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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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2
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Zhou C, Du Y, Zhang H, Wei X, Li R, Wang J. Third-generation sequencing identified a novel complex variant in a patient with rare alpha-thalassemia. BMC Pediatr 2024; 24:330. [PMID: 38741052 DOI: 10.1186/s12887-024-04811-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/06/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Thalassemias represent some of the most common monogenic diseases worldwide and are caused by variations in human hemoglobin genes which disrupt the balance of synthesis between the alpha and beta globin chains. Thalassemia gene detection technology is the gold standard to achieve accurate detection of thalassemia, but in clinical practice, most of the tests are only for common genotypes, which can easily lead to missing or misdiagnosis of rare thalassemia genotypes. CASE PRESENTATION We present the case of an 18-year-old Chinese female with abnormal values of routine hematological indices who was admitted for genetic screening for thalassemia. Genomic DNA was extracted and used for the genetic assays. Gap polymerase chain reaction and agarose gel electrophoresis were performed to detect HBA gene deletions, while PCR-reverse dot blot hybridization was used to detect point mutations in the HBA and HBB genes. Next-generation sequencing and third-generation sequencing (TGS) were used to identify known and potentially novel genotypes of thalassemia. We identified a novel complex variant αHb WestmeadαHb Westmeadαanti3.7/-α3.7 in a patient with rare alpha-thalassemia. CONCLUSIONS Our study identified a novel complex variant that expands the thalassemia gene variants spectrum. Meanwhile, the study suggests that TGS could effectively improve the specificity of thalassemia gene detection, and has promising potential for the discovery of novel thalassemia genotypes, which could also improve the accuracy of genetic counseling. Couples who are thalassemia carriers have the opportunity to reduce their risk of having a child with thalassemia.
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Affiliation(s)
- Cong Zhou
- Department of Medical Genetics/Prenatal Diagnostic Center, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yepei Du
- Department of Medical Genetics/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Haixia Zhang
- Department of Medical Genetics/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xing Wei
- Department of Medical Genetics/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Rui Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Jing Wang
- Department of Medical Genetics/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.
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Zhuang J, Zhang N, Zheng Y, Jiang Y, Chen Y, Mao A, Chen C. Molecular characterization of similar Hb Lepore Boston-Washington in four Chinese families using third generation sequencing. Sci Rep 2024; 14:9966. [PMID: 38693200 PMCID: PMC11063182 DOI: 10.1038/s41598-024-60604-7] [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: 10/05/2023] [Accepted: 04/25/2024] [Indexed: 05/03/2024] Open
Abstract
Hemoglobin (Hb) Lepore is a rare deletional δβ-thalassemia caused by the fusion between delta-beta genes, and cannot be identified by traditional thaltassemia gene testing technology. The aim of this study was to conduct molecular diagnosis and clinical analysis of Hb Lepore in four unrelated Chinese families using third generation sequencing. Decreased levels of mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH) and an abnormal Hb band were observed in the probands of the four families. However, no common α and β-thalassemia variants were detected in the enrolled families using polymerase chain reaction-reverse dot blot hybridization based traditional thalassemia gene testing. Further third-generation sequencing revealed similar Hb Lepore-Boston-Washington variants in all the patients, which were resulted from partial coverage of the HBB and HBD globin genes, leading to the formation of a delta-beta fusion gene. Specific gap-PCR and Sanger sequencing confirmed that all the patients carried a similar Hb Lepore-Boston-Washington heterozygote. In addition, decreased levels of MCH and Hb A2 were observed in the proband's wife of family 2, an extremely rare variant of Hb Nanchang (GGT > AGT) (HBA2:c.46G > A) was identified by third-generation sequencing and further confirmed by Sanger sequencing. This present study was the first to report the similar Hb Lepore-Boston-Washington in Chinese population. By combining the utilization of Hb capillary electrophoresis and third-generation sequencing, the screening and diagnosis of Hb Lepore can be effectively enhanced.
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Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, People's Republic of China.
| | - Na Zhang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, People's Republic of China.
| | - Yu Zheng
- Yaneng BIOscience (Shenzhen) Co. Ltd., Shenzhen, 518000, Guangdong, People's Republic of China
| | - Yuying Jiang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, People's Republic of China
| | - Yu'e Chen
- Department of Ultrasound, Quanzhou Women's and Children's Hospital, Quanzhou, 362000, Fujian Province, People's Republic of China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, 102200, China
| | - Chunnuan Chen
- Department of Neurology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian Province, People's Republic of China.
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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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Zhuang J, Jiang Y, Chen Y, Mao A, Chen J, Chen C. Third-generation sequencing identified two rare α-chain variants leading to hemoglobin variants in Chinese population. Mol Genet Genomic Med 2024; 12:e2365. [PMID: 38284449 PMCID: PMC10801340 DOI: 10.1002/mgg3.2365] [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: 09/23/2023] [Revised: 12/16/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Rare and novel variants of HBA1/2 and HBB genes resulting in thalassemia and hemoglobin (Hb) variants have been increasingly identified. Our goal was to identify two rare Hb variants in Chinese population using third-generation sequencing (TGS) technology. METHODS Enrolled in this study were two Chinese families from Fujian Province. Hematological screening was conducted using routine blood analysis and Hb capillary electrophoresis analysis. Routine thalassemia gene testing was carried out to detect the common mutations of α- and β-thalassemia in Chinese population. Rare or novel α- and β-globin gene variants were further investigated by TGS. RESULTS The proband of family 1 was a female aged 32, with decreased levels of mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), Hb A2, and abnormal Hb bands in zone 5 and zone 12. No common thalassemia mutations were detected by routine thalassemia analysis, while a rare α-globin gene variant Hb Jilin [α139(HC1)Lys>Gln (AAA>CAA); HBA2:c.418A>C] was identified by TGS. Subsequent pedigree analysis showed that the proband's son also harbored the Hb Jilin variant with slightly low levels of MCH, Hb A2, and abnormal Hb bands. The proband of family 2 was a male at 41 years of age, exhibiting normal MCV and MCH, but a low level of Hb A2 and an abnormal Hb band in zone 12 without any common α- and β-thalassemia mutations. The subsequent TGS detection demonstrated a rare Hb Beijing [α16(A14)Lys>Asn (AAG>AAT); HBA2:c.51G>T] variant in HBA2 gene. CONCLUSION In this study, for the first time, we present two rare Hb variants of Hb Jilin and Hb Beijing in Fujian Province, Southeast China, using TGS technology.
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Affiliation(s)
- Jianlong Zhuang
- Prenatal Diagnosis CenterQuanzhou Women's and Children's HospitalQuanzhouFujianChina
| | - Yuying Jiang
- Prenatal Diagnosis CenterQuanzhou Women's and Children's HospitalQuanzhouFujianChina
| | - Yu'e Chen
- Department of UltrasoundQuanzhou Women's and Children's HospitalQuanzhouFujianChina
| | - Aiping Mao
- Department of TGS Research and Development, Berry Genomics CorporationBeijingChina
| | - Junwei Chen
- Department of Children Health CareQuanzhou Women's and Children's HospitalQuanzhouChina
| | - Chunnuan Chen
- Department of NeurologyThe Second Affiliated Hospital of Fujian Medical UniversityQuanzhouFujianChina
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Zhou Y, Jiang Y. Current Advances in Genetic Testing for Spinal Muscular Atrophy. Curr Genomics 2023; 24:273-286. [PMID: 38235355 PMCID: PMC10790334 DOI: 10.2174/0113892029273388231023072050] [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: 07/25/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 01/19/2024] Open
Abstract
Spinal muscular atrophy (SMA) is one of the most common genetic disorders worldwide, and genetic testing plays a key role in its diagnosis and prevention. The last decade has seen a continuous flow of new methods for SMA genetic testing that, along with traditional approaches, have affected clinical practice patterns to some degree. Targeting different application scenarios and selecting the appropriate technique for genetic testing have become priorities for optimizing the clinical pathway for SMA. In this review, we summarize the latest technological innovations in genetic testing for SMA, including MassArray®, digital PCR (dPCR), next-generation sequencing (NGS), and third-generation sequencing (TGS). Implementation recommendations for rationally choosing different technical strategies in the tertiary prevention of SMA are also explored.
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Affiliation(s)
- Yulin Zhou
- United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, P.R. China
- Biobank, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, P.R. China
| | - Yu Jiang
- United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, P.R. China
- Biobank, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, P.R. China
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7
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Xu L, Chen M, Zheng J, Zhang S, Zhang M, Chen L, He Q, Guo D, Lin N, Huang H. Identification of a novel 91.5 kb-deletion (αα) FJ in the α-globin gene cluster using single-molecule real-time (SMRT) sequencing. J Matern Fetal Neonatal Med 2023; 36:2254890. [PMID: 37673790 DOI: 10.1080/14767058.2023.2254890] [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: 04/18/2023] [Revised: 08/01/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023]
Abstract
OBJECTIVES To present a novel 91.5-kb deletion of the α-globin gene cluster (αα)FJ identified by genetic assay and prenatal diagnosis in a Chinese family. SUBJECTS AND METHODS The proband was a 34-year-old G3P1 (Gravida 3, Para 1) female at the gestational age of 21+ weeks with a history of an edematous fetus. A routine genetic assay (reverse dot blot hybridization, RDB) was performed to detect common thalassemia mutations. Multiplex ligation-dependent probe amplification (MLPA) and single-molecule real-time technology (SMRT) were used to detect rare thalassemia mutations. RESULTS The hematological phenotypes of the proband, her mother, elder sister, husband, daughter, and nephew were consistent with the phenotype of α-thalassemia trait. No mutations were found in these family members by RDB, except for the proband's husband who carried an α-globin gene deletion --SEA/αα. MLPA results showed that the proband and other α-thalassemia-suspected relatives had heterozygous deletions around the POLR3K-3-463nt, HS40-178nt, and HBA-HS40-382nt probes. The 5'-breakpoint was out of probe scope and could not be determined. SMRT was performed and a 91.5-kb deletion (NC_000016.10: g.39268_130758del) in the α-globin gene cluster (αα)FJ was identified in the proband and other suspected relatives, which could explain their phenotypes. At the proband's gestational age of 22+ weeks, an amniotic fluid sample was collected and analyzed. As only the 91.5-kb deletion (αα)FJ was identified in the fetus with RDB, MLPA, and SMRT. The proband was suggested to continue the pregnancy. CONCLUSION We first reported a 91.5-kb deletion (NC_000016.10: g.hg38-chr16:39268-_130758del) of the HS-40 region in the α-globin gene cluster (αα)FJ identified in a Chinese family. Since the HS-40 loss of heterozygosity in combination with the heterozygous deletion --SEA might result in Hb Bart's hydrops fetalis, routine genetic assay, and SMRT were recommended to individuals at risk for prenatal diagnosis.
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Affiliation(s)
- Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Meihuan Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Junhao Zheng
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
- Medical Technology and Engineering College, Fujian Medical University, Fuzhou, China
| | - Siwen Zhang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
- Medical Technology and Engineering College, Fujian Medical University, Fuzhou, China
| | - Min Zhang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Qianqian He
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Danhua Guo
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
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Ren ZM, Li WJ, Xing ZH, Fu XY, Zhang JY, Chen YS, Li DF. Detecting rare thalassemia in children with anemia using third-generation sequencing. Hematology 2023; 28:2241226. [PMID: 37548329 DOI: 10.1080/16078454.2023.2241226] [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: 05/29/2023] [Accepted: 07/22/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND In China, conventional genetic testing methods can only detect common thalassemia variants. Accurate detection of rare thalassemia is crucial for clinical diagnosis, especially for children that need long-term blood transfusion. This study aims to explore the application value of third-generation sequencing (TGS) in the diagnosis of rare thalassemia in children with anemia. METHODS We enrolled 20 children with anemia, excluding from iron deficiency anemia (IDA). TGS was employed to identify both known and novel thalassemia genotypes, while sanger sequencing was used to confirm the novel mutation detected. RESULTS Among the 20 samples, we identified 5 cases of rare thalassemia. These included β-4.9 (hg38,Chr11:5226187-5231089) at HBB gene, α-91(HBA2:c.*91delT), αCD30(HBA2:c.91-93delGAG), Chinese Gγ+(Aγδβ)0(NG_000007.3: g .48795-127698 del 78904) and delta - 77(T > C)(HBD:c.-127T>C). Notably, the -SEA/α-91α genotype associated with severe non-deletional hemoglobin H disease (HbH disease) has not been previously reported. Patients with genotypes β654/β-4.9 and -SEA/α-91α necessitate long-term blood transfusions, and those with the -SEA/αCD30α, Chinese Gγ+(Aγδβ)0 and delta thalassemia demonstrate mild anemia. CONCLUSIONS TGS demonstrates promising potential as a diagnostic tool for suspected cases of rare thalassemia in children, especially those suspected to have transfusion-dependent thalassemia (TDT).
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Affiliation(s)
- Zhen-Min Ren
- Department of Laboratory Medicine, Shenzhen Children´s Hospital, Shenzhen, People's Republic of China
| | - Wu-Jiao Li
- Department of Laboratory Medicine, Shenzhen Children´s Hospital, Shenzhen, People's Republic of China
| | - Zhi-Hao Xing
- Department of Laboratory Medicine, Shenzhen Children´s Hospital, Shenzhen, People's Republic of China
| | - Xiao-Ying Fu
- Department of Laboratory Medicine, Shenzhen Children´s Hospital, Shenzhen, People's Republic of China
| | - Ju-Yan Zhang
- Berry Genomics Corporation, Beijing, People's Republic of China
| | - Yun-Sheng Chen
- Department of Laboratory Medicine, Shenzhen Children´s Hospital, Shenzhen, People's Republic of China
| | - De-Fa Li
- Department of Laboratory Medicine, Shenzhen Children´s Hospital, Shenzhen, People's Republic of China
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9
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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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10
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Chen Y, Xie T, Ma M, Yang J, Lv Y, Dong X. Case report: Identification of a novel triplication of alpha-globin gene by the third-generation sequencing: pedigree analysis and genetic diagnosis. Hematology 2023; 28:2277571. [PMID: 38059617 DOI: 10.1080/16078454.2023.2277571] [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: 08/06/2023] [Accepted: 10/25/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Thalassemia, a common autosomal hereditary blood disorder worldwide, mainly contains α- and β-thalassemia. The α-globin gene triplicates allele is harmless for carriers, but aggravates the phenotype of β-thalassemia. Therefore, it is particularly crucial to accurately detect the structural variants of α-globin gene clusters. CASE REPORT We reported a 28-year-old man, the proband, with microcytic hypochromic anemia. From pedigree analysis, his mother and sister had hypochromic microcytosis, and his father was normal. Genetic testing of thalassemia identified a novel α-globin gene triplicate named αααanti4.2del726bp (NC_000016.10:g.170769_174300dupinsAAAAAA) by third-generation sequencing (TGS) in the proband and his father, which was further validated by multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. The genotypes of the proband's mother and sister were both -α3.7/αα compounded with heterozygous HBB:c.126_129delCTTT. They were categorized as silent α-thalassemia with co-inheritance of β-thalassemia trait. The proband's genotype additionally had the α-globin gene triplicates compared with his mother and sister, which increased the imbalance between α/β-globin, so the proband had more severe hematological parameters. The proband's wife was diagnosed as HBA2:c.427T > C heterozygosis, and his daughter had the novel α-globin gene triplicates compounded with HBA2:c.427T > C, therefore the girl might be asymptomatic. CONCLUSION The identification of the novel α-globin gene triplicates provides more insight for the research of thalassemia variants and indicates that TGS has significant advantages on genetic testing of thalassemia for the reliability, accuracy and comprehensiveness.
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Affiliation(s)
- Yujiao Chen
- Dehong Medical Group Hospital of Traditional Chinese Medicine, Dehong Dai and Jingpo Autonomous Prefecture, People's Republic of China
| | - Tiantian Xie
- Berry Genomics Corporation, Beijing, People's Republic of China
| | - Minhui Ma
- Berry Genomics Corporation, Beijing, People's Republic of China
| | - Juan Yang
- Kunming Kingmed Institute for Clinical Laboratory, Kunming, People's Republic of China
| | - Yihang Lv
- Department of Obstetrical, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Xudong Dong
- Department of Obstetrical, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, People's Republic of China
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11
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Tang XW, Jiang F, Li J, Lin XM, Zhou JY, Wan JH, Zuo LD, Qu YX, Li FT, Chen GL, Li DZ. Application of real-time PCR-based multicolor melting curve with automatic analysis system in pregestational and prenatal thalassemia diagnoses. Ann Hum Genet 2023; 87:316-325. [PMID: 37771257 DOI: 10.1111/ahg.12531] [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: 02/08/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND To evaluate the value of the real-time PCR-based multicolor melting curve analysis (MMCA) with an automatic analysis system used in a mass thalassemia screening and prenatal diagnosis program. METHODS A total of 18,912 peripheral blood samples from 9456 couples and 1150 prenatal samples were detected by MMCA assay. All prenatal samples were also tested by a conventional method. Samples with unknown melting peaks, unusual peak height ratios between a wild allele and a mutant allele, or a discordant phenotype-genotype match were further studied by using multiplex ligation-dependent probe amplification (MLPA) or Sanger sequencing. All MMCA results were automatically analyzed and manually checked. The consistency between MMCA assay and conventional methods among prenatal samples was investigated. RESULTS Except for initiation codon (T > G) (HBB:c.2T > G), all genotypes of thalassemia inside the scope of conventional methods were detected by MMCA assay. Additionally, 27 carriers with 10 rare HBB variants, 13 with α fusion gene, 1 with a rare deletion in α globin gene, and 1 with rare HBA variant were detected by using MMCA assay. CONCLUSION MMCA can be an alternative approach used in routine thalassemia carrier screening and prenatal diagnosis for its high throughput, sufficient stability, low cost, and easy operation.
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Affiliation(s)
- Xue-Wei Tang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Jian Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Xiao-Mei Lin
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Jian-Ying Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Jun-Hui Wan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Lian-Dong Zuo
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Yan-Xia Qu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Fa-Tao Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Gui-Lan Chen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
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12
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Lou J, Sun M, Mao A, Liu Y, Zhao Y, Fu Y, Dai Y, Xiong F, Li D, Zhang J, Yan T, Liu Y. Molecular spectrum and prevalence of thalassemia investigated by third-generation sequencing in the Dongguan region of Guangdong Province, Southern China. Clin Chim Acta 2023; 551:117622. [PMID: 37922731 DOI: 10.1016/j.cca.2023.117622] [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: 01/30/2023] [Revised: 10/13/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND PCR, Sanger sequencing and NGS are often employed for carrier screening of thalassemia but all of these methods have limitations. In this study, we evaluated a new third-generation sequencing-based approach termed comprehensive analysis of thalassemia alleles (CATSA) to explore the prevalence of thalassemia in the Dongguan region of southern China. METHODS 19,932 subjects were recruited for thalassemia screening and hemoglobin testing was performed for each of them. Routine PCR was performed for all the hemoglobin testing-positive subjects and CATSA was conducted for randomly selected subjects from hemoglobin testing-positive and negative subjects. RESULTS In the 2716 subjects tested both by PCR and CATSA, 2569 had the same results and 147 had discordant results between the two methods. Sanger sequencing, specially designed PCR and MLPA confirmed the results of CATSA were all correct. In total, CATSA correctly detected 787 subjects with variants while routine PCR correctly detected 640 subjects with variants. CATSA yielded a 5.42% (147 of 2716) increment compared with routine PCR. In the 447 hemoglobin testing-negative subjects, CATSA identified pathogenic variants in 12 subjects. Moreover, CATSA identified a novel deletion (chr16:171262-202032) in the α-globin gene cluster. As a result, the deduced carrier frequency of α-thalassemia,β-thalassemia and α-/β-thalassemia was 5.62%, 3.85% and 0.93%, respectively. CONCLUSIONS Our study demonstrated CATSA was a more comprehensive and precise approach than the routine PCR in a large scale of samples, which is highly beneficial for carrier screening of thalassemia. It provided a broader molecular spectrum of hemoglobinopathies and a better basis for a control program in Dongguan region.
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Affiliation(s)
- Jiwu Lou
- Prenatal Diagnostic Center, Dongguan Maternal and Children Health Hospital, Dongguan, Guangdong, China
| | - Manna Sun
- Department of Obstetrics & Gynecolog, Dongguan Maternal and Children Hospital, Dongguan, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, 102200, China
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, 102200, China
| | - Ying Zhao
- Prenatal Diagnostic Center, Dongguan Maternal and Children Health Hospital, Dongguan, Guangdong, China
| | - Youqing Fu
- Prenatal Diagnostic Center, Dongguan Maternal and Children Health Hospital, Dongguan, Guangdong, China
| | - Yunshi Dai
- Prenatal Diagnostic Center, Dongguan Maternal and Children Health Hospital, Dongguan, Guangdong, China
| | - Fu Xiong
- Department of Medical Genetics, Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Juyan Zhang
- Berry Genomics Corporation, Beijing, 102200, China
| | - Tizhen Yan
- Prenatal Diagnostic Center, Dongguan Maternal and Children Health Hospital, Dongguan, Guangdong, China.
| | - Yanhui Liu
- Prenatal Diagnostic Center, Dongguan Maternal and Children Health Hospital, Dongguan, Guangdong, China; Reproductive Medicine Department,The Third Affiliated Hospital of Shenzhen University,Shenzhen, Guangdong, China.
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13
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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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14
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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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15
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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: 0] [Impact Index Per Article: 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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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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18
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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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19
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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: 6] [Impact Index Per Article: 6.0] [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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20
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Identification of a novel 107 kb deletion in the alpha-globin gene cluster using third-generation sequencing. Clin Biochem 2023; 113:36-39. [PMID: 36572139 DOI: 10.1016/j.clinbiochem.2022.12.010] [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: 09/07/2022] [Revised: 12/11/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To describe the characterization of a novel deletion causing α-thalassemia. METHODS The proband, a 30-year-old female, displayed mild anemia from thalassemia screening. Gap-PCR was used to detect the four common deletional α-thalassemia, and a PCR-reverse dot blot was performed for the three point mutations of the α-globin gene. Multiplex ligation-dependent probe amplification (MLPA) was used to query possible breakpoints of a potential novel deletion. Third-generation sequencing (TGS) was used to identify the novel deletion after the MLPA failed. Gap-PCR and Sanger sequencing were validated for the breakpoint. RESULTS No abnormal results were detected by Gap-PCR and PCR-reverse dot blot. MLPA only showed a large deletion upstream of the HBZ-1 probe, but the scope could not be determined. However, a novel 107 kb deletion at the α-globin gene was discovered by the TGS. The Gap-PCR products with the specific breakpoint fragment of the 107 kb deletion were confirmed by Sanger sequencing. CONCLUSIONS A 107 kb deletion causing α-thalassemia was the first reported worldwide. TGS played an important role in this study and can be recommended as a reliable tool for rare or potential deletions in thalassemia.
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21
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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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22
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Identification of novel mutations in β-thalassemia patients in Maysan Governorate, Iraq. Mol Biol Rep 2023; 50:3053-3062. [PMID: 36683082 DOI: 10.1007/s11033-023-08271-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/10/2023] [Indexed: 01/23/2023]
Abstract
BACKGROUND In homozygous β-thalassemia, the primary genetic modifiers affecting the clinical severity of β-thalassemia are genetic variants and the ability to reduce globin chain imbalance, thus resulting in a milder form of thalassemia. However, there are few reports on the molecular genetics of β-thalassemia in Iraq. METHODS We performed PCR and DNA sequencing on 40 Iraqi patients who were clinically suspected of having β-thalassemia. RESULTS The first genetic sequencing study was conducted in Maysan Governate, Iraq, using patients from various locations to identify novel mutations. There were five novel mutations: 294.T>C 12% (city center and Almajar district), 205. C>T 25% (city center, Alsalam, and Almashrah districts), 289.G>A 38% (Almaymuna and Gleat Salih districts), 49.T>C 32% (city center), and 624.C>A 32% (city center). These mutations were identified among β-thalassemia patients by two regions of HBB gene 696 bp and 861 bp. CONCLUSIONS The discovery of new genetic variants helps predict the severity of β-thalassemia disease. There are relatively few studies in molecular genetics of β-thalassemia in Iraq, and the new mutations reported here will provide valuable data for the prevention and control of β-thalassemia in Maysan Governate, Iraq. The results can lead to new genetic sequencing investigations for other Iraqi regions.
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23
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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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24
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Yuan Y, Zhou X, Deng J, Zhu Q, Peng Z, Chen L, Zou Y, Mao A, Meng W, Ma M, Wu H. Case report: Long-read sequencing identified a novel 14.9-kb deletion of the α-globin gene locus in a family with α-thalassemia in China. Front Genet 2023; 14:1156071. [PMID: 36936435 PMCID: PMC10020366 DOI: 10.3389/fgene.2023.1156071] [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: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Background: Thalassemia is a hereditary blood disease resulting from globin chain synthesis impairment because of α- and/or β-globin gene variants. α-thalassemia is characterized by non-deletional and deletional variants in the HBA gene locus, of which rare deletional variants are difficult to detect by conventional polymerase chain reaction (PCR)-based methods. Case report: We report the case of a one-month-old boy, who and his mother had abnormal hematological parameters, while his father had normal hematology. Conventional PCR-reverse dot blot (RDB) was performed for all family members to analyze the 23 most common thalassemia variants in China, but did not identify any pathologic variants. Single-molecule real-time (SMRT) long-read sequencing (LRS) technology was then performed and identified an unreported 14.9-kb large deletion (hg38 chr16:168,803-183,737) of the α-globin gene locus, which disrupted both HBA1 and HBA2 genes in the proband and his mother. The exact breakpoints of the deletion were confirmed by gap-PCR and Sanger sequencing. Conclusion: We have detected a novel large deletion in α-globin gene locus in China, which not only enriches the variant spectrum of thalassemia, but also demonstrates the accuracy and efficiency of LRS in detecting rare and novel deletions.
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Affiliation(s)
- Yan Yuan
- Department of Medical Genetics, Yueyang Maternal and Child Health Hospital, Yueyang, China
| | - Xia Zhou
- Department of Medical Genetics, Yueyang Maternal and Child Health Hospital, Yueyang, China
| | - Jing Deng
- Department of Medical Genetics, Yueyang Maternal and Child Health Hospital, Yueyang, China
| | - Qun Zhu
- Department of Medical Genetics, Yueyang Maternal and Child Health Hospital, Yueyang, China
| | - Zanping Peng
- Department of Medical Genetics, Yueyang Maternal and Child Health Hospital, Yueyang, China
| | - Liya Chen
- Department of Medical Genetics, Yueyang Maternal and Child Health Hospital, Yueyang, China
| | - Ya Zou
- Department of Medical Genetics, Yueyang Maternal and Child Health Hospital, Yueyang, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, China
| | - Wanli Meng
- Berry Genomics Corporation, Beijing, China
| | - Minhui Ma
- Berry Genomics Corporation, Beijing, China
| | - Hongliang Wu
- Department of Medical Genetics, Yueyang Maternal and Child Health Hospital, Yueyang, China
- *Correspondence: Hongliang Wu,
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25
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Luo P, Liu X, Tang Z, Xiong B. Decreased expression of HBA1 and HBB genes in acute myeloid leukemia patients and their inhibitory effects on growth of K562 cells. Hematology 2022; 27:1003-1009. [DOI: 10.1080/16078454.2022.2117186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- Ping Luo
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
| | - Xiaoyan Liu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
| | - Zehai Tang
- Department of Emergency, The Union Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Bei Xiong
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
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26
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Bao X, Wang J, Qin D, Zhang R, Yao C, Liang J, Liang K, Du L. The -α 3.7III subtype of α +-thalassemia was identified in China. HEMATOLOGY (AMSTERDAM, NETHERLANDS) 2022; 27:826-830. [PMID: 35916627 DOI: 10.1080/16078454.2022.2101913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE The 3.7 kb deletion (-α3.7) in the α-globin cluster, which characterizes α+-thalassemia, has been reported to have a carrier rate of 4.78% in southern China. Three -α3.7 subtypes have been identified worldwide. However, the -α3.7 III subtype has not previously been identified in China. Herein, we reported identification of the -α3.7 III subtype in a Chinese patient. METHODS We used gap-PCR and a liquid chip system to detect α-thalassemia mutations. Multiple ligation-dependent probe amplification was performed to detect the large deletion. We finally used Sanger sequencing and single molecule real-time sequencing to characterize and confirm the genotype. RESULTS The proband, characterized as -α3.7 III heterozygous, showed microcytosis and hypochromic red cells, with a mean corpuscular volume of 78 fL and mean corpuscular hemoglobin of 25.4 pg. The proband's mutation was inherited from her father, who had normal blood parameters. CONCLUSION We first identified the -α3.7 III subtype in China. Consequently, all -α3.7 subtypes have now been identified in the Chinese population. Therefore, attention should be paid to -α3.7 III in clinical prenatal diagnosis, given that commonly used methods such as gap-PCR may lead to misdiagnosis or missed diagnosis.
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Affiliation(s)
- Xiuqin Bao
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China.,Thalassemia Diagnosis 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.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
| | - Danqing Qin
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
| | - Rui Zhang
- Prenatal Diagnosis Center, Huizhou Second Maternal and Child Health Care Hospital, Huizhou, People's Republic of China
| | - Cuize Yao
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
| | - Jie Liang
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
| | - Kailing Liang
- Medical Genetics Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China.,Thalassemia Diagnosis 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.,Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China.,Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, People's Republic of China
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Conlin LK, Aref-Eshghi E, McEldrew DA, Luo M, Rajagopalan R. Long-read sequencing for molecular diagnostics in constitutional genetic disorders. Hum Mutat 2022; 43:1531-1544. [PMID: 36086952 PMCID: PMC9561063 DOI: 10.1002/humu.24465] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022]
Abstract
Long-read sequencing (LRS) has been around for more than a decade, but widespread adoption of the technology has been slow due to the perceived high error rates and high sequencing cost. This is changing due to the recent advancements to produce highly accurate sequences and the reducing costs. LRS promises significant improvement over short read sequencing in four major areas: (1) better detection of structural variation (2) better resolution of highly repetitive or nonunique regions (3) accurate long-range haplotype phasing and (4) the detection of base modifications natively from the sequencing data. Several successful applications of LRS have demonstrated its ability to resolve molecular diagnoses where short-read sequencing fails to identify a cause. However, the argument for increased diagnostic yield from LRS remains to be validated. Larger cohort studies may be required to establish the realistic boundaries of LRS's clinical utility and analytical validity, as well as the development of standards for clinical applications. We discuss the limitations of the current standard of care, and contrast with the applications and advantages of two major LRS platforms, PacBio and Oxford Nanopore, for molecular diagnostics of constitutional disorders, and present a critical argument about the potential of LRS in diagnostic settings.
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Affiliation(s)
- Laura K. Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Deborah A. McEldrew
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Minjie Luo
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ramakrishnan Rajagopalan
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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Ning S, Luo Y, Liang Y, Xie Y, Lu Y, Meng B, Pan J, Xu R, Liu Y, Qin Y. A novel rearrangement of the α-globin gene cluster containing both the -α 3.7 and αααα anti4.2 crossover junctions in a Chinese family. Clin Chim Acta 2022; 535:7-12. [PMID: 35944700 DOI: 10.1016/j.cca.2022.07.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/10/2022] [Accepted: 07/23/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Thalassemia is one of the most common hemoglobinopathies. Thalassemia is mainly caused by the loss and/or deficiency of one or more globin chains in hemoglobin. The copy number variant (CNV) of α-globin gene is one of the important factors affecting the clinical phenotype of β-thalassemia. The precise detection for this type of variation is needed. METHODS Peripheral blood of a 33-year-old man and his family members were collected. Complete blood counts and serum iron levels were measured for participants. Genomic DNA was extracted from all family members. Routine genetic analysis of thalassemia was performed to determine the genotype. Additional PCR-electrophoresis and Multiplex ligation dependent probe amplification (MLPA) were conducted. Single-molecule real-time technology(SMRT) was then performed as a validation assay and further characterization of the variant for family members. RESULTS PCR-electrophoresis and MLPA found a new variant, but the exact genotype could not be determined. At last, SMRT identified the new variant as a rearrangement of the α-globin gene cluster named αHKαα (NC_000016.9:g.169818_174075dup169818_174075dup173302_177105del), which contained both the -α3.7 and ααααanti4.2 crossover junctions. Carriers of the novel CNV show normal clinical phenotype according to the hematological results. CONCLUSION We have identified an unreported CNV (αHKαα) in α-globin gene cluster. The novel CNV not only demonstrates the accuracy and efficiency of our combining strategy in detecting unknown CNVs, but also enriched the variant spectrum of thalassemia.
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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
| | - Yudi Luo
- 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
| | - Binrong Meng
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin, Guangxi Zhuang Autonomous Region, China
| | - Jinjie Pan
- 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
| | - Yunrong Qin
- Department of Clinical Laboratory, Yulin Women and Children Health Care Hospital, Yulin, Guangxi Zhuang Autonomous Region, China.
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Luo H, Huang T, Lu Q, Zhang L, Xu Y, Yang Y, Guo Z, Yuan H, Shen Y, Huang S, Yang B, Zou Y, Liu Y. Molecular prevalence of HBB-associated hemoglobinopathy among reproductive-age adults and the prenatal diagnosis in Jiangxi Province, southern central China. Front Genet 2022; 13:992073. [PMID: 36246595 PMCID: PMC9554255 DOI: 10.3389/fgene.2022.992073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Background and aims: Hemoglobinopathy associated with the HBB gene, with its two general subtypes as thalassemia and abnormal hemoglobin (Hb) variants, is one of the most prevalent hereditary Hb disorders worldwide. Herein we aimed to elucidate the prevalence of ß-thalassemia and abnormal hemoglobin variants and the prenatal diagnosis of the HBB gene in Jiangxi Province, southern central China.Methods: Hematological indices and capillary Hb electrophoresis were conducted for 136,149 subjects who were admitted to Jiangxi Maternal and Child Health Hospital and requested for hemoglobinopathy investigation. Routine α- and ß-globin genotyping were performed by gap-polymerase chain reaction (Gap-PCR) and reverse dot-blot (RDB) hybridization for the 11,549 individuals suspected to be thalassemia carriers. For participants whose genotypes could not explain their hematological indices, further Sanger sequencing and Gap-PCR were conducted for the detection of rare or novel variants in related globin genes. Prenatal diagnosis was performed for 77 pregnant couples both carrying ß-thalassemia trait at appropriate gestational ages.Results: Among the 11,549 subjects, 2,548 individuals were identified with HBB-associated hemoglobinopathy based on molecular analysis. A total of 2,358 subjects were identified as ß-thalassemia heterozygous carriers and nine cases were diagnosed as compound heterozygous ß-thalassemia. Additionally, 125 cases were detected with composite α- and ß-thalassemia and the remaining 56 individuals with abnormal Hb variants in the HBB. A total of 35 types of variants were identified in the HBB gene, including 26 types of ß-thalassemia and nine types of abnormal Hb variants. Four novel variants were firstly reported, including one variant in HBA2 and three variants in HBB. Overall, 77 prenatal samples underwent ß-thalassemia molecular diagnosis; 20 fetuses were identified with normal ß-thalassemia genotypes, 30 fetuses as ß-thalassemia heterozygotes, 11 as homozygotes, and 16 as compound heterozygotes in HBB.Conclusion: We have demonstrated a relatively high prevalence rate at 1.872% of ß-hemoglobinopathies including common and rare ß-thalassemia as well as abnormal Hb variants among large child-bearing population in the Jiangxi area of southern central China for the first time. Our data presents that prenatal diagnosis is an effective way to prevent and control birth defects of ß-thalassemia.
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Affiliation(s)
- Haiyan Luo
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Ting Huang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Qing Lu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Liuyang Zhang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Yonghua Xu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Yan Yang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Zhen Guo
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Department of Ultrasound, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Huizhen Yuan
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Yinqin Shen
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Shuhui Huang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Bicheng Yang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Yongyi Zou
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- *Correspondence: Yongyi Zou, ; Yanqiu Liu,
| | - Yanqiu Liu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China
- *Correspondence: Yongyi Zou, ; Yanqiu Liu,
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Zhong G, Zhong Z, Guan Z, Chen D, Wu Z, Yang K, Chen D, Liu Y, Xu R, Chen J. Case Report: The third-generation sequencing confirmed a novel 7.2 Kb deletion at β-globin gene in a patient with rare β-thalassemia. Front Genet 2022; 13:984996. [PMID: 36171890 PMCID: PMC9511401 DOI: 10.3389/fgene.2022.984996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Thalassemia was the most common monogenic diseases worldwide, which was caused by mutations, deletions or duplications in human globin genes which disturbed the synthesis balance between α- and β-globin chains of hemoglobin. There were many classics methods to diagnose thalassemia, but all of them had limitations. Although variations in the human β-globin gene cluster were mainly point mutations, novel large deletions had been described in recent years along with the development of DNA sequencing technology. Case report: We present a case of 32-year-old male with abnormal hematological results. However, 23 genotypes of the most common thalassemia were not detected by two independent conventional platforms. Finally, using multiplex ligation-dependent probe amplification (MLPA), third-generation sequencing (TGS) and Gap PCR detection methods, we first confirmed the case with a novel 7.2 Kb deletion (Chr11:5222800-5230034, hg38) located at HBB gene. Conclusion: Our results showed that TGS technology was a powerful tool for thalassemia breakpoint detection, had promising potentiality in genetic screening of novel thalassemia, especially for the novel deletions in globin genes.
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Affiliation(s)
- Guoxing Zhong
- 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
| | - Zhiyang Guan
- Department of Medical Genetics and Prenatal Diagnosis, Huizhou First Maternal and Child Health Care Hospital, Huizhou, Guangdong, China
| | - Dina Chen
- Department of Medical Genetics and Prenatal Diagnosis, Huizhou First Maternal and Child Health Care Hospital, Huizhou, Guangdong, China
| | - Zhiyong Wu
- Department of Medical Genetics and Prenatal Diagnosis, Huizhou First Maternal and Child Health Care Hospital, Huizhou, Guangdong, China
| | - Kunxiang Yang
- Department of Medical Genetics and Prenatal Diagnosis, Huizhou First Maternal and Child Health Care Hospital, Huizhou, Guangdong, China
| | - Dan Chen
- Department of Medical Genetics and Prenatal Diagnosis, Huizhou First Maternal and Child Health Care Hospital, Huizhou, Guangdong, China
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, China
| | - Ruofan Xu
- Berry Genomics Corporation, Beijing, China
| | - Jianhong Chen
- Department of Medical Genetics and Prenatal Diagnosis, Huizhou First Maternal and Child Health Care Hospital, Huizhou, Guangdong, China
- *Correspondence: Jianhong Chen,
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Li Y, Liang L, Qin T, Tian M. Detection of hemoglobin H disease by long molecule sequencing. J Clin Lab Anal 2022; 36:e24687. [PMID: 36059093 PMCID: PMC9550979 DOI: 10.1002/jcla.24687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/20/2022] [Accepted: 08/24/2022] [Indexed: 11/11/2022] Open
Abstract
Background Hemoglobin H (Hb H) disease is a moderate‐to‐severe form of α‐thalassemia (α‐thal), and parts of patients may require intermittent transfusion therapy, especially during intercurrent illness. However, rare Hb H diseases remain undetected using routine methods being outside of the testing scope. In this study, we present an approach to detecting Hb H disease by long molecule sequencing (LMS). Methods A total of 206 known genotype samples were collected and carried to blind detected by LMS on the PacBio Sequel platform. Circular consensus sequencing reads were aligned to the hg19 reference genome using Free‐Bayes finished LMS. LMS accuracy would be compared with routine methods, including Gap‐PCR and PCR‐Reverse dot blot hybridization (PCR–RDB). Results The assay could detect carriers of both deletion and point mutations. It had an overall accuracy of 100% when compared with routine methods. In addition, LMS detected six mutations based on routine methods and corrected three case results. Hb H diseases were identified using LMS, whether a common or rare genotype, a deletion or non‐deletion genotype. However, two cases of Hb H disease were misdiagnosed using routine methods. Conclusions Long molecule sequencing can be suggested as a rapid and reliable assay to detect probable carriers of hemoglobinopathies. LMS accurately identified the common and rare genotypes of Hb H disease.
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Affiliation(s)
- Youqiong Li
- Center for Medical Genetics and Prenatal Diagnosis, People Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Liang Liang
- Center for Medical Genetics and Prenatal Diagnosis, People Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Ting Qin
- Center for Medical Genetics and Prenatal Diagnosis, People Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Mao Tian
- Center for Medical Genetics and Prenatal Diagnosis, People Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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Luo S, Chen X, Zeng D, Tang N, Yuan D, Liu B, Chen L, Zhong Q, Li J, Liu Y, Chen J, Wang X, Yan T. Detection of four rare thalassemia variants using Single-molecule realtime sequencing. Front Genet 2022; 13:974999. [PMID: 36159974 PMCID: PMC9493964 DOI: 10.3389/fgene.2022.974999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/01/2022] [Indexed: 11/18/2022] Open
Abstract
Conventional methods for the diagnosis of thalassemia include gap polymerase chain reaction (Gap-PCR), reverse membrane hybridization (RDB), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing. In this study, we used single molecule real-time technology (SMRT) sequencing and discovered four rare variants that have not been identified by conventional diagnostic methods for thalassemia. We also performed genotype and phenotype analyses on family members of thalassemia patients. The SMRT technology detected five cases in which the proband had abnormal results by conventional diagnostic methods or inconsistencies between the genotype and phenotype. The variants included two cases of an α-globin gene cluster 27,311 bp deletion, --27.3/αα (hg38 chr16:158664-185974), one case of an HS-40 region 16,079 bp deletion (hg38 chr16:100600-116678), one case of a rearrangement of -α3.7α1α2 on one allele and one case of a ß-globin gene cluster HBG1-HBG2 4,924 bp deletion (hg38 chr11:5249345-5254268). This study clarified the hematological phenotypes of four rare variants and indicated the application value of SMRT in the diagnosis of rare α-globin and ß-globin gene cluster deletions, gene recombination and deletion breakpoints. The SMRT method is a comprehensive one-step technology for the genetic diagnosis of thalassemia and is particularly suitable for the diagnosis of thalassemia with rare deletions or genetic recombination.
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Affiliation(s)
- Shiqiang Luo
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Xingyuan Chen
- Department of Laboratory Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Academy of Medical Sciences, Nanning, China
| | - Dingyuan Zeng
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, China
| | - Ning Tang
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, Liuzhou, China
| | - Dejian Yuan
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Bailing Liu
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Lizhu Chen
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Qingyan Zhong
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
| | - Jiaqi Li
- Berry Genomics Corporation, Beijing, China
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, China
| | - Jianping Chen
- Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
| | - Xiaoyuan Wang
- Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- *Correspondence: Xiaoyuan Wang, ; Tizhen Yan,
| | - Tizhen Yan
- Liuzhou Key Laboratory of Birth Defects Prevention and Control, Department of Medical Genetics, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, China
- Liuzhou Key Laboratory of Reproductive Medicine, Liuzhou, China
- *Correspondence: Xiaoyuan Wang, ; Tizhen Yan,
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Zhang M, Lin Z, Chen M, Pan Y, Zhang Y, Chen L, Lin N, Ren Y, Jia H, Cai M, Xu L, Huang H. Application of the Single-Molecule Real-Time Technology (SMRT) for Identification of HKαα Thalassemia Allele. Lab Med 2022; 54:65-71. [PMID: 36053226 PMCID: PMC9825284 DOI: 10.1093/labmed/lmac065] [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] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVE Single-molecule real-time technology (SMRT) is a sequencing technology using the DNA polymerases and fluorescently tagged nucleotides to accurately sequence DNA strands. The purpose of this study was to evaluate the detection accuracy of SMRT for identification of the Hong Kongαα (HKαα) thalassemia allele. METHODS We conducted a blinded study of 33 samples of known HKαα alleles. These alleles were detected using SMRT to evaluate accuracy. RESULTS We conducted a blinded study of 33 known HKαα samples and found all HKαα variants detected by SMRT to be concordant with those independently assigned by gap-polymerase chain reaction (gap-PCR), reverse dot blot hybridization, and 2-round nested PCR. In addition, SMRT detected 2 β-thalassemia variants that were missed by conventional techniques. CONCLUSION The results demonstrate that SMRT offers a higher detection accuracy of thalassemia rare and new loci. It is an efficient, reliable, and broad-spectrum test that can be widely used for thalassemia screening in the clinic.
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Affiliation(s)
| | | | - Meihuan Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yali Pan
- Medical Technology and Engineering College of Fujian Medical University, Fuzhou, China
| | - Yanhong Zhang
- Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | | | | | - Meiying Cai
- To whom correspondence should be addressed: , ,
| | - Liangpu Xu
- To whom correspondence should be addressed: , ,
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Bao XQ, Wang JC, Qin DQ, Yao CZ, Liang J, Du L. A Novel 5 kb Deletion in the β-Globin Gene Cluster Identified in a Chinese Patient. Hemoglobin 2022; 46:245-248. [DOI: 10.1080/03630269.2022.2118604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Xiu-Qin Bao
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Ji-Cheng Wang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Dan-Qing Qin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Cui-Ze Yao
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Jie Liang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
| | - Li Du
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
- Thalassemia Diagnosis Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, People’s Republic of China
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A novel 15.8 kb deletion α-thalassemia confirmed by long-read single-molecule real-time sequencing: hematological phenotypes and molecular characterization. Clin Biochem 2022; 108:46-49. [DOI: 10.1016/j.clinbiochem.2022.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022]
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Peng C, Zhang H, Ren J, Chen H, Du Z, Zhao T, Mao A, Xu R, Lu Y, Wang H, Chen X, Liu S. Analysis of rare thalassemia genetic variants based on third-generation sequencing. Sci Rep 2022; 12:9907. [PMID: 35701592 PMCID: PMC9197973 DOI: 10.1038/s41598-022-14038-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/31/2022] [Indexed: 11/22/2022] Open
Abstract
Thalassemia is a group of common hereditary anemias that cause significant morbidity and mortality worldwide. However, precisely diagnosing thalassemia, especially rare thalassemia variants, is still challenging. Long-range PCR and long-molecule sequencing on the PacBio Sequel II platform utilized in this study could cover the entire HBA1, HBA2 and HBB genes, enabling the diagnosis of most of the common and rare types of thalassemia variants. In this study, 100 cases of suspected thalassemia were subjected to traditional thalassemia testing and third-generation sequencing for thalassemia genetic diagnosis. Compared with traditional diagnostic methods, an additional 10 cases of rare clinically significant variants, including 3 cases of structure variants and 7 cases of single nucleotide variations (SNVs) were identified, of which a case with − α3.7 subtype III (− α3.7III) was first identified and validated in the Chinese population. Other rare variants of 11.1 kb deletions (− 11.1/αα), triplicate α-globin genes (aaa3.7/αα) and rare SNVs have also been thoroughly detected. The results showed that rare thalassemia variants are not rare but have been misdiagnosed by conventional methods. The results further validated third-generation sequencing as a promising method for rare thalassemia genetic testing.
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Affiliation(s)
- Cuiting Peng
- Center of Prenatal Diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Haixia Zhang
- Center of Prenatal Diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Jun Ren
- Center of Prenatal Diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Han Chen
- Center of Prenatal Diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Ze Du
- Center of Prenatal Diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Tong Zhao
- Center of Prenatal Diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, 102200, China
| | - Ruofan Xu
- Berry Genomics Corporation, Beijing, 102200, China
| | - Yulin Lu
- Berry Genomics Corporation, Beijing, 102200, China
| | - He Wang
- Center of Prenatal Diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Xinlian Chen
- Center of Prenatal Diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China. .,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China. .,Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, 17 South Renmin Road, Chengdu, China.
| | - Shanling Liu
- Center of Prenatal Diagnosis, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China. .,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China. .,Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, 17 South Renmin Road, Chengdu, China.
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Jiang F, Mao AP, Liu YY, Liu FZ, Li YL, Li J, Zhou JY, Tang XW, Ju AP, Li FT, Wan JH, Zuo LD, Li DZ. Detection of rare thalassemia mutations using long-read single-molecule real-time sequencing. Gene 2022; 825:146438. [PMID: 35306112 DOI: 10.1016/j.gene.2022.146438] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Abstract
Gap- polymerase chain reaction (PCR), reverse dot-blot assay (RDB), real-time PCR based multicolor melting curve analysis (MMCA assay), multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing are conventional methods to diagnose thalassemia but all of them have limitations. In this study, we applied single-molecule real-time (SMRT) sequencing following multiplex long-range PCR to uncover rare mutations in nine patients and their family members. The patients with different results between Gap-PCR and MMCA assay or with phenotype not matching genotype were included. Using SMRT sequencing, we first identified the carriers with αααanti3.7/HKαα, -α762bpα/αα (chr16:172,648-173,409), ααfusion/αQSα (in a trans configuration), two cases with novel gene rearrangements and another case with a novel 341 bp insertion in α-globin gene cluster, respectively. One carrier with --SEA/αααanti4.2, and two carriers with the coexistence of globin variant and an α-globin gene duplication were also found. Most importantly, we could determine two defects in α-globin gene cluster being a cis or trans configuration in a single test. Our results showed that SMRT has great advantages in detection of α-globin gene triplications, rare deletions and determination of a cis or trans configuration. SMRT is a comprehensive and one-step method for thalassemia screening and diagnosis, especially for detection of rare thalassemia mutations.
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Affiliation(s)
- Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Ai-Ping Mao
- Berry Genomics Corporation, Beijing, 102200, China
| | - Yin-Yin Liu
- Berry Genomics Corporation, Beijing, 102200, China
| | - Feng-Zhi Liu
- Medical Genetics Laboratory, Foshan Maternal and Child Health Hospital, Foshan, Guangdong, China
| | - Yan-Lin Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Jian Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Jian-Ying Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Xue-Wei Tang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Ai-Ping Ju
- Clinical Laboratory, Huadu District Maternal and Neonatal Healthcare Hospital of Guangzhou, Hu Zhong Hospital, Guangzhou, Guangdong, China
| | - Fa-Tao Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Jun-Hui Wan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Lian-Dong Zuo
- Scientific Research Department, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China.
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Chen X, Luo M, Pan L, Huang Y, Yan Z, Shen K, Mai G, Liang H, Li J, Chen Y, Xiong L. A novel 4.9 Kb deletion at beta-globin gene is identified by the third-generation sequencing: case report from Baoan, China. Clin Chim Acta 2022; 529:10-16. [PMID: 35150653 DOI: 10.1016/j.cca.2022.01.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Thalassemia is a common inherited haemoglobin disorder worldwide, several methods have been utilized in the step-wise screening. Even though hundreds of mutations in globin genes have been reported, novel mutations are continuously emerging as the development of DNA sequencing. METHODS The case is a 27-year-old female with abnormal values of routine hematological indices, who was admitted for genetic screening of thalassemia. Genomic DNA was extracted and used for genetic assays cover 26 mutations in HBA and HBB genes: gap-PCR and agarose gel electrophoresis were performed to detect deletions, while PCR-reverse dot blot was used to detect point mutations. The next- and third- generation sequencing were used to identify the known and potential novel genotypes of thalassemia, and multiplex ligation-dependent probe amplification (MLPA) was used for genotype validation. RESULTS Hematological results indicate microcytic hypochromic anemia, high HbA2 (7.2%) and high HbF (6.2%). None of the known genotypes of thalassemia were matched for this case, but a novel 4.9 Kb deletion at HBB gene (hg38, Chr11: 5226187-5231089) was discovered by the third-generation sequencing, the novel deletion was also validated by MLPA (8 probes, 11p15.4: 203314-207652). CONCLUSIONS This study suggests the third-generation sequencing has promising potentiality to discover novel genotypes (especially deletions) of thalassemia.
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Affiliation(s)
- Xu Chen
- Central Laboratory, Baoan Women's and Children's Hospital, Shenzhen, China; Shenzhen Key Laboratory of Birth Defects Research, Shenzhen, China
| | - Mingyue Luo
- Central Laboratory, Baoan Women's and Children's Hospital, Shenzhen, China; Shenzhen Key Laboratory of Birth Defects Research, Shenzhen, China
| | - Lei Pan
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Shenzhen, China
| | - Yuting Huang
- Department of Gynecology and Obstetrics, Huiyang Maternity and Child Health Hospital, Huizhou, China
| | - Zehao Yan
- Central Laboratory, Baoan Women's and Children's Hospital, Shenzhen, China; Shenzhen Key Laboratory of Birth Defects Research, Shenzhen, China
| | - Kai Shen
- Central Laboratory, Baoan Women's and Children's Hospital, Shenzhen, China; Shenzhen Key Laboratory of Birth Defects Research, Shenzhen, China
| | - Guangxing Mai
- Central Laboratory, Baoan Women's and Children's Hospital, Shenzhen, China; Shenzhen Key Laboratory of Birth Defects Research, Shenzhen, China
| | - Hui Liang
- Central Laboratory, Baoan Women's and Children's Hospital, Shenzhen, China; Shenzhen Key Laboratory of Birth Defects Research, Shenzhen, China
| | - Jiaqi Li
- Berry Genomics Corporation, Beijing, China
| | - Yiwei Chen
- Berry Genomics Corporation, Beijing, China
| | - Likuan Xiong
- Central Laboratory, Baoan Women's and Children's Hospital, Shenzhen, China; Shenzhen Key Laboratory of Birth Defects Research, Shenzhen, China.
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Luo S, Chen X, Zeng D, Tang N, Yuan D, Zhong Q, Mao A, Xu R, Yan T. The value of single-molecule real-time technology in the diagnosis of rare thalassemia variants and analysis of phenotype-genotype correlation. J Hum Genet 2022; 67:183-195. [PMID: 34690349 PMCID: PMC8948088 DOI: 10.1038/s10038-021-00983-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/19/2021] [Accepted: 09/29/2021] [Indexed: 12/03/2022]
Abstract
To compare single-molecule real-time technology (SMRT) and conventional genetic diagnostic technology of rare types of thalassemia mutations, and to analyze the molecular characteristics and phenotypes of rare thalassemia gene variants, we used 434 cases with positive hematology screening as the cohort, then used SMRT technology and conventional gene diagnosis technology [(Gap-PCR, multiple ligation probe amplification technology (MLPA), PCR-reverse dot blot (RDB)] for thalassemia gene screening. Among the 434 enrolled cases, conventional technology identified 318 patients with variants (73.27%) and 116 patients without variants (26.73%), SMRT identified 361 patients with variants (83.18%), and 73 patients without variants (16.82%). The positive detection rate of SMRT was 9.91% higher than conventional technology. Combination of the two methods identified 485 positive alleles among 49 types of variant. The genotypes of 354 cases were concordant between the two methods, while 80 cases were discordant. Among the 80 cases, 76 cases had variants only identified in SMRT method, 3 cases had variants only identified in conventional method, and 1 false positive result by the traditional PCR detection technology. Except the three variants in HS40 and HBG1-HBG2 loci, which was beyond the design of SMRT method in this study, all the other discordant variants identified by SMRT were validated by further Sanger sequencing or MLPA. The hematological phenotypic parameters of 80 discordant cases were also analyzed. SMRT technology increased the positive detection rate of thalassemia genes, and detected rare thalassemia cases with variable phenotypes, which had great significance for clinical thalassemia gene screening.
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Affiliation(s)
- Shiqiang Luo
- grid.477238.dDepartment of Medical Genetics, Liuzhou Key Laboratory of Birth Defects Prevention and Control, Liuzhou Maternity and Child Healthcare Hospital, 545001 Liuzhou, Guangxi China ,Liuzhou Key Laboratory of Reproductive Medicine, 545001 Liuzhou, Guangxi China
| | - Xingyuan Chen
- grid.410652.40000 0004 6003 7358Department of Laboratory Medicine, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi Zhuang Autonomous Region China ,Guangxi Academy of Medical Sciences, Nanning, Guangxi Zhuang Autonomous Region China
| | - Dingyuan Zeng
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, 545001 Liuzhou, Guangxi China
| | - Ning Tang
- Guangxi Health Commission Key Laboratory of Birth Cohort Study in Pregnant Women of Advanced Age, 545001 Liuzhou, Guangxi China
| | - Dejian Yuan
- grid.477238.dDepartment of Medical Genetics, Liuzhou Key Laboratory of Birth Defects Prevention and Control, Liuzhou Maternity and Child Healthcare Hospital, 545001 Liuzhou, Guangxi China ,Liuzhou Key Laboratory of Reproductive Medicine, 545001 Liuzhou, Guangxi China
| | - Qingyan Zhong
- grid.477238.dDepartment of Medical Genetics, Liuzhou Key Laboratory of Birth Defects Prevention and Control, Liuzhou Maternity and Child Healthcare Hospital, 545001 Liuzhou, Guangxi China ,Liuzhou Key Laboratory of Reproductive Medicine, 545001 Liuzhou, Guangxi China
| | - Aiping Mao
- Berry Genomics Corporation, 102200 Beijing, China
| | - Ruofan Xu
- Berry Genomics Corporation, 102200 Beijing, China
| | - Tizhen Yan
- Department of Medical Genetics, Liuzhou Key Laboratory of Birth Defects Prevention and Control, Liuzhou Maternity and Child Healthcare Hospital, 545001, Liuzhou, Guangxi, China. .,Liuzhou Key Laboratory of Reproductive Medicine, 545001, Liuzhou, Guangxi, China.
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Suhaimi SA, Zulkipli IN, Ghani H, Abdul-Hamid MRW. Applications of next generation sequencing in the screening and diagnosis of thalassemia: A mini-review. Front Pediatr 2022; 10:1015769. [PMID: 36245713 PMCID: PMC9557073 DOI: 10.3389/fped.2022.1015769] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Thalassemias are a group of inherited blood disorders that affects 5-7% of the world population. Comprehensive screening strategies are essential for the management and prevention of this disorder. Today, many clinical and research laboratories have widely utilized next-generation sequencing (NGS) technologies to identify diseases, from germline and somatic disorders to infectious diseases. Yet, NGS application in thalassemia is limited and has just recently surfaced due to current demands in seeking alternative DNA screening tools that are more efficient, versatile, and cost-effective. This review aims to understand the several aspects of NGS technology, including its most current and expanding uses, advantages, and limitations, along with the issues and solutions related to its integration into routine screening and diagnosis of thalassemias. Hitherto, NGS has been a groundbreaking technology that offers tremendous improvements as a diagnostic tool for thalassemia in terms of its higher throughput, accuracy, and adaptability. The superiority of NGS in detecting rare variants, solving complex hematological problems, and providing non-invasive alternatives to neonatal diagnosis cannot be overlooked. However, several pitfalls still preclude its use as a stand-alone technique over conventional methods.
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Affiliation(s)
| | | | - Hazim Ghani
- PAPRSB Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei
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Vijian D, Wan Ab Rahman WS, Ponnuraj KT, Zulkafli Z, Mohd Noor NH. Molecular Detection of Alpha Thalassemia: A Review of Prevalent Techniques. Medeni Med J 2021; 36:257-269. [PMID: 34915685 PMCID: PMC8565582 DOI: 10.5222/mmj.2021.14603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/07/2021] [Indexed: 12/14/2022] Open
Abstract
Alpha thalassemia (α-thalassemia) is an autosomal recessive disorder due to the reduction or absence of α globin chain production. Laboratory diagnosis of α-thalassemia requires molecular analysis for the confirmatory diagnosis. A screening test, comprising complete blood count, blood smear and hemoglobin quantification by high performance liquid chromatography and capillary electrophoresis, may not possibly detect all the thalassemia diseases. This review focused on the molecular techniques used to detect α-thalassemia, and the advantages and disadvantages of each technique were highlighted. Multiplex gap-polymerase chain reaction, single-tube multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification, and loop-mediated isothermal amplification were used to detect common deletion of α-thalassemia. Furthermore, the reverse dot blot analysis and a single tube multiplex polymerase chain reaction could detect non-deletion mutation of the α-globin gene. Sanger sequencing is widely used to detect non-deletion mutations of α-thalassemia. Recently, next-generation sequencing was introduced in the diagnosis of both deletion and point mutations of α-thalassemia. Despite the advantages and disadvantages of different techniques, the routine method employed in the laboratory should be based on the facility, expertise, available equipment, and economic conditions.
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Affiliation(s)
- Divashini Vijian
- Universiti Sains Malaysia, School of Dental Sciences, Kubang Kerian Kelantan, Malaysia
| | - Wan Suriana Wan Ab Rahman
- Universiti Sains Malaysia, Health campus, School of Dental Sciences, Kubang Kerian, Kelantan, Malaysia
| | | | - Zefarina Zulkafli
- Universiti Sains Malaysia, School of Medical Sciences, Department of Hematology, Kubang Kerian Kelantan, Malaysia
| | - Noor Haslina Mohd Noor
- Universiti Sains Malaysia, School of Medical Sciences, Department of Hematology, Kubang Kerian Kelantan, Malaysia
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Liang Q, Gu W, Chen P, Li Y, Liu Y, Tian M, Zhou Q, Qi H, Zhang Y, He J, Li Q, Tang L, Tang J, Teng Y, Zhou Y, Huang S, Lu Z, Xu M, Hou W, Huang T, Li Y, Li R, Hu L, Li S, Guo Q, Zhuo Z, Mou Y, Cram DS, Wu L. A More Universal Approach to Comprehensive Analysis of Thalassemia Alleles (CATSA). J Mol Diagn 2021; 23:1195-1204. [PMID: 34293487 DOI: 10.1016/j.jmoldx.2021.06.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/24/2021] [Accepted: 06/10/2021] [Indexed: 11/18/2022] Open
Abstract
The aim of the study was to assess the clinical utility of a third-generation sequencing (TGS) approach termed comprehensive analysis of thalassemia alleles (CATSA) for identifying both α and β thalassemia genetic carrier status. Prospective blood samples (n = 1759) with abnormal hemoglobin parameters were screened for pathogenic thalassemia variants by CATSA on the PacBio TGS platform. In 1159 individuals, a total of 1317 pathogenic thalassemia variants were identified and confirmed by independent PCR-based tests. Of the total thalassemia variants detected, the α-variant --SEA (35.4%) and β-variant c.126_129delCTTT (15%) were the most common. CATSA was also able to detect three types of rare HBA structural variants as well as five rare HBA2, three HBA1, and 10 HBB single-nucleotide variations/insertions and deletions. Compared with standard thalassemia variant PCR panel testing, CATSA identified all panel variants present, with no false-negative results. Carrier assignment was improved through identification of rare variants missed by the panel test. On the basis of allelic coverage, reliability, and accuracy, TGS with long-range PCR presents a comprehensive approach with the potential to provide a universal solution for thalassemia genetic carrier screening. It is proposed that CATSA has immediate clinical utility as an effective carrier screening approach for at-risk couples.
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Affiliation(s)
- Qiaowei Liang
- Department of Molecular Genetics, Hunan Jiahui Genetics Hospital, Changsha, China
| | - Wanqian Gu
- Department of Reproductive Genetics, Yunnan Maternal and Child Health Care Hospital, Kunming, China
| | - Ping Chen
- Key Laboratory of Thalassemia Medicine, Chinese Academy of Medical Sciences, Guangxi Key Laboratory of Thalassemia Research, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | | | - Yanqiu Liu
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Mao Tian
- Center for Medical Genetic and Prenatal Diagnosis, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qiaomiao Zhou
- Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, China
| | - Hongbo Qi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yuhong Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun He
- Department of Molecular Genetics, Changsha Hospital for Maternal and Child Health Care Genetic Eugenics, Changsha, China
| | - Qing Li
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lingfang Tang
- Department of Pregnancy Health, Guilin Women and Children Health Care Hospital, Guilin, China
| | - Juan Tang
- Laboratory of Genetics and Metabolism, Guilin Women and Children Health Care Hospital, Guilin, China
| | - Yanling Teng
- Department of Molecular Genetics, Hunan Jiahui Genetics Hospital, Changsha, China
| | - Yulin Zhou
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine and School of Public Health, Xiamen University, Xiamen, China
| | - Shengwen Huang
- Department of Genetics and Prenatal Diagnosis, Guizhou Provincial People's Hospital, Guiyang, China
| | - Zongjie Lu
- Department of Obstetrics, Suining Central Hospital, Suining, China
| | | | - Wei Hou
- Key Laboratory of Thalassemia Medicine, Chinese Academy of Medical Sciences, Guangxi Key Laboratory of Thalassemia Research, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ting Huang
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Youqiong Li
- Center for Medical Genetic and Prenatal Diagnosis, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Rong Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lanping Hu
- Department of Molecular Genetics, Changsha Hospital for Maternal and Child Health Care Genetic Eugenics, Changsha, China
| | - Shaoying Li
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiwei Guo
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine and School of Public Health, Xiamen University, Xiamen, China
| | - Zhaozhen Zhuo
- Department of Genetics and Prenatal Diagnosis, Guizhou Provincial People's Hospital, Guiyang, China
| | - Yan Mou
- Department of Obstetrics, Suining Central Hospital, Suining, China
| | | | - Lingqian Wu
- Department of Molecular Genetics, Hunan Jiahui Genetics Hospital, Changsha, China; Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.
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Jiang F, Lyu GZ, Zhang VW, Li DZ. Identification of thalassemia gene cluster deletion by long-read whole-genome sequencing (LR-WGS). Int J Lab Hematol 2021; 43:859-865. [PMID: 33400392 DOI: 10.1111/ijlh.13452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/18/2020] [Accepted: 12/14/2020] [Indexed: 01/10/2023]
Abstract
INTRODUCTION At present, a variety of molecular detection methods are obtained to diagnose thalassemia accurately. Although exome sequencing or specific panels have been widely used in clinical diagnosis of genetic diseases, the positive rate is about 25%-30%. Because the detection range is limited to exons and splice sites, and the read length is usually 100-150 bp, there are limitations in the detection of globin gene clusters with pseudogenes. METHODS In this study, seven thalassemia patients were selected to perform whole-genome sequencing (WGS) with long read at 400 bp to make accurate detection for thalassemia deletions. And we used PCR and Sanger sequencing to confirm the gene deletions in the patients. RESULTS WGS analysis detected a rare 172 kb deletion on the α-globin gene cluster at chr16: 57 009-330 001, 19 kb deletion at chr16: 215 396-234 699, 11 kb deletion at chr16:220 861-231 981; and 27 kb deletion on the β-globin gene deletion at chr11: 5 222 878-5 250 288, 21.4 kb deletion at chr11: 5 236 361-5 257 771, 78.9 kb deletion at chr11: 5 191 121-5 270 050. All the seven patients carried heterozygous deletions, including three in α-gene cluster, three in β-gene cluster, and one in both globin clusters. CONCLUSION Our results indicate that long-read WGS will be beneficial to the diagnosis of genetic diseases with pseudogenes or highly duplicated sequences and will enable clinical geneticists to inform high-risk couples and provide prenatal diagnosis.
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Affiliation(s)
- Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center Affiliated to Guangzhou Medical University, Guangzhou, China
| | | | | | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center Affiliated to Guangzhou Medical University, Guangzhou, China
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