hbs, highly specialized genetic based techniques like PCR, reverse transcribed (RT)-PCR, DNA microarray, sequencing of genomic DNA, and sequencing of RT-PCR amplified globin cDNA of the gene of interest have been used. Hence, adequate utilization and improvement of available diagnostic and screening technologies are important for the control and management of hemoglobinopathies.
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Affiliation(s)
- Ali Sani
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Muhammad Idrees Khan
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Saud Shah
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Youli Tian
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; School of Life Science and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Genhan Zha
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liuyin Fan
- Student Innovation Center, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Qiang Zhang
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Chengxi Cao
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; School of Life Science and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China.
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19
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Hsu JS, Wu DC, Shih SH, Liu JF, Tsai YC, Lee TL, Chen WA, Tseng YH, Lo YC, Lin HY, Chen YC, Chen JY, Chou TH, Chang DTH, Su MW, Guo WH, Mao HH, Chen CY, Chen PL. Complete genomic profiles of 1496 Taiwanese reveal curated medical insights. J Adv Res 2023:S2090-1232(23)00405-8. [PMID: 38159844 DOI: 10.1016/j.jare.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/03/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024] Open
Abstract
INTRODUCTION The population of Taiwan has a long history of ethno-cultural evolution. The Taiwanese population was isolated from other large populations such as the European, Han Chinese, and Japanese population. The Taiwan Biobank (TWB) project has built a nationwide database, particularly for personal whole-genome sequence (WGS) to facilitate basic and clinical collaboration nationally and internationally, making it one of the most valuable public datasets of the East Asian population. OBJECTIVES This study provides comprehensive medical genomic findings from TWB WGS data, for better characterization of disease susceptibility and the choice of ideal treatment regimens in Taiwanese population. METHODS We reanalyzed 1496 WGS using a PrecisionFDA Truth challenge winner method Sentieon DNAscope. Single nucleotide variants (SNV) and small insertions/deletions (INDEL) were benchmarked. We also analyzed pharmacogenomic (PGx) drug-associated alleles, and copy number variants (CNV). Multiple practicing clinicians reviewed and curated the clinically significant variants. Variant annotations can be browsed at TaiwanGenomes (https://genomes.tw). RESULTS We found that each participant had an average of 6,870.7 globally novel variants and 75.3% (831/1103) of the participants harbored at least one PharmGKB-selected high evidence level human leukocyte antigen (HLA) risk allele. 54 PharmGKB-reported high-level instances of evidence of Cytochrome P450 variant-drug pairs, with a population frequency of over 13.2%. We also identified 23 variants in the ACMG secondary finding V3 gene list from 25 participants, suggesting that 1.67% (25/1496) of the population is harboring at least one medical actionable variant. Our carrier status analyses suggest that one in 25 couples (3.94%) would risk having offspring with at least one pathogenic variant, which is in line with rates found in Japan and Singapore. For pathogenic CNV, we detected 6.88% and 2.02% carrier rates for alpha thalassemia and spinal muscular atrophy, respectively. CONCLUSION Our study highlights the overall medical insights of a complete Taiwanese genomic profile.
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Affiliation(s)
- Jacob Shujui Hsu
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan; Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei 100233, Taiwan
| | - Dung-Chi Wu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Shang-Hung Shih
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Jen-Feng Liu
- Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei 100233, Taiwan
| | - Ya-Chen Tsai
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Tung-Lin Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 100226, Taiwan
| | - Wei-An Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 100226, Taiwan
| | - Yi-Hsuan Tseng
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan
| | - Yi-Chung Lo
- Department of Electrical Engineering, National Cheng-Kung University, Tainan 701401, Taiwan
| | - Hong-Ye Lin
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Chieh Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan
| | - Jing-Yi Chen
- Department of Electrical Engineering, National Cheng-Kung University, Tainan 701401, Taiwan
| | - Ting-Hsuan Chou
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan
| | - Darby Tien-Hao Chang
- Department of Electrical Engineering, National Cheng-Kung University, Tainan 701401, Taiwan; Digital Technology Division, SinoPac Holdings, Taiwan
| | - Ming Wei Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan
| | - Wei-Hong Guo
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Hsin-Hsiang Mao
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Chien-Yu Chen
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan; Department of Biomechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 100025, Taiwan; Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei 100233, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei 100226, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 100233, Taiwan.
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20
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Bao X, Qin D, Wang J, Chen J, Yao C, Liang J, Liang K, Wang Y, Wang Y, Du L, Yin A. Two novel deletion mutations in β-globin gene cause β-thalassemia trait in two Chinese families. Hum Genomics 2023; 17:111. [PMID: 38062488 PMCID: PMC10704694 DOI: 10.1186/s40246-023-00559-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND β-Thalassemia is mainly caused by point mutations in the β-globin gene cluster. With the rapid development of sequencing technic, more and more variants are being discovered. RESULTS In this study, we found two novel deletion mutations in two unrelated families, HBB: c.180delG (termed βCD59) and HBB: c.382_402delCAGGCTGCCTATCAGAAAGTG (termed βCD128-134) in family A and B, respectively. Both the two novel mutations lead to β-thalassemia trait. However, when compounded with other β0-thalassemia, it may behave with β-thalassemia intermedia or β-thalassemia major. CONCLUSION Our study broadens the variants spectral of β-thalassemia in Chinese population and provides theoretical guidance for the prenatal diagnosis.
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Affiliation(s)
- Xiuqin Bao
- Medical Genetic Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Danqing Qin
- Medical Genetic Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Jicheng Wang
- Medical Genetic Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Jing Chen
- Prenatal Diagnosis Center, The Second People's Hospital of Zhaoqing, Zhaoqing, Guangdong, People's Republic of China
| | - Cuize Yao
- Medical Genetic Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Jie Liang
- Medical Genetic Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Kailing Liang
- Medical Genetic Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Yixia Wang
- Medical Genetic Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Yousheng Wang
- Grassroots Guidance and Collaboration Section, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Li Du
- Medical Genetic Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China.
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China.
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China.
| | - Aihua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China.
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China.
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China.
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Tang B, Wang J, Qin D, Yao C, Chen K, Liang L, Chai H, Guo H, Du L. Hb Chapel Hill or Alpha2 74(EF3) Asp>Gly, a mildly unstable variant found in a Chinese family. Hematology 2023; 28:2187154. [PMID: 36939273 DOI: 10.1080/16078454.2023.2187154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 02/28/2023] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Hb Chapel Hill [Alpha2 74(EF3) Asp > Gly] results from an GAC > GGC substitution at codon 74 of the HBA1 or HBA2 genes. Hb Chapel Hill has not been reported since 1986. METHODS A heterozygous mutation, HBA2: c.224A > G, was identified in the proband, her father and sister. We compared the haematological and clinical data of this family with the data reported in the limited number of individuals. RESULTS Having excluded iron deficiency, the Hb Chapel Hill was asymptomatic in heterozygous state. The cases presented here characterize cases in new techniques including capillary electrophoresis (CE). Two aberrant peaks were identified by CE, a major peak migrating in the zone 7 that correspond to Hb Chapel Hill (αChapel Hill 2β2) and a minor peak migrating in the zone 1 that correspond to Hb Chapel Hill2 (αChapel Hill 2δ2). Focusing on the variant expression, the Hb Chapel Hill plus Hb A2 variant were around 18.9-20.6% of total Hb in three members. CONCLUSION This data will be useful for providing up-to-date and high quality information on the Hb Chapel Hill.
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Affiliation(s)
- Bin Tang
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
| | - Jicheng Wang
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
| | - Danqinq Qin
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
| | - Cuize Yao
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
| | - Keyi Chen
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
| | - Lihua Liang
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
| | - Huiying Chai
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
| | - Hao Guo
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
| | - Li Du
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
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22
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Qin D, Wang J, Yao C, Bao X, Liang J, Du L. Hb Q-Thailand heterozygosity unlinked with the (-α 4.2/) α +-thalassemia deletion allele identified by long-read SMRT sequencing: hematological and molecular analyses. Hematology 2023; 28:2184118. [PMID: 36867091 DOI: 10.1080/16078454.2023.2184118] [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: 03/04/2023] Open
Abstract
OBJECTIVE In the present study, two unrelated cases of Hb Q-Thailand heterozygosity unlinked with the (-α4.2/) α+-thalassemia deletion allele were identified by long-read single molecule real-time (SMRT) sequencing in southern China. The aim of this study was to report the hematological and molecular features as well as diagnostic aspects of the rare manifestation. METHODS Hematological parameters and hemoglobin analysis results were recorded. A suspension array system for routine thalassemia genetic analysis and long-read SMRT sequencing were applied in parallel for thalassemia genotyping. Traditional methods, including Sanger sequencing, multiplex gap-polymerase chain reaction (gap-PCR) and multiplex ligation-dependent probe amplification (MLPA), were used together to confirm the thalassemia variants. RESULTS Long-read SMRT sequencing was used to diagnose two Hb Q-Thailand heterozygous patients for whom the hemoglobin variant was unlinked to the (-α4.2/) allele for the first time. The hitherto undescribed genotypes were verified by traditional methods. Hematological parameters were compared with those of Hb Q-Thailand heterozygosity linked with the (-α4.2/) deletion allele in our study. For the positive control samples, long-read SMRT sequencing revealed a linkage relationship between the Hb Q-Thailand allele and the (-α4.2/) deletion allele. CONCLUSIONS Identification of the two patients confirms that the linkage relationship between the Hb Q-Thailand allele and the (-α4.2/) deletion allele is a common possibility but not a certainty. Remarkably, as it is superior to traditional methods, SMRT technology may eventually serve as a more comprehensive and precise method that holds promising prospects in clinical practice, especially for rare variants.
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Affiliation(s)
- Danqing Qin
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China
| | - Jicheng Wang
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China
| | - Cuize Yao
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China
| | - Xiuqin Bao
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China
| | - Jie Liang
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China
| | - Li Du
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, People's Republic of China
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23
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Zhang W, Han X, Deng J, Zhou R, Du X, Wu C, Li M. Two Novel α-Thalassemia Mutations CD 39 -C [Thr > Pro] and CD 109 ACC > CCC [Thr > Pro] Identified in Two Chinese Families: A Case Report. Hemoglobin 2023; 47:172-179. [PMID: 37818638 DOI: 10.1080/03630269.2023.2263365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/09/2023] [Indexed: 10/12/2023]
Abstract
We reported the identification of two rare α-thalassemia silent carriers with novel HBA1 mutations of CD 39 -C [Thr > Pro] (HBA1: c.114del; p.Thr39Profs*11) and CD 109 ACC > CCC [Thr > Pro] (HBA1: c.325A > C; p. Thr109Pro), respectively. The two probands were pregnant women diagnosed with mild hypochromic anemia or microcytic hypochromic anemia by routine blood tests. They started iron therapy before taking differential diagnosis from iron deficiency anemia. After wait and watch approach, they both accepted thalassemia genetic screening, which identified CD 39 -C [Thr > Pro] and CD 109 ACC > CCC [Thr > Pro], respectively. Due to inappropriate iron therapy, worse anemia and iron overload were noticed in the first proband, but no obvious side effect was found in both probands. Functional analysis showed that, relative to the wild type, CD 39 -C [Thr > Pro] considerably reduced the expression of the HBA1 protein while CD 109 ACC > CCC [Thr > Pro] only had a minor impact. Our study highlighted the importance of gestational thalassemia screening based on next-generation sequencing for identifying novel rare thalassemia variants and increased our understanding about the relationship between genotype and phenotype of α-thalassemia.
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Affiliation(s)
- Wenqian Zhang
- BGI Genomics, Shenzhen, China
- Clin Lab, BGI Genomics, Wuhan, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaoqiang Han
- Department of Obstetrics and Gynecology, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, China
| | - Jie Deng
- Department of Obstetrics and Gynecology, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, China
| | - Rui Zhou
- BGI Genomics, Shenzhen, China
- Clin Lab, BGI Genomics, Wuhan, China
| | - Xiaoyun Du
- BGI Genomics, Shenzhen, China
- Clin Lab, BGI Genomics, Wuhan, China
| | - Cheng Wu
- BGI Genomics, Shenzhen, China
- Clin Lab, BGI Genomics, Wuhan, China
| | - Mingqun Li
- Department of Obstetrics and Gynecology, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, China
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Feng J, Cui D, Li C, Yang Y, Li Q, Li X, Tan S, Li Z, Meng W, Li H, Zhang Y. The comprehensive analysis of thalassemia alleles (CATSA) based on single-molecule real-time technology (SMRT) is a more powerful strategy in the diagnosis of thalassemia caused by rare variants. Clin Chim Acta 2023; 551:117619. [PMID: 38375625 DOI: 10.1016/j.cca.2023.117619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 02/21/2024]
Abstract
Thalassemia is one of the most widely distributed monogenic disorders in the world and affects the largest number of people. It can manifest a wide spectrum of phenotypes from asymptomatic to fatal, which is associated with the degree of imbalance between α- and β-globin chains. Therefore, individuals with different genotypes could present with a similar phenotype. Genetic analysis is always needed to make a correct diagnosis. However, routine genetic analysis of thalassemia used in the Chinese population identifies only 23 common variants, resulting in many cases undiagnosed or being misdiagnosed. In this study, we applied a long-read sequencing-based approach termed comprehensive analysis of thalassemia alleles (CATSA) to 30 subjects whose hematologic screening results could not be explained by the routine genetic test results. The identification of additional variants and the correction of genotypes allowed the interpretation of the clinical phenotype in 24 subjects, which have been confirmed to be correct by independent experiments. Moreover, we identified a novel 8.4-kb deletion containing the entire HBB and HBD genes as well as part of the HBBP1 gene, expanding the genotype spectrum of β-thalassemia. CATSA showed a great advantage over other genetic tests in the diagnosis of thalassemia caused by rare variants.
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Affiliation(s)
- Jianjiang Feng
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Di Cui
- Berry Genomics Corporation, Beijing 102200, China
| | - Caipeng Li
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Yingsong Yang
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Qiuli Li
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Xiaomin Li
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Shuming Tan
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Zhiming Li
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Wanli Meng
- Berry Genomics Corporation, Beijing 102200, China
| | - Haoxian Li
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China.
| | - Yanghui Zhang
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China.
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Feng J, Mao A, Lu Y, Shi H, Meng W, Liang C. Molecular characterization of a novel 83.9-kb deletion of the α-globin upstream regulatory elements by long-read sequencing. Blood Cells Mol Dis 2023; 103:102764. [PMID: 37336681 DOI: 10.1016/j.bcmd.2023.102764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Inherited deletions of upstream regulatory elements of α-globin genes give rise to α-thalassemia, which is an autosomal recessive monogenic disease. However, conventional thalassemia target diagnosis often fails to identify these rare deletions. Here we reported a family with two previous pregnancies of Hb Bart's hydrops fetalis and was seeking for prenatal diagnosis during the third pregnancy. Both parents had low level of Hemoglobin A2 indicating α-thalassemia. Conventional Gap-PCR and PCR-reverse dot blot showed the father carried -SEA deletion but did not identify any variants in the mother. Multiplex ligation-dependent probe amplification identified a deletion containing two HS-40 probes but could not determine the exact region. Finally, a long-read sequencing (LRS)-based approach directly identified that the exact deletion region was chr16: 48,642-132,584, which was located in the α-globin upstream regulatory elements and named (αα)JM after the Jiangmen city. Gap-PCR and Sanger sequencing confirmed the breakpoint. Both the mother and fetus from the third pregnancy carried heterozygous (αα)JM, and the fetus was normally delivered at gestational age of 39 weeks. This study demonstrated that LRS technology had great advantages over conventional target diagnosis methods for identifying rare thalassemia variants and assisted better carrier screening and prenatal diagnosis of thalassemia.
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Affiliation(s)
- Jianjiang Feng
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing 102200, China
| | - Ye Lu
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Haihong Shi
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Wanli Meng
- Berry Genomics Corporation, Beijing 102200, China
| | - Chen Liang
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China.
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Ye Y, Sun G, Ren Z, Liang Y, Luo H, Lin P, Wang X, Dong Z, Huang L, Qin L, Yu W, Wang G, Zhou Y, Tang J, Lou J, Liu Y, Zeng X, Chen Y, Li Y, Zhang Q, Huang J, Zhu P, Lin L, Zhang X, Xu X. Quantification of human embryonic ζ-globin chains in Southeast Asian deletion (-- SEA) carriers. J Clin Pathol 2023; 76:784-789. [PMID: 36008105 DOI: 10.1136/jcp-2022-208159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/12/2022] [Indexed: 11/04/2022]
Abstract
AIMS Reactivation of embryonic ζ-globin is a promising strategy for genetic treatment of α-thalassaemia. However, quantification of ζ-globin as a quantitative trait in α-thalassaemia carriers and patients remains incompletely understood. In this study, we aimed to set up a reliable approach for the quantification of ζ-globin in α-thalassaemia carriers, followed by a population study to investigate its expression patterns. METHODS ζ-globin was purified as monomers from cord blood haemolysate of a Hb Bart's fetus, followed by absolute protein quantification, which was then tested by in-house ELISA system and introduced as protein standard. It was then used for large-scale quantification in peripheral blood samples from 6179 individuals. Finally, liquid chromatography-tandem mass spectrometry (LC-MS/MS) introduced as an independent validating approach by measuring ζ-globin expression in a second cohort of 141-SEA/αα carriers. RESULTS The ELISA system was proved sensitive in distinguishing individuals with varied extent of ζ-globin. Large scale quantitative study of this --SEA/αα carrier cohort indicated the high diversity of ζ-globin expression ranging from 0.00155 g/L to 1.48778 g/L. Significant positive correlation between ELISA and LC-MS/MS (R=0.400, p<0.001) was observed and it is more sensitive in distinguishing the samples with extreme expression of ζ-globin (R=0.650, p<0.001). CONCLUSION Our study has reported reliable approaches for the quantification of ζ-globin and presented the expression patterns of ζ-globin among the --SEA/αα carrier population, which might lay a foundation on subsequent genotype-phenotype studies on mechanisms of delayed haemoglobin switch in α-thalassaemia.
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Affiliation(s)
- Yuhua Ye
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Genetics Testing Engineering Research Center, Guangzhou, People's Republic of China
| | - Guoying Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, People's Republic of China
| | - Zhe Ren
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, People's Republic of China
| | - Yidan Liang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Genetics Testing Engineering Research Center, Guangzhou, People's Republic of China
| | - Hualei Luo
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Genetics Testing Engineering Research Center, Guangzhou, People's Republic of China
| | - Peng Lin
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Genetics Testing Engineering Research Center, Guangzhou, People's Republic of China
| | - Xingmin Wang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Genetics Testing Engineering Research Center, Guangzhou, People's Republic of China
| | - Zejun Dong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Genetics Testing Engineering Research Center, Guangzhou, People's Republic of China
| | - Li Huang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Genetics Testing Engineering Research Center, Guangzhou, People's Republic of China
| | - Lang Qin
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Genetics Testing Engineering Research Center, Guangzhou, People's Republic of China
| | - Wenfang Yu
- Department of Blood Transfusion, Shanghai General Hospital, Shanghai, People's Republic of China
| | - Ge Wang
- Department of Clinical Laboratory, Zhuhai Municipal Maternal and Child Healthcare Hospital, Zhuhai, Guangdong, People's Republic of China
| | - Yuqiu Zhou
- Department of Clinical Laboratory, Zhuhai Municipal Maternal and Child Healthcare Hospital, Zhuhai, Guangdong, People's Republic of China
| | - Jia Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute, Guangzhou, People's Republic of China
| | - Jiwu Lou
- Dongguan Institute of Reproduction and Genetics, Dongguan Maternal and Children Health Hospital, Dongguan, People's Republic of China
| | - Yanhui Liu
- Dongguan Institute of Reproduction and Genetics, Dongguan Maternal and Children Health Hospital, Dongguan, People's Republic of China
| | - Xianqi Zeng
- Women and Children's Health Hospital of Shaoguan, Shaoguan, Guangdong, People's Republic of China
| | - Yajun Chen
- Women and Children's Health Hospital of Shaoguan, Shaoguan, Guangdong, People's Republic of China
| | - Yihong Li
- Department of Gynecology and Obstetrics, Southern Medical University, Guangzhou, People's Republic of China
| | - Qianqian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Genetics Testing Engineering Research Center, Guangzhou, People's Republic of China
| | - Jin Huang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Genetics Testing Engineering Research Center, Guangzhou, People's Republic of China
| | - Ping Zhu
- Department of Immunology, Southern Medical University, Guangzhou, People's Republic of China
| | - Liang Lin
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, People's Republic of China
| | - Xinhua Zhang
- Department of Hematology, 923rd Hospital of the People's Liberation Army, Nanning, Guangxi, People's Republic of China
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Genetics Testing Engineering Research Center, Guangzhou, People's Republic of China
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Wang X, Sun Y, Guan XW, Wang YY, Hong DY, Zhang ZL, Li YH, Yang PY, Jiang T, Xu ZF. Newborn genetic screening is highly effective for high-risk infants: A single-centre study in China. J Glob Health 2023; 13:04128. [PMID: 37824171 PMCID: PMC10569371 DOI: 10.7189/jogh.13.04128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Background Newborn genetic screening (NBGS) is promising for early detection of genetic diseases in newborns. However, little is known about its clinical effectiveness in special groups like high-risk infants. To address this gap, we aimed to investigate the impact of NBGS on high-risk infants. Methods We screened 10 334 healthy newborns from the general maternity unit and 886 high-risk infants from the neonatal ward using both traditional newborn screening (tNBS) and NBGS, and collected clinical data from electronic medical records. Results We found that high-risk infants had a higher proportion of eutocia (P < 0.01) and prematurity (P < 0.01). For high-risk infants vs healthy newborns screened by tNBS, the primary screening positive rate was 3.84% vs 1.31%, the false positive rate (FPR) was 3.62% vs 1.18% (P < 0.001), and the positive predictive value (PPV) was 5.88% vs 8.27%. For NBGS vs tNBS in high-risk infants, the primary screening positive rate was 0.54% vs 3.68%, the FPR was 0.22% vs 3.47%, and the PPV was 60.00% vs 5.88%. Conclusions We found that combined newborn screening can effectively reduce the FPR caused by the high-risk symptoms and improve the PPV in high-risk infants, sufficient for more accurately showing the true status of the disease.
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Affiliation(s)
| | | | - Xian-Wei Guan
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Yan-Yun Wang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Dong-Yang Hong
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Zhi-Lei Zhang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Ya-Hong Li
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Pei-Ying Yang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
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Chen T, Fan C, Huang Y, Feng J, Zhang Y, Miao J, Wang X, Li Y, Huang C, Jin W, Tang C, Feng L, Yin Y, Zhu B, Sun M, Liu X, Xiang J, Tan M, Jia L, Chen L, Huang H, Peng H, Sun X, Gu X, Peng Z, Zhu B, Zou H, Han L. Genomic Sequencing as a First-Tier Screening Test and Outcomes of Newborn Screening. JAMA Netw Open 2023; 6:e2331162. [PMID: 37656460 PMCID: PMC10474521 DOI: 10.1001/jamanetworkopen.2023.31162] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/10/2023] [Indexed: 09/02/2023] Open
Abstract
Importance Newborn screening via biochemical tests is in use worldwide. The availability of genetic sequencing has allowed rapid screening for a substantial number of monogenic disorders. However, the outcomes of this strategy have not been evaluated in a general newborn population. Objective To evaluate the outcomes of applying gene panel sequencing as a first-tier newborn screening test. Design, Setting, and Participants This cohort study included newborns who were prospectively recruited from 8 screening centers in China between February 21 and December 31, 2021. Neonates with positive results were followed up before July 5, 2022. Exposures All participants were concurrently screened using dried blood spots. The screen consisted of biochemical screening tests and a targeted gene panel sequencing test for 128 conditions. The biochemical and genomic tests could both detect 43 of the conditions, whereas the other 85 conditions were screened solely by the gene panel. Main Outcomes and Measures The primary outcomes were the number of patients detected by gene panel sequencing but undetected by the biochemical test. Results This study prospectively recruited 29 601 newborns (15 357 [51.2%] male). The mean (SD) gestational age was 39.0 (1.5) weeks, and the mean (SD) birth weight was 3273 (457) g. The gene panel sequencing screened 813 infants (2.7%; 95% CI, 2.6%-2.9%) as positive. By the date of follow-up, 402 infants (1.4%; 95% CI, 1.2%-1.5%) had been diagnosed, indicating the positive predictive value was 50.4% (95% CI, 50.0%-53.9%). The gene panel sequencing identified 59 patients undetected by biochemical tests, including 20 patients affected by biochemically and genetically screened disorders and 39 patients affected by solely genetically screened disorders, which translates into 1 out of every 500 newborns (95% CI, 1/385-1/625) benefiting from the implementation of gene panels as a first-tier screening test. Conclusions and Relevance In this cohort study, the use of gene panel sequencing in a general newborn population as a first-tier screening test improved the detection capability of traditional screening, providing an evidence-based suggestion that it could be considered as a crucial method for first-tier screening.
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Affiliation(s)
- Ting Chen
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research & Center for Clinical Innovation and Research, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chunna Fan
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yonglan Huang
- Guangzhou Newborn Screening Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jizhen Feng
- Department of Genetics, Shijiazhuang Maternal and Child Health Hospital, Shijiazhuang, Hebei, China
| | - Yinhong Zhang
- Department of Medical Genetics, NHC Key Laboratory of Preconception Health Birth in Western China, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Jingkun Miao
- Department of Pediatrics, Chongqing Health Center for Women and Children & Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaohua Wang
- Department of Genetics, Inner Mongolia Maternity and Child Health Care Hospital, Hohhot, Inner Mongolia, China
| | - Yulin Li
- Neonatal Disease Screening Center, Jinan Maternity and Child Health Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Cidan Huang
- Neonatal Disease Screening Center, Hainan Women and Children’s Medical Center, Haikou, Hainan, China
| | - Weiwei Jin
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Chengfang Tang
- Guangzhou Newborn Screening Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lulu Feng
- Department of Genetics, Shijiazhuang Maternal and Child Health Hospital, Shijiazhuang, Hebei, China
| | - Yifan Yin
- Department of Pediatrics, Chongqing Health Center for Women and Children & Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Bo Zhu
- Department of Genetics, Inner Mongolia Maternity and Child Health Care Hospital, Hohhot, Inner Mongolia, China
| | - Meng Sun
- Neonatal Disease Screening Center, Jinan Maternity and Child Health Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xiulian Liu
- Neonatal Disease Screening Center, Hainan Women and Children’s Medical Center, Haikou, Hainan, China
| | | | - Minyi Tan
- Guangzhou Newborn Screening Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Liyun Jia
- Department of Genetics, Shijiazhuang Maternal and Child Health Hospital, Shijiazhuang, Hebei, China
| | - Lei Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hui Huang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Xin Sun
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research & Center for Clinical Innovation and Research, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xuefan Gu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research & Center for Clinical Innovation and Research, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Baosheng Zhu
- Department of Medical Genetics, NHC Key Laboratory of Preconception Health Birth in Western China, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hui Zou
- Neonatal Disease Screening Center, Jinan Maternity and Child Health Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Lianshu Han
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research & Center for Clinical Innovation and Research, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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29
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Qin J, He J, Li Y, Liu N, Tao F, Zhang P, Guo W, Qin Q, Zhou W. One-step genotyping of α-thalassaemia by multiplex symmetric PCR melting curve. J Clin Pathol 2023; 76:632-636. [PMID: 35701141 DOI: 10.1136/jclinpath-2022-208363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/31/2022] [Indexed: 11/03/2022]
Abstract
AIMS Alpha-thalassaemia is one of the most common monogenic disorders worldwide. Due to high guanine-cytosine (GC) content and high mutation diversity in α-globin gene cluster, deletional and non-deletional mutations were usually separately detected with different methods. The aim of this study was to develop a novel one-step method for α-thalassaemia genotyping. METHODS A multiplex symmetric PCR melting curve strategy was designed for one-step α-thalassaemia genotyping. Based on this strategy, a novel method was developed to simultaneously detect four common deletional (-α3.7 , -α4.2 , _ _SEA , --THAI ) and five common non-deletional (αCD30(-GAG)α, αCD31(G>A)α, αWSα, αQSα, αCSα) α-thalassaemia mutations in a closed-tube reaction. This method was also evaluated by double-blind detection of 235 genotype-known samples and 1630 clinical samples. RESULTS All nine α-thalassaemia mutations could be accurately identified by this novel method within 3 hours. The evaluation results also showed a 100% concordance with comparison methods. CONCLUSIONS This method is rapid, accurate, low-cost and easy to operate, which can be used for molecular screening and genetic diagnosis of α-thalassaemia in clinical practice. The multiplex symmetric PCR melting curve strategy designed in this study can also provide an effective approach to the method development for high GC content templates and multiple mutations.
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Affiliation(s)
- Jiachun Qin
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Jun He
- Department of Genetics, Changsha Hospital for Maternal and Child Health Care, Changsha, China
| | - Yang Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Nansong Liu
- Research and Development Center, Yaneng BIOscience (Shenzhen) Co Ltd, Shenzhen, Guangdong, China
| | - Fangchao Tao
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Pengyi Zhang
- Neonatal Screening Center, Maternal and Child Health Hospital, Fushan, China
| | - Weilin Guo
- Research and Development Center, Yaneng BIOscience (Shenzhen) Co Ltd, Shenzhen, Guangdong, China
| | - Qiongzhen Qin
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Wanjun Zhou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Department of Laboratory Medicine, Southern Medical University Nanfang Hospital, Guangzhou, Guangdong, China
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Zhang Y, Xie H, Liang G, Qin Y, Wei X, Ning S, Liang Y, Liang X, Xie Y, Lin Z, Zhu D, Lin J, Xiong F, Xu X, Shang X. A novel gain-of-function PIP4K2A mutation elevates the expression of β-globin and aggravates the severity of α-thalassemia. Br J Haematol 2023; 202:1018-1023. [PMID: 37423903 DOI: 10.1111/bjh.18967] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023]
Abstract
Haemoglobin H (Hb H) disease (intermediate status of α-thalassemia) shows marked phenotypic variability from asymptomatic to severe anaemia. Apart from the combined β-thalassemia allele ameliorating clinical severity, reports of genetic modifier genes affecting the phenotype of Hb H disease are scarce which bring inconvenience to precise diagnosis and genetic counselling of the patients. Here, we present a novel mutation (c.948C>A, p.S316R) in the PIP4K2A gene in a female Hb H disease patient who displayed moderate anaemia and a relatively high Hb H level. Haematological analysis in her family members revealed that individuals carrying this mutation have upregulated β-globin expression, leading to a more imbalanced β/α-globin ratio and more Hb H inclusion bodies in peripheral red blood cells. According to functional experiments, the mutant PIP4K2A protein exhibits enhanced protein stability, increased kinase activity and a stronger regulatory effect on downstream proteins, suggesting a gain-of-function mutation. Moreover, introduction of the S316R mutation into HUDEP-2 cells increased expression of β-globin, further inhibiting erythroid differentiation and terminal enucleation. Thus, the S316R mutation is a novel genetic factor associated with β-globin expression, and the PIP4K2A gene is a new potential modifier gene affecting the α-thalassemia phenotype.
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Affiliation(s)
- Yanxia Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hongting Xie
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Guanxia Liang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yunrong Qin
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin, China
| | - Xiaofeng Wei
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Sisi Ning
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin, China
| | - Yi Liang
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin, China
| | - Xiongda Liang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yuling Xie
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin, China
| | - Zezhang Lin
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Dina Zhu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jiaqiong Lin
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Fu Xiong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiangming Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuan Shang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Yang T, Luo X, Liu Y, Lin M, Zhao Q, Zhang W, Chen Z, Dong M, Wang J, Wang Q, Zhang X, Zhong T. Next-generation sequencing analysis of the molecular spectrum of thalassemia in Southern Jiangxi, China. Hum Genomics 2023; 17:77. [PMID: 37592328 PMCID: PMC10436446 DOI: 10.1186/s40246-023-00520-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/26/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Thalassemia is an extremely prevalent monogenic inherited blood disorder in southern China. It is important to comprehensively understand the molecular spectrum of thalassemia in an area with such a high prevalence of thalassemia before taking appropriate actions for the prevention and treatment of this disorder. Herein, we explored the clinical feasibility of using next-generation sequencing (NGS) for large-scale population screening to illustrate the prevalence and spectrum of thalassemia in Southern Jiangxi. METHODS Blood samples collected from 136,312 residents of reproductive age in Southern Jiangxi were characterized for thalassemia by NGS. A retrospective analysis was then conducted on blood samples determined to be positive for thalassemia. RESULTS In total, 19,827 (14.545%) subjects were diagnosed as thalassemia carriers, and the thalassemia prevalence rate significantly varied by geographical region (p < 0.001). A total of 40 α-thalassemia genotypes including 21 rare genotypes were identified, with -@-SEA/αα being the most prevalent genotype. 42 β-thalassemia genotypes including 27 rare genotypes were identified, with the most common mutation IVS II-654 C > T accounting for 35.257% of these β-thalassemia genotypes. Furthermore, 74 genotypes were identified among 608 individuals with combined α- and β-thalassemia. Notably, most individuals with rare thalassemia mutations had mildly abnormal hematologic parameters including microcytic hypochromia. CONCLUSIONS Our findings demonstrate the great heterogeneity and diverse spectrum of thalassemia in Southern Jiangxi, emphasizing the importance and necessity of persistent prevention and control of thalassemia in this region. Additionally, our findings further suggest that NGS can effectively identify rare mutations and reduce the misdiagnosis rate of thalassemia.
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Affiliation(s)
- Tong Yang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Xuemei Luo
- Ganzhou Municipal Health Commission, Ganzhou, China
| | - Yanqiu Liu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Min Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Qinfei Zhao
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Wenqian Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Zhigang Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Minghua Dong
- School of Public Health and Health Management, Gannan Medical University, Ganzhou, China
| | - Junli Wang
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Qi Wang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Xiaokang Zhang
- School of Public Health and Health Management, Gannan Medical University, Ganzhou, China.
| | - Tianyu Zhong
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China.
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, Jiangxi, China.
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Carrier Screening Programs for Cystic Fibrosis, Fragile X Syndrome, Hemoglobinopathies and Thalassemia, and Spinal Muscular Atrophy: A Health Technology Assessment. ONTARIO HEALTH TECHNOLOGY ASSESSMENT SERIES 2023; 23:1-398. [PMID: 37637488 PMCID: PMC10453298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Background We conducted a health technology assessment to evaluate the safety, effectiveness, and cost-effectiveness of carrier screening programs for cystic fibrosis (CF), fragile X syndrome (FXS), hemoglobinopathies and thalassemia, and spinal muscular atrophy (SMA) in people who are considering a pregnancy or who are pregnant. We also evaluated the budget impact of publicly funding carrier screening programs, and patient preferences and values. Methods We performed a systematic literature search of the clinical evidence. We assessed the risk of bias of each included study using the Cochrane Risk of Bias tool and the Risk of Bias Assessment tool for Non-randomized Studies (RoBANS), and the quality of the body of evidence according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) Working Group criteria. We performed a systematic economic literature search and conducted cost-effectiveness analyses comparing preconception or prenatal carrier screening programs to no screening. We considered four carrier screening strategies: 1) universal screening with standard panels; 2) universal screening with a hypothetical expanded panel; 3) risk-based screening with standard panels; and 4) risk-based screening with a hypothetical expanded panel. We also estimated the 5-year budget impact of publicly funding preconception or prenatal carrier screening programs for the given conditions in Ontario. To contextualize the potential value of carrier screening, we spoke with 22 people who had sought out carrier screening. Results We included 107 studies in the clinical evidence review. Carrier screening for CF, hemoglobinopathies and thalassemia, FXS, and SMA likely results in the identification of couples with an increased chance of having an affected pregnancy (GRADE: Moderate). Screening likely impacts reproductive decision-making (GRADE: Moderate) and may result in lower anxiety among pregnant people, although the evidence is uncertain (GRADE: Very low).We included 21 studies in the economic evidence review, but none of the study findings were directly applicable to the Ontario context. Our cost-effectiveness analyses showed that in the short term, preconception or prenatal carrier screening programs identified more at-risk pregnancies (i.e., couples that tested positive) and provided more reproductive choice options compared with no screening, but were associated with higher costs. While all screening strategies had similar values for health outcomes, when comparing all strategies together, universal screening with standard panels was the most cost-effective strategy for both preconception and prenatal periods. The incremental cost-effectiveness ratios (ICERs) of universal screening with standard panels compared with no screening in the preconception period were $29,106 per additional at-risk pregnancy detected and $367,731 per affected birth averted; the corresponding ICERs in the prenatal period were about $29,759 per additional at-risk pregnancy detected and $431,807 per affected birth averted.We estimated that publicly funding a universal carrier screening program in the preconception period over the next 5 years would require between $208 million and $491 million. Publicly funding a risk-based screening program in the preconception period over the next 5 years would require between $1.3 million and $2.7 million. Publicly funding a universal carrier screening program in the prenatal period over the next 5 years would require between $128 million and $305 million. Publicly funding a risk-based screening program in the prenatal period over the next 5 years would require between $0.8 million and $1.7 million. Accounting for treatment costs of the screened health conditions resulted in a decrease in the budget impact of universally provided carrier screening programs or cost savings for risk-based programs.Participants value the perceived potential positive impact of carrier screening programs such as medical benefits from early detection and treatment, information for reproductive decision-making, and the social benefit of awareness and preparation. There was a strong preference expressed for thorough, timely, unbiased information to allow for informed reproductive decision-making. Conclusions Carrier screening for CF, FXS, hemoglobinopathies and thalassemia, and SMA is effective at identifying at-risk couples, and test results may impact preconception and reproductive decision-making.The cost-effectiveness and budget impact of carrier screening programs are uncertain for Ontario. Over the short term, carrier screening programs are associated with higher costs, and also higher chances of detecting at-risk pregnancies compared with no screening. The 5-year budget impact of publicly funding universal carrier screening programs is larger than that of risk-based programs. However, accounting for treatment costs of the screened health conditions results in a decrease in the total additional costs for universal carrier screening programs or in cost savings for risk-based programs.The people we spoke with who had sought out carrier screening valued the potential medical benefits of early detection and treatment, particularly the support and preparation for having a child with a potential genetic condition.
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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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Shao M, Wan Y, Cao W, Yang J, Cui D, Ma M, Hu W. Case report: A novel 10.8-kb deletion identified in the β-globin gene through the long-read sequencing technology in a Chinese family with abnormal hemoglobin testing results. Front Med (Lausanne) 2023; 10:1192279. [PMID: 37521358 PMCID: PMC10374251 DOI: 10.3389/fmed.2023.1192279] [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: 03/23/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Background Thalassemia is a common inherited hemoglobin disorder caused by a deficiency of one or more globin subunits. Substitution variants and deletions in the HBB gene are the major causes of β-thalassemia, of which large fragment deletions are rare and difficult to be detected by conventional polymerase chain reaction (PCR)-based methods. Case report In this study, we reported a 26-year-old Han Chinese man, whose routine blood parameters were found to be abnormal. Hemoglobin testing was performed on the proband and his family members, of whom only the proband's mother had normal parameters. The comprehensive analysis of thalassemia alleles (CATSA, a long-read sequencing-based approach) was performed to identify the causative variants. We finally found a novel 10.8-kb deletion including the β-globin (HBB) gene (Chr11:5216601-5227407, GRch38/hg38) of the proband and his father and brother, which were consistent with their hemoglobin testing results. The copy number and exact breakpoints of the deletion were confirmed by multiplex ligation-dependent probe amplification (MLPA) and gap-polymerase chain reaction (Gap-PCR) as well as Sanger sequencing, respectively. Conclusion With this novel large deletion found in the HBB gene in China, we expand the genotype spectrum of β-thalassemia and show the advantages of long-read sequencing (LRS) for comprehensive and precise detection of thalassemia variants.
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Affiliation(s)
- Mingkun Shao
- Department of OB and GYN, The Second Affiliated Hospital of Kunming Medical University, Yunnan, China
| | - Yaoyao Wan
- Department of Cardiovascular Medicine, The Second People's Hospital of Honghe Autonomous Prefecture, Yunnan, China
| | - Weipeng Cao
- Jinyu Medical Laboratory Co., Ltd., Yunnan, China
| | - Juan Yang
- Jinyu Medical Laboratory Co., Ltd., Yunnan, China
| | - Di Cui
- Berry Genomics Corporation, Beijing, China
| | - Minhui Ma
- Berry Genomics Corporation, Beijing, China
| | - Wanqin Hu
- Department of OB and GYN, The Second Affiliated Hospital of Kunming Medical University, Yunnan, China
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Wang WD, Hu F, Zhou DH, Gale RP, Lai YR, Yao HX, Li C, Wu BY, Chen Z, Fang JP, Chen SJ, Liang Y. Thalassaemia in China. Blood Rev 2023; 60:101074. [PMID: 36963988 DOI: 10.1016/j.blre.2023.101074] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 02/15/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
Because of successful thalassaemia prevention programmes in resource-rich countries and it's huge population China now has the greatest number of new cases of thalassaemia globally as well as more people with thalassaemia than any other country. 30 million Chinese have thalassaemia-associated mutations and about 300,000 have thalassaemia major or intermedia requiring medical intervention. Over the past 2 decades there has been tremendous economic growth in China including per capita spending on health care. There is now nation-wide availability and partial or full insurance for prenatal genetic testing, RBC-transfusions, iron-chelating drugs and haematopoietic cell transplants. Prenatal screening and educational programmes have reduced the incidence of new cases. However, substantial challenges remain. For example, regional differences in access to medical care and unequal economic development require innovations to reduce the medical, financial and psychological burdens of Chinese with thalassaemia and their families. In this review we discuss success in preventing and treating thalassaemia in China highlighting remaining challenges. Our discussion has important implications for resource-poor geospaces challenged with preventing and treating thalassaemia.
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Affiliation(s)
- Wei-da Wang
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Fang Hu
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Dun-Hua Zhou
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Robert Peter Gale
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Department of Immunology and Inflammation, Haematology Research Centre, Imperial College London, London, UK
| | - Yong-Rong Lai
- Department of Hematology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hong-Xia Yao
- Department of Hematology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, Hainan, China
| | - Chunfu Li
- Nanfang-Chunfu Children's Institute of Hematology and Oncology, Taixin Hospital, Dongguan, China
| | - Bing-Yi Wu
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jian-Pei Fang
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Yang Liang
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
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Laufer VA, Glover TW, Wilson TE. Applications of advanced technologies for detecting genomic structural variation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108475. [PMID: 37931775 PMCID: PMC10792551 DOI: 10.1016/j.mrrev.2023.108475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.
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Affiliation(s)
- Vincent A Laufer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas W Glover
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas E Wilson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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Sabath DE. The role of molecular diagnostic testing for hemoglobinopathies and thalassemias. Int J Lab Hematol 2023. [PMID: 37211360 DOI: 10.1111/ijlh.14089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/27/2023] [Indexed: 05/23/2023]
Abstract
Hemoglobin disorders are among the most common genetic diseases worldwide. Molecular diagnosis is helpful in cases where the diagnosis is uncertain and for genetic counseling. Protein-based diagnostic techniques are frequently adequate for initial diagnosis. Molecular genetic testing is pursued in some cases, particularly when a definitive diagnosis is not possible and especially for the purpose of assessing genetic risk for couples wanting to have children. The expertise available in the clinical hematology laboratory is essential for the diagnosis of patients with hemoglobin abnormalities. Initial diagnoses are made using protein-based techniques such as electrophoresis and chromatography. Based on these findings, genetic risk to an individual's offspring can be assessed. In the setting of β-thalassemia and other β-globin disorders, coincident α-thalassemia may be difficult to diagnose, which can have potentially serious consequences. In addition, unusual forms of β-thalassemia caused by deletions in the β-globin locus cannot be definitively characterized using standard techniques. Molecular diagnostic testing has an important role in the diagnosis of hemoglobin disorders and is important in the setting of genetic counseling. Molecular testing also has a role in prenatal diagnosis to identify fetuses affected by severe hemoglobinopathies and thalassemias.
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Affiliation(s)
- Daniel E Sabath
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
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Ning S, Qin Y, Liang Y, Liang Y, Xie Y, Lu Y, Wei G, Xu R, Liu Y, Li J. The frequency of HKαα allele in silent deletional α-thalassemia carriers in the Yulin region of southern China using the third-generation sequencing. Gene 2023; 875:147505. [PMID: 37217151 DOI: 10.1016/j.gene.2023.147505] [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: 02/24/2023] [Revised: 04/21/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
OBJECTIVES α-thalassemia is relatively prevalent in Yulin Region in southern China. In order to accurately detect α-globin gene aberrations for genetic counseling, the prevalence of HKαα (Hong Kong αα) allele in this subpopulation of silent deletional α-thalassemia were examined. MATERIALS AND METHODS A total of 1845 subjects were selected in Yulin Region from January 2021 to March 2021. Peripheral blood was collected from each participant for routine genetic analysis of thalassemia. The HKαα allele was determined using the Single-molecule real-time (SMRT) technology for samples with -α3.7/αα, βN/βN genotype. RESULTS Two samples were identified with HKαα allele from 100 samples with -α3.7/αα, βN/βN genotype. The frequency of HKαα allele was 2.0% (2/100) in -α3.7/αα, βN/βN carriers in Yulin Region. One sample was identified with a novel variant of the α-globin gene cluster named αHKαα by SMRT technology. One rare HBA2 variant and six HBB variants were found by SMRT technology, including -α3.7/HBA2:c.300+34G>A, HBB:c.316-45G>C/βN, HBB:c.315+180T>C/βN, HBB:c.316-179A>C/βN. CONCLUSION A certain proportion of HKαα allele had been detected in Yulin Region. SMRT technology plays a crucial role for improving the diagnostic accuracy and positive detection rate of thalassemia. The completion of this study has great meaning for strengthening the prevention and control of thalassemia in Yulin Region.
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Affiliation(s)
- Sisi Ning
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin,Guangxi Zhuang Autonomous Region, China
| | - Yunrong Qin
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin,Guangxi Zhuang Autonomous Region, China
| | - Yunning Liang
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin,Guangxi Zhuang Autonomous Region, China
| | - Yi Liang
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin,Guangxi Zhuang Autonomous Region, China
| | - Yuling Xie
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin,Guangxi Zhuang Autonomous Region, China
| | - Yinghong Lu
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin,Guangxi Zhuang Autonomous Region, China
| | - Guanghong Wei
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin,Guangxi Zhuang Autonomous Region, China
| | - Ruofan Xu
- Berry Genomics Corporation, Beijing, China
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, China
| | - Jihui Li
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin,Guangxi Zhuang Autonomous Region, China.
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Zhang S, Zhou L, Zhang L, Wang Y, Wang H. Molecular genetic screening of full-term small for gestational age. BMC Pediatr 2023; 23:217. [PMID: 37147621 PMCID: PMC10161501 DOI: 10.1186/s12887-023-04030-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 04/24/2023] [Indexed: 05/07/2023] Open
Abstract
OBJECTIVE To examine the clinical application of genomic screening in newborns small for gestational age (SGA), hoping to provide an efficient technique for early discovery of neonatal diseases, which is necessary to elevate survival rates and the quality of life in infants. METHODS Totally 93 full-term SGA newborns were assessed. Dried blood spot (DBS) samples were obtained at 72 h after birth, and tandem mass spectrometry (TMS) and Angel Care genomic screening (GS, using Targeted next generation sequencing) were carried out. RESULTS All 93 subjects were examined by Angel Care GS and TMS. No children showing inborn errors of metabolism (IEM) were detected by TMS, while 2 pediatric cases (2.15%, 2/93) were confirmed as thyroid dyshormonogenesis 6 (TDH6) by Angel Care GS. Additionally, 45 pediatric cases (48.4%) had one or more variants conferring a carrier status for recessive childhood-onset disorders, with 31 genes and 42 variants associated with 26 diseases. The top three gene-related diseases with carrier status were autosomal recessive deafness (DFNB), abnormal thyroid hormone and Krabbe disease. CONCLUSIONS SGA is tightly associated with genetic variation. Molecular Genetic Screening allows early detection of congenital hypothyroidism and may be a potent genomic sequencing technique for screening newborns.
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Affiliation(s)
- Shuman Zhang
- Department of Neonatology, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu Province, China
| | - Lingna Zhou
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu Province, China
| | - Lin Zhang
- Department of Neonatology, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu Province, China
| | - Yu Wang
- Department of Neonatology, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu Province, China.
| | - Huaiyan Wang
- Department of Neonatology, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, Jiangsu Province, China.
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Bao X, Wang J, Qin D, Yao C, Liang J, Liang K, Zeng Y, Du L. Identification of four novel large deletions and complex variants in the α-globin locus in Chinese population. Hum Genomics 2023; 17:38. [PMID: 37098594 PMCID: PMC10127377 DOI: 10.1186/s40246-023-00486-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 04/20/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND At present, the methods generally used to detect α-thalassemia mutations are confined to detecting common mutations, which may lead to misdiagnosis or missed diagnosis. The single-molecule real-time (SMRT) sequencing enables long-read single-molecule sequencing with high detection accuracy, and long-length DNA chain reads in high-fidelity read mode. This study aimed to identify novel large deletions and complex variants in the α-globin locus in Chinese population. METHODS We used SMRT sequencing to detect rare and complex variants in the α-globin locus in four individuals whose hematological data indicated microcytic hypochromic anemia. However, the conventional thalassemia detection result was negative. Multiplex ligation-dependent probe amplification and droplet digital polymerase chain reaction were used to confirm SMRT sequencing results. RESULTS Four novel large deletions were observed ranging from 23 to 81 kb in the α-globin locus. One patient also had a duplication of upstream of HBZ in the deletional region, while another, with a 27.31-kb deletion on chromosome 16 (hg 38), had abnormal hemoglobin Siriraj (Hb Siriraj). CONCLUSION We first identified the four novel deletions in the α-globin locus using SMRT sequencing. Considering that the conventional methods might lead to misdiagnosis or missed diagnosis, SMRT sequencing proved to be an excellent method to discover rare and complex variants in thalassemia, especially in prenatal diagnosis.
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Affiliation(s)
- Xiuqin Bao
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Jicheng Wang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Danqing Qin
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Cuize Yao
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Jie Liang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Kailing Liang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Yukun Zeng
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China
| | - Li Du
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, People's Republic of China.
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China.
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, People's Republic of China.
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Zulkeflee RH, Bahar R, Abdullah M, Mohd Radzi MAR, Md Fauzi A, Hassan R. Application of Targeted Next-Generation Sequencing for the Investigation of Thalassemia in a Developing Country: A Single Center Experience. Diagnostics (Basel) 2023; 13:diagnostics13081379. [PMID: 37189480 DOI: 10.3390/diagnostics13081379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Thalassemia is identified as a prevalent disease in Malaysia, known to be one of the developing countries. Fourteen patients with confirmed cases of thalassemia were recruited from the Hematology Laboratory. The molecular genotypes of these patients were tested using the multiplex-ARMS and GAP-PCR methods. The samples were repeatedly investigated using the Devyser Thalassemia kit (Devyser, Sweden), a targeted NGS panel targeting the coding regions of hemoglobin genes, namely the HBA1, HBA2, and HBB genes, which were used in this study. There were many different genetic variants found in 14 unrelated cases. Out of all fourteen cases, NGS was able to determine an additional -50 G>A (HBB:c.-100G>A) that were not identified by the multiplex-ARMS method, including HBA2 mutations, namely CD 79 (HBA2:c.239C>G). Other than that, CD 142 (HBA2:c.427T>C) and another non-deletional alpha thalassemia and alpha triplication were also not picked up by the GAP-PCR methods. We illustrated a broad, targeted NGS-based test that proposes benefits rather than using traditional screening or basic molecular methods. The results of this study should be heeded, as this is the first report on the practicality of targeted NGS concerning the biological and phenotypic features of thalassemia, especially in a developing population. Discovering rare pathogenic thalassemia variants and additional secondary modifiers may facilitate precise diagnosis and better disease prevention.
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Affiliation(s)
- Razan Hayati Zulkeflee
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Department of Hematology, School of Medical Sciences, Universiti Sains Malaysia (USM), Kubang Kerian 16150, Malaysia
| | - Rosnah Bahar
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Department of Hematology, School of Medical Sciences, Universiti Sains Malaysia (USM), Kubang Kerian 16150, Malaysia
| | - Marne Abdullah
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Department of Hematology, School of Medical Sciences, Universiti Sains Malaysia (USM), Kubang Kerian 16150, Malaysia
| | - Muhammad Amiro Rasheeq Mohd Radzi
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Department of Paediatrics, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Alina Md Fauzi
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Bandar Baru Nilai, Nilai 71800, Malaysia
| | - Rosline Hassan
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Department of Hematology, School of Medical Sciences, Universiti Sains Malaysia (USM), Kubang Kerian 16150, Malaysia
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Yang Z, Yang X, Sun Y, Wang Y, Song L, Qiao Z, Fang Z, Wang Z, Liu L, Chen Y, Yan S, Guo X, Zhang J, Fan C, Liu F, Peng Z, Peng H, Sun J, Chen W. Test development, optimization and validation of a WGS pipeline for genetic disorders. BMC Med Genomics 2023; 16:74. [PMID: 37020281 PMCID: PMC10077614 DOI: 10.1186/s12920-023-01495-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND With advances in massive parallel sequencing (MPS) technology, whole-genome sequencing (WGS) has gradually evolved into the first-tier diagnostic test for genetic disorders. However, deployment practice and pipeline testing for clinical WGS are lacking. METHODS In this study, we introduced a whole WGS pipeline for genetic disorders, which included the entire process from obtaining a sample to clinical reporting. All samples that underwent WGS were constructed using polymerase chain reaction (PCR)-free library preparation protocols and sequenced on the MGISEQ-2000 platform. Bioinformatics pipelines were developed for the simultaneous detection of various types of variants, including single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs) and balanced rearrangements, mitochondrial (MT) variants, and other complex variants such as repeat expansion, pseudogenes and absence of heterozygosity (AOH). A semiautomatic pipeline was developed for the interpretation of potential SNVs and CNVs. Forty-five samples (including 14 positive commercially available samples, 23 laboratory-held positive cell lines and 8 clinical cases) with known variants were used to validate the whole pipeline. RESULTS In this study, a whole WGS pipeline for genetic disorders was developed and optimized. Forty-five samples with known variants (6 with SNVs and Indels, 3 with MT variants, 5 with aneuploidies, 1 with triploidy, 23 with CNVs, 5 with balanced rearrangements, 2 with repeat expansions, 1 with AOHs, and 1 with exon 7-8 deletion of SMN1 gene) validated the effectiveness of our pipeline. CONCLUSIONS This study has been piloted in test development, optimization, and validation of the WGS pipeline for genetic disorders. A set of best practices were recommended using our pipeline, along with a dataset of positive samples for benchmarking.
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Affiliation(s)
- Ziying Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Xu Yang
- Department of Paediatrics, Pu'er People's Hospital, Pu'er, 665000, China
| | - Yan Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lijie Song
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- DTU Bioengineering, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Zhihong Qiao
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhonghai Fang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhonghua Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lipei Liu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yunmei Chen
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Saiying Yan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Xueqin Guo
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 430074, China
| | - Junqing Zhang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Chunna Fan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Fengxia Liu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huanhuan Peng
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.
- BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.
| | - Wei Chen
- Pu'er People's Hospital, Pu'er, 665000, China.
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Wang G, Zou S, Li J, Wang X, Wu H, Tao Z, Zhang Q, Xu X, Zhou Y. The diagnosis and molecular analysis of a novel 27.2 kb deletion causing α 0-thalassemia. Clin Biochem 2023; 116:20-23. [PMID: 36878345 DOI: 10.1016/j.clinbiochem.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023]
Abstract
BACKGROUND Thalassemia, one of the most prevalent monogenic diseases worldwide, is caused by an imbalance of α-like and non-α-like globin chain production. Copy number variations, which cause the most common genotype of α-thalassemia, can be detected by multiple diagnostic methods. CASE REPORT The proband was a 31-year-old female who was diagnosed with microcytic hypochromic anemia by antenatal screening. Hematological analysis and molecular genotyping were conducted on the proband and the proband's family members. Gap-polymerase chain reaction, Sanger sequencing, multiplex ligation-dependent probe amplification, and next-generation sequencing were used to detect potentially pathogenic genes. Familial studies and genetic analyses revealed a novel deletion of 27.2 kb located in the α-globin gene cluster (NC_000016.9: g. 204538_231777delinsTAACA). CONCLUSIONS We reported a novel α-thalassemia deletion and described the process of molecular diagnosis. The novel deletion extends the thalassemia mutation spectrum, which may be helpful in genetic counseling and clinical diagnosis in the future.
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Affiliation(s)
- Ge Wang
- Zhuhai Institute of Medical Genetics, Zhuhai Women and Children's Hospital, Zhuhai, Guangdong, China
| | - Shaomin Zou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Jialong Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Xingmin Wang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Hongqiu Wu
- Zhuhai Institute of Medical Genetics, Zhuhai Women and Children's Hospital, Zhuhai, Guangdong, China
| | - Zhenzhong Tao
- Guangzhou Jiexu Gene Technology Co., Ltd., Guangzhou, Guangdong, China
| | - Qianqian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Innovative Research Center for Diagnosis and Therapy of Thalassemias, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Yuqiu Zhou
- Zhuhai Institute of Medical Genetics, Zhuhai Women and Children's Hospital, Zhuhai, Guangdong, China..
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Zhou QM, Jiang F, Xu J, Lin D, Huang RL, Zhou JY, Qu YX, Li DZ. High accuracy of single-molecule real-time sequencing in detecting a rare α-globin fusion gene in carrier screening population. Ann Hum Genet 2023; 87:9-17. [PMID: 36317495 DOI: 10.1111/ahg.12486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
INTRODUCTION The α-globin fusion gene between the HBA2 and HBAP1 genes becomes clinically important in thalassemia screening because this fusion gene can cause severe hemoglobin (Hb) H disease when combining with α0 -thalassemia (α0 -thal). Due to its uncommon rearrangement in the α gene cluster without dosage changes, this fusion gene is undetectable by common molecular testing approaches used for α-thal diagnosis. METHODS In this study, we used the single-molecule real-time (SMRT) sequencing technique to detect this fusion gene in 23 carriers identified by next-generation sequencing (NGS) among 16,504 screened individuals. Five primers for α and β thalassemia were utilized. RESULTS According to the NGS results, the 23 carriers include 14 pure heterozygotes, eight compound heterozygotes with common α-thal alleles, and one homozygote. By using SMRT, the fusion mutant was successfully detected in all 23 carriers. Furthermore, SMRT corrected the diagnosis in two "pure" heterozygotes: one was compound heterozygote with anti-3.7 triplication, and the other was homozygote. CONCLUSION Our results indicate that SMRT is a superior method compared to NGS in detecting the α fusion gene, attributing to its efficient, accurate, and one-step properties.
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Affiliation(s)
- Qiao-Miao Zhou
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, People's Republic of China
| | - Jing Xu
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Dan Lin
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Ren-Liang Huang
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Jian-Ying Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, People's Republic of China
| | - Yan-Xia Qu
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, People's Republic of China
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Liang Q, He J, Li Q, Zhou Y, Liu Y, Li Y, Tang L, Huang S, Li R, Zeng F, Mao A, Liu Y, Liang D, Wu L. Evaluating the Clinical Utility of a Long-Read Sequencing-Based Approach in Prenatal Diagnosis of Thalassemia. Clin Chem 2023; 69:239-250. [PMID: 36683393 DOI: 10.1093/clinchem/hvac200] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/02/2022] [Indexed: 01/24/2023]
Abstract
BACKGROUND The aim is to evaluate the clinical utility of a long-read sequencing-based approach termed comprehensive analysis of thalassemia alleles (CATSA) in prenatal diagnosis of thalassemia. METHODS A total of 278 fetuses from at-risk pregnancies identified in thalassemia carrier screening by PCR-based methods were recruited from 9 hospitals, and PCR-based methods were employed for prenatal diagnosis. CATSA was performed retrospectively and blindly for all 278 fetuses. RESULTS Among the 278 fetuses, 263 (94.6%) had concordant results and 15 (5.4%) had discordant results between the 2 methods. Of the 15 fetuses, 4 had discordant thalassemia variants within the PCR detection range and 11 had additional variants identified by CATSA. Independent PCR and Sanger sequencing confirmed the CATSA results. In total, CATSA and PCR-based methods correctly detected 206 and 191 fetuses with variants, respectively. Thus, CATSA yielded a 7.9% (15 of 191) increment as compared with PCR-based methods. CATSA also corrected the predicted phenotype in 8 fetuses. Specifically, a PCR-based method showed one fetus had homozygous HBB c.52A > T variants, while CATSA determined the variant was heterozygous, which corrected the predicted phenotype from β-thalassemia major to trait, potentially impacting the pregnancy outcome. CATSA additionally identified α-globin triplicates in 2 fetuses with the heterozygous HBB c.316-197C > T variant, which corrected the predicted phenotype from β-thalassemia trait to intermedia and changed the disease prognosis. CONCLUSIONS CATSA represents a more comprehensive and accurate approach that potentially enables more informed genetic counseling and improved clinical outcomes compared to PCR-based methods.
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Affiliation(s)
- Qiaowei Liang
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Jun He
- Changsha Hospital for Maternal and Child Health Care, Changsha, Hunan, China
| | - Qing Li
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yulin Zhou
- Women and Children's Hospital, School of Medicine and School of Public Health, Xiamen University, Xiamen, China
| | - Yanqiu Liu
- Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Youqiong Li
- Center for Medical Genetics and Prenatal Diagnosis, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Lingfang Tang
- Guilin Women and Children Health Care Hospital, Guilin, Guangxi, China
| | | | - Rong Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Fanqian Zeng
- Yunnan Maternal and Child Health Care Hospital, Kunming, Yunnan, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, China
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, China
| | - Desheng Liang
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lingqian Wu
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
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Identification of a novel 10.3 kb deletion causing α 0-thalassemia by third-generation sequencing: Pedigree analysis and genetic diagnosis. Clin Biochem 2023; 113:64-69. [PMID: 36610469 DOI: 10.1016/j.clinbiochem.2022.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/29/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023]
Abstract
BACKGROUND α-thalassemia is an inherited blood disorder caused by variants in the α-globin gene cluster. Identification of the pathogenic α-globin gene variants is important for the diagnosis and management of thalassemia. METHODS Two suspected families from Xiantao, Hubei Province were recruited in this study. The family members underwent hemoglobin testing. Polymerase Chain Reaction based reverse dot blot (PCR-RDB) was employed to identify the known variants. Next-generation sequencing (NGS) and third-generation sequencing (TGS) were performed to screen the potential disease-causing variants, which were validated by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). RESULTS Hematological analysis suggested that proband A had α-thalassemia traits, and proband B had HbH disease traits. However, only a -α3.7 mutation had been detected by PCR-RDB and NGS in the proband of family B. Subsequent TGS identified a novel 10.3 kb deletion (NC_000016.10:g.172342-182690del) covering the HBA1, HBQ1 and HBA2 genes in the α-globin gene cluster in both family A and B, which was confirmed by Sanger sequencing and MLPA. These results indicated that the novel deletion is likely responsible for α-thalassemia. CONCLUSION A novel α-thalassemia deletion was identified for the two families by TGS. Our work broadened the molecular spectrum of α-thalassemia, and was beneficial for the diagnosis, genetic counseling and management of α-thalassemia.
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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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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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Zhu D, Xu L, Zhang Y, Liang G, Wei X, Li L, Jin W, Shang X. Investigation of the mechanism of copy number variations involving the α-globin gene cluster on chromosome 16: two case reports and literature review. Mol Genet Genomics 2023; 298:131-141. [PMID: 36326959 DOI: 10.1007/s00438-022-01968-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
Abstract
Thalassemia is one of the most common single-gene disorder worldwide. An important genetic cause of thalassemia is copy number variations (CNVs) in the α-globin gene cluster. However, there is no unified summary and discussion on the detailed information and mechanisms of these CNVs. In this study, two novel CNVs, a tandem duplication (αααα159) and deletion (--259), were identified in two Chinese families with thalassemia patients, according to the results of hematologic analysis, routine genetic testing for thalassemia, multiplex ligation-dependent probe amplification (MLPA), next-generation sequencing (NGS) and other molecular methods. Co-inherited with βCD41-42 mutation and --SEA deletion separately, αααα159 and --259 resulted in a patient with β-thalassemia intermedia and a lethal fetus with Hb Bart's hydrops fetalis syndrome, respectively. Next, a literature review was performed to summarize all known CNVs involving the α-globin gene cluster. The molecular structure characteristics of these CNVs were analyzed and the possible mechanism was explored. It is the first time to analyze the generation mechanism of genome arrangements in the α-globin gene cluster systematically.
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Affiliation(s)
- Dina Zhu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Linlin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yanxia Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Guanxia Liang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaofeng Wei
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Liyan Li
- Department of Gynecology and Obstetrics, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wangjie Jin
- Department of Gynecology and Obstetrics, Technology Center of Prenatal Diagnosis and Genetic Diseases Diagnosis, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xuan Shang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
- Innovation Center for Diagnostics and Treatment of Thalassemia, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, 510515, China.
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515, China.
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50
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Wu J, Xie D, Wang L, Kuang Y, Luo S, Ren L, Li D, Mao A, Li J, Chen L, An B, Huang S. Application of third-generation sequencing for genetic testing of thalassemia in Guizhou Province, Southwest China. Hematology 2022; 27:1305-1311. [DOI: 10.1080/16078454.2022.2156720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Jiangfen Wu
- School of Medicine, Guizhou University, Guiyang, People’s Republic of China
| | - Dan Xie
- School of Medicine, Guizhou University, Guiyang, People’s Republic of China
| | - Lei Wang
- School of Medicine, Guizhou University, Guiyang, People’s Republic of China
| | - Ying Kuang
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, People’s Republic of China
| | - Shulin Luo
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, People’s Republic of China
| | - Lingyan Ren
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, People’s Republic of China
| | - Di Li
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, People’s Republic of China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, People’s Republic of China
| | - Jiaqi Li
- Berry Genomics Corporation, Beijing, People’s Republic of China
| | - Libao Chen
- Berry Genomics Corporation, Beijing, People’s Republic of China
| | - Bangquan An
- Discipline Inspection and Supervision Office, Guizhou provincial people’s hospital, Guiyang, People’s Republic of China
| | - Shengwen Huang
- School of Medicine, Guizhou University, Guiyang, People’s Republic of China
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, People’s Republic of China
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People’s Hospital, Guiyang, People’s Republic of China
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