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Huang R, Liu Y, Xu J, Lin D, Mao A, Yang L, Zhong G, Wang H, Xu R, Chen Y, Zhou Q. Back-to-Back Comparison of Third-Generation Sequencing and Next-Generation Sequencing in Carrier Screening of Thalassemia. Arch Pathol Lab Med 2024; 148:797-804. [PMID: 36630651 DOI: 10.5858/arpa.2022-0168-oa] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2022] [Indexed: 01/13/2023]
Abstract
CONTEXT.— Recently, new technologies, such as next-generation sequencing and third-generation sequencing, have been used in carrier screening of thalassemia. However, there is no direct comparison between the 2 methods in carrier screening of thalassemia. OBJECTIVE.— To compare the clinical performance of third-generation sequencing with next-generation sequencing in carrier screening of thalassemia. DESIGN.— Next-generation sequencing and third-generation sequencing were simultaneously conducted for 1122 individuals in Hainan Province. RESULTS.— Among 1122 genetic results, 1105 (98.48%) were concordant and 17 (1.52%) were discordant between the 2 methods. Among the 17 discordant results, 4 were common thalassemia variants, 9 were rare thalassemia variants, and 4 were variations with unknown pathogenicity. Sanger sequencing and polymerase chain reaction for discordant samples confirmed all the results of third-generation sequencing. Among the 685 individuals with common and rare thalassemia variants detected by third-generation sequencing, 512 (74.74%) were carriers of α-thalassemia, 110 (16.06%) were carriers of β-thalassemia, and 63 (9.20%) had coinheritance of α-thalassemia and β-thalassemia. Three thalassemia variants were reported for the first time in Hainan Province, including -THAI, -α2.4, and ααααanti3.7. Eleven variants with potential pathogenicity were identified in 36 patients with positive hemoglobin test results. Among 52 individuals with negative hemoglobin test results, 17 were identified with thalassemia variants. In total, third-generation sequencing and next-generation sequencing correctly detected 763 and 746 individuals with variants, respectively. Third-generation sequencing yielded a 2.28% (17 of 746) increment compared with next-generation sequencing. CONCLUSIONS.— Third-generation sequencing was demonstrated to be a more accurate and reliable approach in carrier screening of thalassemia compared with next-generation sequencing.
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Affiliation(s)
- Renliang Huang
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Jing Xu
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Dan Lin
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Liuqing Yang
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Gaobu Zhong
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Huoniao Wang
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
| | - Ruofan Xu
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Yiwei Chen
- Berry Genomics Corporation, Beijing, 102200, China (Liu, Mao, R. Xu, Chen)
| | - Qiaomiao Zhou
- From the Department of Genetics and Prenatal Diagnosis, Hainan Women and Children's Medical Center, Haikou, 571100, China (Huang, J. Xu, Lin, Yang, Zhong, Wang, Zhou)
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Traisrisilp K, Zheng Y, Choy KW, Chareonkwan P. Thalassemia screening by third-generation sequencing: Pilot study in a Thai population. Obstet Med 2024; 17:101-107. [PMID: 38784187 PMCID: PMC11110746 DOI: 10.1177/1753495x231207676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 09/27/2023] [Indexed: 05/25/2024] Open
Abstract
Background Conventional thalassemia screening takes a stepwise approach and has limitations in comprehensively identifying all spectrums of mutations. This study aimed to investigate the performance of third-generation sequencing (TGS) compared to conventional molecular testing. Methods TGS was applied to validate all known variants detected by conventional testing and to detect missing variants in undiagnosed cases. The study was conducted at Maharaj Nakorn Chiang Mai Hospital between December 2021 and April 2022. Results In total, 19 cases were included in this study, among which 52.6% (10/19) had known thalassemia variants, while 47.7% (9/19) cases were undiagnosed by conventional methods. All 16 variants previously detected were validated by TGS, and TGS additionally detected 43.8% (7/16) thalassemia variants for 36.8% (7/19) cases. Conclusion TGS could provide additional genetic diagnoses compared with conventional methods. Further cost-effectiveness studies with a larger sample size are needed to explore the role of TGS in clinical practices.
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Affiliation(s)
- Kuntharee Traisrisilp
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Yu Zheng
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Pimlak Chareonkwan
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
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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 PMCID: PMC11089783 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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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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Yu SY, Xi YL, Xu FQ, Zhang J, Liu YS. Application of long read sequencing in rare diseases: The longer, the better? Eur J Med Genet 2023; 66:104871. [PMID: 38832911 DOI: 10.1016/j.ejmg.2023.104871] [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: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 06/06/2024]
Abstract
Rare diseases encompass a diverse group of genetic disorders that affect a small proportion of the population. Identifying the underlying genetic causes of these conditions presents significant challenges due to their genetic heterogeneity and complexity. Conventional short-read sequencing (SRS) techniques have been widely used in diagnosing and investigating of rare diseases, with limitations due to the nature of short-read lengths. In recent years, long read sequencing (LRS) technologies have emerged as a valuable tool in overcoming these limitations. This minireview provides a concise overview of the applications of LRS in rare disease research and diagnosis, including the identification of disease-causing tandem repeat expansions, structural variations, and comprehensive analysis of pathogenic variants with LRS.
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Affiliation(s)
- Si-Yan Yu
- Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China; The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu-Lin Xi
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Fu-Qiang Xu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jian Zhang
- Department of Medical Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China.
| | - Yan-Shan Liu
- Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China; Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
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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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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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Feng J, Cui D, Li C, Yang Y, Li Q, Li X, Tan S, Li Z, Meng W, Li H, Zhang Y. The comprehensive analysis of thalassemia alleles (CATSA) based on single-molecule real-time technology (SMRT) is a more powerful strategy in the diagnosis of thalassemia caused by rare variants. Clin Chim Acta 2023; 551:117619. [PMID: 38375625 DOI: 10.1016/j.cca.2023.117619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 02/21/2024]
Abstract
Thalassemia is one of the most widely distributed monogenic disorders in the world and affects the largest number of people. It can manifest a wide spectrum of phenotypes from asymptomatic to fatal, which is associated with the degree of imbalance between α- and β-globin chains. Therefore, individuals with different genotypes could present with a similar phenotype. Genetic analysis is always needed to make a correct diagnosis. However, routine genetic analysis of thalassemia used in the Chinese population identifies only 23 common variants, resulting in many cases undiagnosed or being misdiagnosed. In this study, we applied a long-read sequencing-based approach termed comprehensive analysis of thalassemia alleles (CATSA) to 30 subjects whose hematologic screening results could not be explained by the routine genetic test results. The identification of additional variants and the correction of genotypes allowed the interpretation of the clinical phenotype in 24 subjects, which have been confirmed to be correct by independent experiments. Moreover, we identified a novel 8.4-kb deletion containing the entire HBB and HBD genes as well as part of the HBBP1 gene, expanding the genotype spectrum of β-thalassemia. CATSA showed a great advantage over other genetic tests in the diagnosis of thalassemia caused by rare variants.
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Affiliation(s)
- Jianjiang Feng
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Di Cui
- Berry Genomics Corporation, Beijing 102200, China
| | - Caipeng Li
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Yingsong Yang
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Qiuli Li
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Xiaomin Li
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Shuming Tan
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Zhiming Li
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Wanli Meng
- Berry Genomics Corporation, Beijing 102200, China
| | - Haoxian Li
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China.
| | - Yanghui Zhang
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China.
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Feng J, Mao A, Lu Y, Shi H, Meng W, Liang C. Molecular characterization of a novel 83.9-kb deletion of the α-globin upstream regulatory elements by long-read sequencing. Blood Cells Mol Dis 2023; 103:102764. [PMID: 37336681 DOI: 10.1016/j.bcmd.2023.102764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Inherited deletions of upstream regulatory elements of α-globin genes give rise to α-thalassemia, which is an autosomal recessive monogenic disease. However, conventional thalassemia target diagnosis often fails to identify these rare deletions. Here we reported a family with two previous pregnancies of Hb Bart's hydrops fetalis and was seeking for prenatal diagnosis during the third pregnancy. Both parents had low level of Hemoglobin A2 indicating α-thalassemia. Conventional Gap-PCR and PCR-reverse dot blot showed the father carried -SEA deletion but did not identify any variants in the mother. Multiplex ligation-dependent probe amplification identified a deletion containing two HS-40 probes but could not determine the exact region. Finally, a long-read sequencing (LRS)-based approach directly identified that the exact deletion region was chr16: 48,642-132,584, which was located in the α-globin upstream regulatory elements and named (αα)JM after the Jiangmen city. Gap-PCR and Sanger sequencing confirmed the breakpoint. Both the mother and fetus from the third pregnancy carried heterozygous (αα)JM, and the fetus was normally delivered at gestational age of 39 weeks. This study demonstrated that LRS technology had great advantages over conventional target diagnosis methods for identifying rare thalassemia variants and assisted better carrier screening and prenatal diagnosis of thalassemia.
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Affiliation(s)
- Jianjiang Feng
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing 102200, China
| | - Ye Lu
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Haihong Shi
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China
| | - Wanli Meng
- Berry Genomics Corporation, Beijing 102200, China
| | - Chen Liang
- Center for Medical Genetics, Jiangmen Maternal & Child Health Care Hospital, Jiangmen 529000, Guangdong, China.
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Ling X, Wang C, Li L, Pan L, Huang C, Zhang C, Huang Y, Qiu Y, Lin F, Huang Y. Third-generation sequencing for genetic disease. Clin Chim Acta 2023; 551:117624. [PMID: 37923104 DOI: 10.1016/j.cca.2023.117624] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
Third-generation sequencing (TGS) has led to a brave new revolution in detecting genetic diseases over the last few years. TGS has been rapidly developed for genetic disease applications owing to its significant advantages such as long read length, rapid detection, and precise detection of complex and rare structural variants. This approach greatly improves the efficiency of disease diagnosis and complements the shortcomings of short-read sequencing. In this paper, we first briefly introduce the working mechanism of one of the most important representatives of TGS, single-molecule real-time (SMRT) sequencing by Pacific Bioscience (PacBio), followed by a review and comparison of the advantages and disadvantages of different sequencing technologies. Finally, we focused on the progress of SMRT sequencing applications in genetic disease detection. Future perspectives on the applications of TGS in other fields were also presented. With the continuous innovation of the SMRT technologies and the expansion of their fields of application, SMRT sequencing has broad clinical application prospects in genetic diseases detection, and is expected to become an important tool for the molecular diagnosis of other diseases.
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Affiliation(s)
- Xiaoting Ling
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Chenghan Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Linlin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Liqiu Pan
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Chaoyu Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Caixia Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Yunhua Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Yuling Qiu
- NHC Key Laboratory of Thalassemia Medicine, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Thalassemia Research, Guangxi Medical University, Nanning 530021, China
| | - Faquan Lin
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China.
| | - Yifang Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China.
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11
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Huang W, Qu S, Qin Q, Yang X, Han W, Lai Y, Chen J, Zhou S, Yang X, Zhou W. Nanopore Third-Generation Sequencing for Comprehensive Analysis of Hemoglobinopathy Variants. Clin Chem 2023; 69:1062-1071. [PMID: 37311260 DOI: 10.1093/clinchem/hvad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/03/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND Oxford Nanopore Technology (ONT) third-generation sequencing (TGS) is a versatile genetic diagnostic platform. However, it is nonetheless challenging to prepare long-template libraries for long-read TGS, particularly the ONT method for analysis of hemoglobinopathy variants involving complex structures and occurring in GC-rich and/or homologous regions. METHODS A multiplex long PCR was designed to prepare library templates, including the whole-gene amplicons for HBA2/1, HBG2/1, HBD, and HBB, as well as the allelic amplicons for targeted deletions and special structural variations. Library construction was performed using long-PCR products, and sequencing was conducted on an Oxford Nanopore MinION instrument. Genotypes were identified based on integrative genomics viewer (IGV) plots. RESULTS This novel long-read TGS method distinguished all single nucleotide variants and structural variants within HBA2/1, HBG2/1, HBD, and HBB based on the whole-gene sequence reads. Targeted deletions and special structural variations were also identified according to the specific allelic reads. The result of 158 α-/β-thalassemia samples showed 100% concordance with previously known genotypes. CONCLUSIONS This ONT TGS method is high-throughput, which can be used for molecular screening and genetic diagnosis of hemoglobinopathies. The strategy of multiplex long PCR is an efficient strategy for library preparation, providing a practical reference for TGS assay development.
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Affiliation(s)
- Weilun Huang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shoufang Qu
- Division of In Vitro Diagnostics for Non-infectious diseases, National Institutes for Food and Drug Control, Beijing, China
| | - Qiongzhen Qin
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xu Yang
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Wanqing Han
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Yongli Lai
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jiaqi Chen
- Department of Pediatrics, Southern Medical University Nanfang Hospital, Guangzhou, China
| | - Shihao Zhou
- Department of Genetics, Changsha Hospital for Maternal and Child Health Care, Changsha, China
| | - Xuexi Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Wanjun Zhou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Department of Laboratory Medicine, Southern Medical University Nanfang Hospital, Guangzhou, China
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12
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Jiang F, Zhou J, Zuo L, Tang X, Li J, Li F, Yang T, Qu Y, Wan J, Liao C, Li D. Utilization of multiple genetic methods for prenatal diagnosis of rare thalassemia variants. Front Genet 2023; 14:1208102. [PMID: 37529778 PMCID: PMC10387553 DOI: 10.3389/fgene.2023.1208102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
Background: Thalassemia is the most prevalent monogenic disorder caused by an imbalance between the α- and β-globin chains as a result of pathogenic variants in the α- or β-globin genes. Novel or complex structural changes in globin genes are major hurdles for genetic consulting and prenatal diagnosis. Methods: From 2020 to 2022, genetic analysis was performed on 1,316 families suspected of having children with thalassemia major, including 42 pregnant couples suspected of being thalassemia carriers with rare variants. Multiple techniques including multiplex ligation-dependent probe amplification (MLPA), Sanger sequencing, targeted next-generation sequencing, and single-molecule real-time (SMRT) sequencing were used to diagnose rare thalassemia. Results: The rate of prenatal diagnosis for rare thalassemia variants was 3.19% (42/1,316). The most prevalent alleles of α- and β-thalassemia are Chinese Gγ(Aγδβ)0and -- THAI deletion. In addition, ten rare complex genotypes include one Chinese Gγ(Aγδβ)0 deletion combined with HBG1-HBG2 fusion, two rare deletions at HBB gene (hg38, Chr11: 5224211-5232470, hg38, Chr11: 5224303-5227790), one complete 7,412 bp fusion gene for anti-Lepore Hong Kong, two complex rearrangements of the α-globin gene cluster, two novel duplications, and two rare large deletions in the α-globin gene cluster. Conclusion: Accurate gene diagnosis for probands with combined molecular biology techniques is the key to prenatal diagnosis of rare thalassemia.
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Affiliation(s)
- Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jianying Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Liandong Zuo
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xuewei Tang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jian Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fatao Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Tianhe Yang
- Xiangya School of Nursing, Central South University, Changsha, Hunan, China
| | - Yanxia Qu
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Junhui Wan
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Can Liao
- *Correspondence: Can Liao, ; Dongzhi Li,
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center Affiliated with Guangzhou Medical University, Guangzhou, Guangdong, China
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13
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Zhan L, Gui C, Wei W, Liu J, Gui B. Third generation sequencing transforms the way of the screening and diagnosis of thalassemia: a mini-review. Front Pediatr 2023; 11:1199609. [PMID: 37484768 PMCID: PMC10357962 DOI: 10.3389/fped.2023.1199609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
Thalassemia is an inherited blood disorder imposing a significant social and economic burden. Comprehensive screening strategies are essential for the prevention and management of this disease. Third-generation sequencing (TGS), a breakthrough technology, has shown great potential for screening and diagnostic applications in various diseases, while its application in thalassemia detection is still in its infancy. This review aims to understand the latest and most widespread uses, advantages of TGS technologies, as well as the challenges and solutions associated with their incorporation into routine screening and diagnosis of thalassemia. Overall, TGS has exhibited higher rates of positive detection and diagnostic accuracy compared to conventional methods and next-generation sequencing technologies, indicating that TGS will be a feasible option for clinical laboratories conducting in-house thalassemia testing. The implementation of TGS technology in thalassemia diagnosis will facilitate the development of effective prevention and management strategies, thereby reducing the burden of this disease on individuals and society.
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Affiliation(s)
- Lixia Zhan
- The Second School of Medicine, Guangxi Medical University, Nanning, China
- Child Healthcare Department, The Second People's Hospital of Beihai, Beihai, China
| | - Chunrong Gui
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wei Wei
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Juliang Liu
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Baoheng Gui
- The Second School of Medicine, Guangxi Medical University, Nanning, China
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
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14
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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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15
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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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16
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Zhou QM, Jiang F, Xu J, Lin D, Huang RL, Zhou JY, Qu YX, Li DZ. High accuracy of single-molecule real-time sequencing in detecting a rare α-globin fusion gene in carrier screening population. Ann Hum Genet 2023; 87:9-17. [PMID: 36317495 DOI: 10.1111/ahg.12486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
INTRODUCTION The α-globin fusion gene between the HBA2 and HBAP1 genes becomes clinically important in thalassemia screening because this fusion gene can cause severe hemoglobin (Hb) H disease when combining with α0 -thalassemia (α0 -thal). Due to its uncommon rearrangement in the α gene cluster without dosage changes, this fusion gene is undetectable by common molecular testing approaches used for α-thal diagnosis. METHODS In this study, we used the single-molecule real-time (SMRT) sequencing technique to detect this fusion gene in 23 carriers identified by next-generation sequencing (NGS) among 16,504 screened individuals. Five primers for α and β thalassemia were utilized. RESULTS According to the NGS results, the 23 carriers include 14 pure heterozygotes, eight compound heterozygotes with common α-thal alleles, and one homozygote. By using SMRT, the fusion mutant was successfully detected in all 23 carriers. Furthermore, SMRT corrected the diagnosis in two "pure" heterozygotes: one was compound heterozygote with anti-3.7 triplication, and the other was homozygote. CONCLUSION Our results indicate that SMRT is a superior method compared to NGS in detecting the α fusion gene, attributing to its efficient, accurate, and one-step properties.
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Affiliation(s)
- Qiao-Miao Zhou
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, People's Republic of China
| | - Jing Xu
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Dan Lin
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Ren-Liang Huang
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Jian-Ying Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, People's Republic of China
| | - Yan-Xia Qu
- Prenatal Diagnosis Center, Hainan Women and Children's Medical Center, Haikou, Hainan, People's Republic of China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, People's Republic of China
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17
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Identification of a novel 10.3 kb deletion causing α 0-thalassemia by third-generation sequencing: Pedigree analysis and genetic diagnosis. Clin Biochem 2023; 113:64-69. [PMID: 36610469 DOI: 10.1016/j.clinbiochem.2022.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/29/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023]
Abstract
BACKGROUND α-thalassemia is an inherited blood disorder caused by variants in the α-globin gene cluster. Identification of the pathogenic α-globin gene variants is important for the diagnosis and management of thalassemia. METHODS Two suspected families from Xiantao, Hubei Province were recruited in this study. The family members underwent hemoglobin testing. Polymerase Chain Reaction based reverse dot blot (PCR-RDB) was employed to identify the known variants. Next-generation sequencing (NGS) and third-generation sequencing (TGS) were performed to screen the potential disease-causing variants, which were validated by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). RESULTS Hematological analysis suggested that proband A had α-thalassemia traits, and proband B had HbH disease traits. However, only a -α3.7 mutation had been detected by PCR-RDB and NGS in the proband of family B. Subsequent TGS identified a novel 10.3 kb deletion (NC_000016.10:g.172342-182690del) covering the HBA1, HBQ1 and HBA2 genes in the α-globin gene cluster in both family A and B, which was confirmed by Sanger sequencing and MLPA. These results indicated that the novel deletion is likely responsible for α-thalassemia. CONCLUSION A novel α-thalassemia deletion was identified for the two families by TGS. Our work broadened the molecular spectrum of α-thalassemia, and was beneficial for the diagnosis, genetic counseling and management of α-thalassemia.
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18
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Li N, Wu B, Wang J, Yan Y, An P, Li Y, Liu Y, Hou Y, Qing X, Niu L, Ding X, Xie Z, Zhang M, Guo X, Chen X, Cai T, Luo J, Wang F, Yang F. Differential proteomic patterns of plasma extracellular vesicles show potential to discriminate β-thalassemia subtypes. iScience 2023; 26:106048. [PMID: 36824279 PMCID: PMC9941134 DOI: 10.1016/j.isci.2023.106048] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/01/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
The observed specificity of β-thalassemia-subtype phenotypes makes new diagnostic strategies that complement current screening methods necessary to determine each subtype and facilitate therapeutic regimens for different patients. Here, we performed quantitative proteomics of plasma-derived extracellular vesicles (EVs) of β-thalassemia major (TM) patients, β-thalassemia intermedia (TI) patients, and healthy controls to explore subgroup characteristics and potential biomarkers. Plasma quantitative proteomics among the same cohorts were analyzed in parallel to compare the biomarker potential of both specimens. EV proteomics showed significantly more abnormalities in immunity and lipid metabolism in TI and TM, respectively. The differential proteomic patterns of EVs were consistent with but more striking than those of plasma. Notably, we also found EV proteins to have a superior performance for discriminating β-thalassemia subtypes. These findings allowed us to propose a diagnostic model consisting of five proteins in EVs with subtyping potential, demonstrating the ability of plasma-derived EVs for the diagnosis of β-thalassemia patients.
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Affiliation(s)
- Na Li
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bowen Wu
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jifeng Wang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yumeng Yan
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng An
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Yuezhen Li
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Yuning Liu
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Yanfei Hou
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Xiaoqing Qing
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lili Niu
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiang Ding
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhensheng Xie
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengmeng Zhang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojing Guo
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tanxi Cai
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianming Luo
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021 China
| | - Fudi Wang
- The Fourth Affiliated Hospital, School of Public Health, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Corresponding author
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19
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Liu Q, Chen Q, Zhang Z, Peng S, Liu J, Pang J, Jia Z, Xi H, Li J, Chen L, Liu Y, Peng Y. Identification of rare thalassemia variants using third-generation sequencing. Front Genet 2023; 13:1076035. [PMID: 36685902 PMCID: PMC9845392 DOI: 10.3389/fgene.2022.1076035] [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: 10/21/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
Routine PCR, Sanger sequencing, and specially designed GAP-PCR are often used in the genetic analysis of thalassemia, but all these methods have limitations. In this study, we evaluated a new third-generation sequencing-based approach termed comprehensive analysis of thalassemia alleles (CATSA) in subjects with no variants identified by routine PCR, Sanger sequencing, and specially designed GAP-PCR. Hemoglobin testing and routine PCR tests for 23 common variants were performed for 3,033 subjects. Then, Sanger sequencing and specially designed GAP-PCR were performed for a subject with no variants identified by routine PCR, no iron deficiency, and positive hemoglobin testing. Finally, the new CATSA method was conducted for the subjects with no variants identified by Sanger sequencing and specially designed GAP-PCR. In the 49 subjects tested by CATSA, eight subjects had variants identified. Sanger sequencing and independent PCR confirmed the CATSA result. In addition, it is the first time that Hb Lepore was identified in Hunan Province. In total, traditional methods identified variants in 759 of the 3,033 subjects, while CATSA identified additional variants in eight subjects. CATSA showed great advantages compared to the other genetic testing methods.
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Affiliation(s)
- Qin Liu
- Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Qianting Chen
- Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Zonglei Zhang
- Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Shiyi Peng
- Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Jing Liu
- Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Jialun Pang
- Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Zhengjun Jia
- Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Hui Xi
- Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Jiaqi Li
- Berry Genomics Corporation, Beijing, China
| | - Libao Chen
- Berry Genomics Corporation, Beijing, China
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, China,*Correspondence: Yinyin Liu, ; Ying Peng,
| | - Ying Peng
- Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China,*Correspondence: Yinyin Liu, ; Ying Peng,
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20
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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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21
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Wu J, Xie D, Wang L, Kuang Y, Luo S, Ren L, Li D, Mao A, Li J, Chen L, An B, Huang S. Application of third-generation sequencing for genetic testing of thalassemia in Guizhou Province, Southwest China. Hematology 2022; 27:1305-1311. [DOI: 10.1080/16078454.2022.2156720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Jiangfen Wu
- School of Medicine, Guizhou University, Guiyang, People’s Republic of China
| | - Dan Xie
- School of Medicine, Guizhou University, Guiyang, People’s Republic of China
| | - Lei Wang
- School of Medicine, Guizhou University, Guiyang, People’s Republic of China
| | - Ying Kuang
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, People’s Republic of China
| | - Shulin Luo
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, People’s Republic of China
| | - Lingyan Ren
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, People’s Republic of China
| | - Di Li
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, People’s Republic of China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, People’s Republic of China
| | - Jiaqi Li
- Berry Genomics Corporation, Beijing, People’s Republic of China
| | - Libao Chen
- Berry Genomics Corporation, Beijing, People’s Republic of China
| | - Bangquan An
- Discipline Inspection and Supervision Office, Guizhou provincial people’s hospital, Guiyang, People’s Republic of China
| | - Shengwen Huang
- School of Medicine, Guizhou University, Guiyang, People’s Republic of China
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, People’s Republic of China
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People’s Hospital, Guiyang, People’s Republic of China
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22
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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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Liang Q, Liu Y, Liu Y, Duan R, Meng W, Zhan J, Xia J, Mao A, Liang D, Wu L. Comprehensive Analysis of Fragile X Syndrome: Full Characterization of the FMR1 Locus by Long-Read Sequencing. Clin Chem 2022; 68:1529-1540. [PMID: 36171182 DOI: 10.1093/clinchem/hvac154] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/21/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND Fragile X syndrome (FXS) is the most frequent cause of inherited X-linked intellectual disability. Conventional FXS genetic testing methods mainly focus on FMR1 CGG expansions and fail to identify AGG interruptions, rare intragenic variants, and large gene deletions. METHODS A long-range PCR and long-read sequencing-based assay termed comprehensive analysis of FXS (CAFXS) was developed and evaluated in Coriell and clinical samples by comparing to Southern blot analysis and triplet repeat-primed PCR (TP-PCR). RESULTS CAFXS accurately detected the number of CGG repeats in the range of 93 to at least 940 with mass fraction of 0.5% to 1% in the background of normal alleles, which was 2-4-fold analytically more sensitive than TP-PCR. All categories of mutations detected by control methods, including full mutations in 30 samples, were identified by CAFXS for all 62 clinical samples. CAFXS accurately determined AGG interruptions in all 133 alleles identified, even in mosaic alleles. CAFXS successfully identified 2 rare intragenic variants including the c.879A > C variant in exon 9 and a 697-bp microdeletion flanking upstream of CGG repeats, which disrupted primer annealing in TP-PCR assay. In addition, CAFXS directly determined the breakpoints of a 237.1-kb deletion and a 774.0-kb deletion encompassing the entire FMR1 gene in 2 samples. CONCLUSIONS Long-read sequencing-based CAFXS represents a comprehensive assay for identifying FMR1 CGG expansions, AGG interruptions, rare intragenic variants, and large gene deletions, which greatly improves the genetic screening and diagnosis for FXS.
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Affiliation(s)
- Qiaowei Liang
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Yingdi Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yaning Liu
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Ranhui Duan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Wanli Meng
- Berry Genomics Corporation, Beijing, China
| | | | - Jiahui Xia
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Aiping Mao
- 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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24
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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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25
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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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26
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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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27
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Long J, Sun L, Gong F, Zhang C, Mao A, Lu Y, Li J, Liu E. Third-generation sequencing: A novel tool detects complex variants in the α-thalassemia gene. Gene 2022; 822:146332. [PMID: 35181504 DOI: 10.1016/j.gene.2022.146332] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/23/2022] [Accepted: 02/11/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Thalassemia is a monogenic disorder with a high carrier rate in the southern region of China. Most laboratories currently follow the protocol of testing hematologic indicators in individuals with positive hematologic indicators and then using the hot-spot mutation test kit. A novel thalassemia gene test is performed if there is a mismatch between the hematology and hot-spot mutation test results. However, due to the large population in southern China, some individuals carry complex α-globin gene cluster (CAGC) variants in NG_000006.1, which are difficult to detect using conventional thalassemia genetic analysis protocols, leading to missed or false genetic test results for individuals carrying these complex α-globin gene cluster variants. When an individual carries a complex α-thalassemia gene variant, and an individual carries a β- thalassemia gene variant, there may be clinical symptoms that might complicate clinical consultation and prenatal diagnosis if not accurately detected. Third-generation sequencing (TGS) enables long-read single-molecule sequencing with high detection accuracy, and long-length DNA chain reads in high-fidelity reads mode. TGS can be used to analyze high homology and rich GC DNA sequences. RESULTS Four samples that showed abnormalities in the thalassemia genetic test were studied using TGS, revealing that they carried genotypes with complex α-globin gene cluster variants, one of which was a complex variant αα anti3.7 α anti3.7 α 17.2. CONCLUSIONS TGS detects complex α-globin gene cluster variants. This study may provide a reference protocol for the use of TGS for the detection of complex α-globin gene cluster variants. TGS can reveal individuals with complex α-thalassemia genotypes in the population and improve the accuracy of genetic counseling and prenatal diagnosis.
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Affiliation(s)
- Ju Long
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China.
| | - Lei Sun
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China
| | - Feifei Gong
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China
| | - Chenghong Zhang
- Laboratory of Medical Genetics, Qinzhou Maternal and Child Health Care Hospital, Qinzhou, Guangxi 535099, PR China
| | - Aiping Mao
- Third-Generation Sequencing BU, Berry Genomics Corporation, Beijing 102200, China
| | - Yulin Lu
- Third-Generation Sequencing BU, Berry Genomics Corporation, Beijing 102200, China
| | - Jiaqi Li
- Third-Generation Sequencing BU, Berry Genomics Corporation, Beijing 102200, China
| | - Enqi Liu
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China.
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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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