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Li JW, Mao SJ, Chao YQ, Hu CX, Qian YJ, Dai YL, Huang K, Shen Z, Zou CC. Application of tandem mass spectrometry in the screening and diagnosis of mucopolysaccharidoses. Orphanet J Rare Dis 2024; 19:179. [PMID: 38685110 PMCID: PMC11059687 DOI: 10.1186/s13023-024-03195-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/19/2024] [Indexed: 05/02/2024] Open
Abstract
Mucopolysaccharidoses (MPSs) are caused by a deficiency in the enzymes needed to degrade glycosaminoglycans (GAGs) in the lysosome. The storage of GAGs leads to the involvement of several systems and even to the death of the patient. In recent years, an increasing number of therapies have increased the treatment options available to patients. Early treatment is beneficial in improving the prognosis, but children with MPSs are often delayed in their diagnosis. Therefore, there is an urgent need to develop a method for early screening and diagnosis of the disease. Tandem mass spectrometry (MS/MS) is an analytical method that can detect multiple substrates or enzymes simultaneously. GAGs are reliable markers of MPSs. MS/MS can be used to screen children at an early stage of the disease, to improve prognosis by treating them before symptoms appear, to evaluate the effectiveness of treatment, and for metabolomic analysis or to find suitable biomarkers. In the future, MS/MS could be used to further identify suitable biomarkers for MPSs for early diagnosis and to detect efficacy.
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Affiliation(s)
- Jing-Wen Li
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Shao-Jia Mao
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Yun-Qi Chao
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Chen-Xi Hu
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Yan-Jie Qian
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Yang-Li Dai
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Ke Huang
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Zheng Shen
- Lab Center, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Chao-Chun Zou
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China.
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Sun Y, Guan XW, Wang YY, Hong DY, Zhang ZL, Li YH, Yang PY, Wang X, Jiang T, Chi X. Newborn genetic screening for Fabry disease: Insights from a retrospective analysis in Nanjing, China. Clin Chim Acta 2024; 557:117889. [PMID: 38531466 DOI: 10.1016/j.cca.2024.117889] [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: 01/11/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 03/28/2024]
Abstract
Fabry disease (FD), an X-linked disorder resulting from dysfunction of α-galactosidase A, can result in significant complications. Early intervention yields better outcomes, but misdiagnosis or delayed diagnosis is common, impacting prognosis. Thus, early detection is crucial in the clinical diagnosis and treatment of FD. While newborn screening for FD has been implemented in certain regions, challenges persist in enzyme activity detection techniques, particularly for female and late-onset patients. Further exploration of improved screening strategies is warranted. This study retrospectively analyzed genetic screening results for pathogenic GLA variants in 17,171 newborns. The results indicated an estimated incidence of FD in the Nanjing region of China of approximately 1 in 1321. The most prevalent pathogenic variant among potential FD patients was c.640-801G > A (46.15 %). Furthermore, the residual enzyme activity of the pathogenic variant c.911G > C was marginally higher than that of other variants, and suggesting that genetic screening may be more effective in identifying potential female and late-onset patients compared to enzyme activity testing. This research offers initial insights into the effectiveness of GLA genetic screening and serves as a reference for early diagnosis, treatment, and genetic counseling in FD.
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Affiliation(s)
- Yun Sun
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, China
| | - Xian-Wei Guan
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, China
| | - Yan-Yun Wang
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, China
| | - Dong-Yang Hong
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, China
| | - Zhi-Lei Zhang
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, China
| | - Ya-Hong Li
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, China
| | - Pei-Ying Yang
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, China
| | - Xin Wang
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, China.
| | - Tao Jiang
- Genetic Medicine Center, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, China.
| | - Xia Chi
- Department of Child Healthcare, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, China.
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Tang C, Li L, Chen T, Li Y, Zhu B, Zhang Y, Yin Y, Liu X, Huang C, Miao J, Zhu B, Wang X, Zou H, Han L, Feng J, Huang Y. Newborn Screening for Inborn Errors of Metabolism by Next-Generation Sequencing Combined with Tandem Mass Spectrometry. Int J Neonatal Screen 2024; 10:28. [PMID: 38651393 PMCID: PMC11036227 DOI: 10.3390/ijns10020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024] Open
Abstract
The aim of this study was to observe the outcomes of newborn screening (NBS) in a certain population by using next-generation sequencing (NGS) as a first-tier screening test combined with tandem mass spectrometry (MS/MS). We performed a multicenter study of 29,601 newborns from eight screening centers with NBS via NGS combined with MS/MS. A custom-designed panel targeting the coding region of the 142 genes of 128 inborn errors of metabolism (IEMs) was applied as a first-tier screening test, and expanded NBS using MS/MS was executed simultaneously. In total, 52 genes associated with the 38 IEMs screened by MS/MS were analyzed. The NBS performance of these two methods was analyzed and compared respectively. A total of 23 IEMs were diagnosed via NGS combined with MS/MS. The incidence of IEMs was approximately 1 in 1287. Within separate statistical analyses, the positive predictive value (PPV) for MS/MS was 5.29%, and the sensitivity was 91.3%. However, for genetic screening alone, the PPV for NGS was 70.83%, with 73.91% sensitivity. The three most common IEMs were methylmalonic academia (MMA), primary carnitine deficiency (PCD) and phenylketonuria (PKU). The five genes with the most common carrier frequencies were PAH (1:42), PRODH (1:51), MMACHC (1:52), SLC25A13 (1:55) and SLC22A5 (1:63). Our study showed that NBS combined with NGS and MS/MS improves the performance of screening methods, optimizes the process, and provides accurate diagnoses.
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Affiliation(s)
- Chengfang Tang
- Department of Guangzhou Newborn Screening Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510180, China;
| | - Lixin Li
- Department of Genetic, Shijiazhuang Maternal and Child Health Hospital, Shijiazhuang 050090, China;
| | - Ting Chen
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China;
| | - Yulin Li
- Neonatal Disease Screening Center, Jinan Maternity and Child Health Hospital Affiliated to Shandong First Medical University, Jinan 250001, China; (Y.L.); (H.Z.)
| | - Bo Zhu
- Department of Genetics, Inner Mongolia Maternity and Child Health Care Hospital, Hohhot 750306, China; (B.Z.); (X.W.)
| | - Yinhong Zhang
- Department of Medical Genetics, NHC Key Laboratory of Preconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Yunnan Provincial Clinical Research Center for Birth Defects and Rare Diseases, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, China; (Y.Z.); (B.Z.)
| | - Yifan Yin
- Department of Pediatrics, Chongqing Health Center for Women and Children &Women and Children’s Hospital of Chongqing Medical University, Chongqing 401147, China; (Y.Y.); (J.M.)
| | - Xiulian Liu
- Neonatal Disease Screening Center, Hainan Women and Children’s Medical Center, Haikou 570206, China; (X.L.); (C.H.)
| | - Cidan Huang
- Neonatal Disease Screening Center, Hainan Women and Children’s Medical Center, Haikou 570206, China; (X.L.); (C.H.)
| | - Jingkun Miao
- Department of Pediatrics, Chongqing Health Center for Women and Children &Women and Children’s Hospital of Chongqing Medical University, Chongqing 401147, China; (Y.Y.); (J.M.)
| | - Baosheng Zhu
- Department of Medical Genetics, NHC Key Laboratory of Preconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Yunnan Provincial Clinical Research Center for Birth Defects and Rare Diseases, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, China; (Y.Z.); (B.Z.)
| | - Xiaohua Wang
- Department of Genetics, Inner Mongolia Maternity and Child Health Care Hospital, Hohhot 750306, China; (B.Z.); (X.W.)
| | - Hui Zou
- Neonatal Disease Screening Center, Jinan Maternity and Child Health Hospital Affiliated to Shandong First Medical University, Jinan 250001, China; (Y.L.); (H.Z.)
| | - Lianshu Han
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China;
| | - Jizhen Feng
- Department of Genetic, Shijiazhuang Maternal and Child Health Hospital, Shijiazhuang 050090, China;
| | - Yonglan Huang
- Department of Guangzhou Newborn Screening Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510180, China;
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Zhu ZX, Genchev GZ, Wang YM, Ji W, Ren YY, Tian GL, Sriswasdi S, Lu H. Improving the second-tier classification of methylmalonic acidemia patients using a machine learning ensemble method. World J Pediatr 2024:10.1007/s12519-023-00788-6. [PMID: 38401044 DOI: 10.1007/s12519-023-00788-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/10/2023] [Indexed: 02/26/2024]
Abstract
INTRODUCTION Methylmalonic acidemia (MMA) is a disorder of autosomal recessive inheritance, with an estimated prevalence of 1:50,000. First-tier clinical diagnostic tests often return many false positives [five false positive (FP): one true positive (TP)]. In this work, our goal was to refine a classification model that can minimize the number of false positives, currently an unmet need in the upstream diagnostics of MMA. METHODS We developed machine learning multivariable screening models for MMA with utility as a secondary-tier tool for false positives reduction. We utilized mass spectrometry-based features consisting of 11 amino acids and 31 carnitines derived from dried blood samples of neonatal patients, followed by additional ratio feature construction. Feature selection strategies (selection by filter, recursive feature elimination, and learned vector quantization) were used to determine the input set for evaluating the performance of 14 classification models to identify a candidate model set for an ensemble model development. RESULTS Our work identified computational models that explore metabolic analytes to reduce the number of false positives without compromising sensitivity. The best results [area under the receiver operating characteristic curve (AUROC) of 97%, sensitivity of 92%, and specificity of 95%] were obtained utilizing an ensemble of the algorithms random forest, C5.0, sparse linear discriminant analysis, and autoencoder deep neural network stacked with the algorithm stochastic gradient boosting as the supervisor. The model achieved a good performance trade-off for a screening application with 6% false-positive rate (FPR) at 95% sensitivity, 35% FPR at 99% sensitivity, and 39% FPR at 100% sensitivity. CONCLUSIONS The classification results and approach of this research can be utilized by clinicians globally, to improve the overall discovery of MMA in pediatric patients. The improved method, when adjusted to 100% precision, can be used to further inform the diagnostic process journey of MMA and help reduce the burden for patients and their families.
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Affiliation(s)
- Zhi-Xing Zhu
- Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Center for Biomedical Informatics, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Georgi Z Genchev
- Center of Excellence in Computational Molecular Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yan-Min Wang
- Newborn Screening Center, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Ji
- Newborn Screening Center, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yong-Yong Ren
- SJTU-Yale Joint Center for Biostatistics and Data Science, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guo-Li Tian
- Newborn Screening Center, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Sira Sriswasdi
- Center of Excellence in Computational Molecular Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Center for Artificial Intelligence in Medicine, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | - Hui Lu
- Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Center for Biomedical Informatics, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- SJTU-Yale Joint Center for Biostatistics and Data Science, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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Yu B, Yang Y, Zhou L, Wang Q. Evaluating a Novel Newborn Screening Methodology: Combined Genetic and Biochemical Screenings. Arch Med Res 2024; 55:102959. [PMID: 38295467 DOI: 10.1016/j.arcmed.2024.102959] [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: 09/21/2023] [Revised: 11/20/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024]
Abstract
PURPOSE Analysis of four newborn screening modes using newborn genomic sequencing (nGS) and traditional biochemical screening (TBS). METHODS Prospective clinical study with a total of 1,012 newborn samples from retrospective TBS. Three independent groups performed the study under strict double-blind conditions according to the screening modes: independent biochemical (IBS), independent NeoSeq (INS), sequential (SS), and combined (CS) screening. Using targeted sequencing, the NeoSeq panel included 154 pathogenic genes covering 86 diseases. RESULTS Of the 1,012 newborns, 120 were diagnosed were diagnosed with genetic diseases Among them, 52 cases were within the scope of TBS and 68 additional cases were identified through nGS. The number of cases detected per screening mode was 50, 113, 56, and 119 for IBS, INS, SS, and CS, respectively. CS was the most satisfactory screening mode, with the detection rate of 99.17%, the specificity and positive predictive value of 100%, and the negative predictive value of 99.89%. In addition, of the 68 cases identified by nGS (96 variants in 31 pathogenic genes), only four participants (5.9%) had clinical manifestations consistent with the disease. The experimental reporting cycles of CS and INS were the shortest. CONCLUSIONS CS was the most satisfactory method for newborn screening, which combined nGS with TBS to improve early diagnosis.
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Affiliation(s)
- Bin Yu
- Department of Medical Genetics, Changzhou Maternal and Child Health Hospital, Changzhou Medical Center of Nanjing Medical University, Changzhou, Jiangsu Province, China.
| | - Yuqi Yang
- Department of Medical Genetics, Changzhou Maternal and Child Health Hospital, Changzhou Medical Center of Nanjing Medical University, Changzhou, Jiangsu Province, China
| | - Lingna Zhou
- Department of Medical Genetics, Changzhou Maternal and Child Health Hospital, Changzhou Medical Center of Nanjing Medical University, Changzhou, Jiangsu Province, China
| | - Qiuwei Wang
- Department of Neonatology, Changzhou Children's Hospital of Nantong Medical University, Changzhou, Jiangsu Province, China.
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Cao Z, He X, Wang D, Gu M, Suo F, Qiang R, Zhang R, Song C, Wang X, Zhu B, Cao D, Yu H, Qu Y, Shen G, Wu J, Wang P, Wang J, Zhang H, Yan Z, Yu G, Zou L. Targeted exome sequencing strategy (NeoEXOME) for Chinese newborns using a pilot study with 3423 neonates. Mol Genet Genomic Med 2024; 12:e2357. [PMID: 38284445 PMCID: PMC10795095 DOI: 10.1002/mgg3.2357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 09/15/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Newborn screening (NBS) aims to detect congenital anomalies, and next-generation sequencing (NGS) has shown promise in this aspect. However, the NBS strategy for monogenic inherited diseases in China remains insufficient. METHODS We developed a NeoEXOME panel comprising 601 genes that are relevant to the Chinese population found through extensive research on available databases. An interpretation system to grade the results into positive (high-risk, moderate-risk, and low-risk genotypes), negative, and carrier according to the American College of Medical Genetics (ACMG) guidelines was also developed. We validated the panel to evaluate its efficacy by using data from the "1000 Genomes Project" and conducted a pilot multicenter study involving 3423 neonates. RESULTS The NGS positive rate in the 1000 Genomes Project was 7.6% (23/301), whereas the rate was 12.0% in the multicenter study, including 3249 recruited neonates. Notably, in 200 neonates, positive per conventional NBS, 58.5% (69/118) showed results consistent with NGS. In the remaining 3049 neonates showing negative results in conventional NBS, 271 (8.9%) were positive per NGS, and nine of them were clinically diagnosed with diseases in the follow-up. CONCLUSION We successfully designed a NeoEXOME panel for targeted sequencing of monogenic inherited diseases in NBS. The panel demonstrated high performance in the Chinese population, particularly for the early detection of diseases with no biochemical markers.
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Affiliation(s)
- Ziyang Cao
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiaoyan He
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Dongjuan Wang
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical UniversityChongqingChina
| | - Maosheng Gu
- Center of Medical GeneticsXuzhou Maternal and Child Health Care HospitalXuzhouChina
| | - Feng Suo
- Center of Medical GeneticsXuzhou Maternal and Child Health Care HospitalXuzhouChina
| | - Rong Qiang
- Center of Medical GeneticsNorthwest Women and Children's HospitalXi'anChina
| | - Ruixue Zhang
- Center of Medical GeneticsNorthwest Women and Children's HospitalXi'anChina
| | - Chengrong Song
- Center of Medical GeneticsNorthwest Women and Children's HospitalXi'anChina
| | - Xiaohua Wang
- Center of Medical GeneticsInner Mongolia Maternal and Child Health Care HospitalHohhotChina
| | - Bo Zhu
- Center of Medical GeneticsInner Mongolia Maternal and Child Health Care HospitalHohhotChina
| | - Donghua Cao
- Medical Genetic LaboratoryDalian Municipal Women and Children's Medical Center (Group)DalianChina
- Genetic LaboratoryShenyang Jinghua Hospital Co., LtdShenyangChina
| | - Haihua Yu
- Medical Genetic LaboratoryDalian Municipal Women and Children's Medical Center (Group)DalianChina
| | - Yiping Qu
- Newborn Screening Center of Children's Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Guosong Shen
- Medical Laboratory Center of Huzhou Maternal and Child Health Care HospitalHuzhouChina
| | - Jian Wu
- Research and Development DepartmentMyGenostics Inc.BeijingChina
| | - Pengpeng Wang
- Research and Development DepartmentMyGenostics Inc.BeijingChina
| | - Jinxia Wang
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Hongyang Zhang
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zijun Yan
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Guangjun Yu
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Lin Zou
- Clinical Research Unit, Shanghai Children's HospitalShanghai Jiao Tong University Medical SchoolShanghaiChina
- Institute of Pediatric Infection, Immunity, and Critical Care MedicineShanghai Jiao Tong University School of MedicineShanghaiChina
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical UniversityChongqingChina
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Jiang H, Yang R, Dong A, Wu B, Zhao Z. Progress of newborn screening in China. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 52:673-682. [PMID: 38115737 PMCID: PMC10764191 DOI: 10.3724/zdxbyxb-2023-0467] [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: 09/28/2023] [Accepted: 12/10/2023] [Indexed: 12/21/2023]
Abstract
Newborn screening (NBS) plays a significant role in reducing the risk of birth defects. NBS in China began in the early 1980s. Under the protection of laws and regulations and the leadership of the national health administration, approved screening centers in public hospitals took the responsibility for publicity, screening, diagnosis, treatment, follow-up and management of birth defects. As of 2022, 31 provinces (autonomous regions and municipalities directly under the central government) have carried out NBS for phenylketonuria, congenital hypothyroidism, and hearing loss, 23 provinces have carried out screening for glucose-6-phosphate dehydrogenase (with a screening rate of 89.24%), and 24 provinces have carried out screening for congenital adrenal cortical hyperplasia (91.45% screening rate). Over the past four decades, screening techniques have evolved from bacterial inhibition, fluorescence analysis, and tandem mass spectrometry for the detection of biochemical markers to genetic testing, which has greatly contributed to the expansion of the types of diseases screened for. The combined use of metabolomics and genomics is currently being explored. Effective management and rigorous quality control of NBS are prerequisites for improving the quality and ensuring the accuracy of screening. The Quality Management System for Newborn Screening System Network (QMS-NBS), established by the National Center for Clinical Laboratories, covers all screening centers and related blood collection agencies. The operation of the QMS-NBS allows the quality and performance of screening to be transparent and measurable, ensuring the quality and efficiency of screening. This article provides an overview of the history of NBS, especially the evolution of policies for the NBS in China, the construction of screening institutions, the number of newborns screened, the incidence rates of screened diseases, the changes in screening technology, the expansion of new diseases screened for, and the quality control of NBS. Overall, the progress in NBS in China has not only benefited from the development and standardization at the technological level, but also benefited from the construction of policies, regulations and ethics.
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Affiliation(s)
- Hongli Jiang
- Department of Pediatrics, Shenzhen Guangming District People's Hospital, Shenzhen 518034, Guangdong Province, China.
| | - Rulai Yang
- Department of Genetics and Metabolism, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Ao Dong
- Department of Clinical Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Benqing Wu
- Department of Pediatrics, Shenzhen Guangming District People's Hospital, Shenzhen 518034, Guangdong Province, China
| | - Zhengyan Zhao
- Department of Genetics and Metabolism, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China.
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Xin-Yi Z, Yang-Li D, Ling-Hui Z. Review of the phenotypes and genotypes of Bardet-Biedl syndrome from China. Front Genet 2023; 14:1247557. [PMID: 38034494 PMCID: PMC10684923 DOI: 10.3389/fgene.2023.1247557] [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: 07/15/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Objective: To analyze the phenotypes, genotypes, and the relationship of phenotypes and genotypes for Chinese patients with Bardet-Biedl syndrome (BBS). Methods: The Chinese Wanfang and Weipu data, and PubMed were searched up to December 2022. Patients with detailed clinical feature data were involved in the analysis. Results: A total of 153 Chinese patients, including 87 males, 53 females, and 12 unknown, were enrolled. Their ages ranged from 1.2 to 44 years old with a mean of 16.70 ± 9.90 years old. Among these patients, 80 (52.29%) were reported by ophthalmologists, and only 24 (15.68%) reported by pediatricians. Most patients (132/137, 96.35%) had visual problems; 131/153 (85.62%) had polydactyly; 124/132 (93.93%) were overweight or obese; 63/114 (55.26%) had renal abnormalities; kidney dysfunction was found in 33 (21.57%); 83/104 (79.81%) had hypogonadism and/or genital hypoplasia; and 111/136 (81.62%) had mental retardation. In this series, genetic analysis was performed in 90 (58.82%) patients, including 22 BBS7 (24.71%), 20 BBS2 (22.73%), and 10 BBS10 (11.24%) patients. Moreover, 11 fetuses were diagnosed prenatally in the last 4 years except for one patient in 2004 year. It was noted that BBS7 had higher penetrance. BBS2 had higher hearing impairment and lower renal abnormality penetrance. BBS10 also had lower renal abnormality penetrance as well. Conclusion: Misdiagnosis or miss diagnosis of BBS may be common in China. In patients with polydactyly, visual impairment, obesity, renal abnormalities, hypogonadism, and mental retardation, or in fetuses with polydactyly and/or renal abnormalities, BBS should be considered in the differential diagnosis. Other deformities should be evaluated carefully and genetic analysis should be performed as early as possible.
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Affiliation(s)
- Zou Xin-Yi
- Department of Clinical Medicine, Medical School of Hangzhou City University, Hangzhou, China
| | - Dai Yang-Li
- Department of Endocrinology, The Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Zeng Ling-Hui
- Department of Clinical Medicine, Medical School of Hangzhou City University, Hangzhou, China
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Wang X, Sun Y, Guan XW, Wang YY, Hong DY, Zhang ZL, Li YH, Yang PY, Jiang T, Xu ZF. Newborn genetic screening is highly effective for high-risk infants: A single-centre study in China. J Glob Health 2023; 13:04128. [PMID: 37824171 PMCID: PMC10569371 DOI: 10.7189/jogh.13.04128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Background Newborn genetic screening (NBGS) is promising for early detection of genetic diseases in newborns. However, little is known about its clinical effectiveness in special groups like high-risk infants. To address this gap, we aimed to investigate the impact of NBGS on high-risk infants. Methods We screened 10 334 healthy newborns from the general maternity unit and 886 high-risk infants from the neonatal ward using both traditional newborn screening (tNBS) and NBGS, and collected clinical data from electronic medical records. Results We found that high-risk infants had a higher proportion of eutocia (P < 0.01) and prematurity (P < 0.01). For high-risk infants vs healthy newborns screened by tNBS, the primary screening positive rate was 3.84% vs 1.31%, the false positive rate (FPR) was 3.62% vs 1.18% (P < 0.001), and the positive predictive value (PPV) was 5.88% vs 8.27%. For NBGS vs tNBS in high-risk infants, the primary screening positive rate was 0.54% vs 3.68%, the FPR was 0.22% vs 3.47%, and the PPV was 60.00% vs 5.88%. Conclusions We found that combined newborn screening can effectively reduce the FPR caused by the high-risk symptoms and improve the PPV in high-risk infants, sufficient for more accurately showing the true status of the disease.
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Affiliation(s)
| | | | - Xian-Wei Guan
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Yan-Yun Wang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Dong-Yang Hong
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Zhi-Lei Zhang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Ya-Hong Li
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
| | - Pei-Ying Yang
- Genetic Medicine Center, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu Province of China, China
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Guo Y, Jiang J, Xu Z. Chinese genetic variation database of inborn errors of metabolism: a systematic review of published variants in 13 genes. Orphanet J Rare Dis 2023; 18:148. [PMID: 37308883 DOI: 10.1186/s13023-023-02726-1] [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: 08/19/2022] [Accepted: 05/14/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Population-specific variation database of inborn errors of metabolism (IEMs) is essential for precise genetic diagnosis and disease prevention. Here we presented a systematic review of clinically relevant variants of 13 IEMs genes reported among Chinese patients. METHODS A systematic search of the following electronic databases for 13 IEMs genes was conducted: PubMed-NCBI, China national knowledge infrastructure and Wanfang databases. Patient data was extracted from articles eligible for inclusion and recorded in Excel electronic form using a case-by-case approach. RESULTS A total of 218 articles, 93 published in English and 125 in Chinese, were retrieved. After variant annotation and deduplication, 575 unique patients (241 from articles published in Chinese) were included in the population-specific variation database. Patients identified by newborn screening and symptomatic presentation were 231 (40.17%) and 344 (59.83%), respectively. Biallelic variants were observed in 525/575 (91.3%). Among the 581 unique variants identified, 83 (14.28%) were described ≥ 3 times and 97 (16.69%) were not recorded in Clinvar or HGMD. Four variants were reclassified as benign and dozens of confusing variants deserved further research. CONCLUSION This review provides a unique resource of the well-characterized diseases and causative variants that have accumulated in Chinese population and is a preliminary attempt to build the Chinese genetic variation database of IEMs.
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Affiliation(s)
- Yongchao Guo
- Shenzhen Uni-medica Technology Co., Ltd, Liuxian Culture Park, Nanshan District, 5180553, Shenzhen, China
| | - Jianhui Jiang
- Maternal and Child Health Hospital of Guangdong Province, No.13 Guangyuan West Road, Yuexiu District, 510010, Guangzhou, Guangdong Province, China
| | - Zhongyao Xu
- Shenzhen Uni-medica Technology Co., Ltd, Liuxian Culture Park, Nanshan District, 5180553, Shenzhen, China.
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Ye L, Yin Y, Chen M, Gong N, Peng Y, Liu H, Miao J. Combined genetic screening and traditional newborn screening to improve the screening efficiency of congenital hypothyroidism. Front Pediatr 2023; 11:1185802. [PMID: 37252044 PMCID: PMC10213735 DOI: 10.3389/fped.2023.1185802] [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: 03/14/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023] Open
Abstract
Background Congenital hypothyroidism (CH) is an neonatal endocrine disorder. Traditional newborn screening is the mainstream method of CH screening, so as to ensure the early detection and treatment of CH. This method is limited as it has high rates of false positives and negatives. Genetic screening can be used to address the shortcomings of traditional newborn Screening (NBS); however, the comprehensive clinical value of genetic screening is yet to be systematically studied. Methods A total of 3,158 newborns who accepted the newborn screening and genetic screening were recruited for this study. Biochemical screening and genetic screening were performed at the same time. The level of TSH with the DBS was detected by time-resolved immunofluorescence assay. High-throughput sequencing technology based on targeted gene capture was used for genetic screening. The suspected neonatal was recalled and tested serum TSH, and FT4. Finally, the effectiveness of traditional NBS and combined screening was compared. Results In this study, 16 cases were diagnosed by traditional NBS. 10 cases of DUOX2 mutation were found in newborn CH-related genetic screening, including 5 homozygous and 5 compound heterozygous variations. We found that the c.1588A > T mutations in DUOX2 constituting the predominant site in the present cohort.Compared with NBS and genetic screening, the sensitivity of combined screening increased by 11.1% and 55.6%, respectively. Compared with NBS and genetic screening, the negative predictive value of combined screening increased by 0.1% and 0.4%, respectively. Conclusions Combined traditional NBS and genetic screening reduces the false negative rate of CH screening and improves the early and accurate identification of neonates with CH. Our research explains the mutation spectrum of CH in this region, and provisionally demonstrates the necessity, feasibility and significance of genetic screening in newborns and provides a solid basis for future clinical developments.
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Affiliation(s)
- Liang Ye
- Department of Pediatrics, Women and Children’ Hospital of Chongqing Medical University, Chongqing, China
- Department of Pediatrics, Chongqing Health Center for Women and Children, Chongqing, China
| | - Yifan Yin
- Department of Pediatrics, Women and Children’ Hospital of Chongqing Medical University, Chongqing, China
- Department of Pediatrics, Chongqing Health Center for Women and Children, Chongqing, China
| | - Min Chen
- Department of Pediatrics, Women and Children’ Hospital of Chongqing Medical University, Chongqing, China
- Department of Pediatrics, Chongqing Health Center for Women and Children, Chongqing, China
| | - Nian Gong
- Department of Pediatrics, Women and Children’ Hospital of Chongqing Medical University, Chongqing, China
- Department of Pediatrics, Chongqing Health Center for Women and Children, Chongqing, China
| | - Yong Peng
- Department of Pediatrics, Women and Children’ Hospital of Chongqing Medical University, Chongqing, China
- Department of Pediatrics, Chongqing Health Center for Women and Children, Chongqing, China
| | - Hao Liu
- Department of Pediatrics, Women and Children’ Hospital of Chongqing Medical University, Chongqing, China
- Department of Pediatrics, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jingkun Miao
- Department of Pediatrics, Women and Children’ Hospital of Chongqing Medical University, Chongqing, China
- Department of Pediatrics, Chongqing Health Center for Women and Children, Chongqing, China
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Jia A, Lei Y, Liu DP, Pan L, Guan HZ, Yang B. A Retrospective Analysis of Clinically Focused Exome Sequencing Results of 372 Infants with Suspected Monogenic Disorders in China. Pharmgenomics Pers Med 2023; 16:81-97. [PMID: 36755623 PMCID: PMC9901461 DOI: 10.2147/pgpm.s387767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
Objective The context was designed to optimize the diagnostic utility of clinically focused exome sequencing (CFES) and shorten the diagnostic odyssey among pediatric patients suspected of monogenic disorders (MDs). Methods Here, we retrospectively analyzed the clinical notes of 372 patients from different areas in the Jiangxi province that were referred for a diagnostic CFES and analysis from June 2018 to March 2022 with symptoms suggestive of MDs. In our study, preliminary tests using the proband-only clinical exome sequencing as a cost-effective first-tier diagnostic test for pediatric patients with unidentified MDs, supplemented by family segregation studies for targeted variants when indicated. Results Probands with confirmed diagnostic (CD) or likely diagnostic (LD) genetic influences accounted for 12% of all cases, whereas those with an uncertain diagnosis accounted for 48%. We also found that systemic primary carnitine deficiency (CDSP) (SLC22A5 gene) and phenylketonuria (PAH gene) were relatively more prevalent, and these patients with CDSP had the most frequent c.1400C > G variant (p.S467C) and c.51C > G variant (p. F17L) in this study. In addition, statistical analysis revealed that the estimates of diagnostic yields varied across certain phenotypic features of patients, and patients with specific phenotypic traits tended to benefit more from CFES. Conclusion The CFES may be a first-line genetic test for diagnosing young children with suspected genetic conditions, as it validates the identification of molecular genetics alterations and facilitates comprehensive medical management. Moreover, we found that infants exhibiting metabolism/homeostasis abnormalities, craniofacial /otolaryngology/ ophthalmologic abnormalities, and/or the integument were significantly more likely to receive a genetic diagnosis via CFES than infants without such features. However, due to the current study's low diagnostic yield and inherent limitations, high-quality clinical studies with larger sample sizes are still needed to provide more likely results and confirm our findings.
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Affiliation(s)
- An Jia
- Medical School, Huanghe Science and Technology College, Zhengzhou, People’s Republic of China
| | - Yi Lei
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Dan-Ping Liu
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Lu Pan
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Hui-Zhen Guan
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China
| | - Bicheng Yang
- Medical School, Huanghe Science and Technology College, Zhengzhou, People’s Republic of China,Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, People’s Republic of China,Correspondence: Bicheng Yang, Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, 330006, People’s Republic of China, Tel +86 15350402147, Email
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A Survival Status Classification Model for Osteosarcoma Patients Based on E-CNN-SVM and Multisource Data Fusion. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:9464182. [PMID: 35855803 PMCID: PMC9288314 DOI: 10.1155/2022/9464182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 12/01/2022]
Abstract
Traditional algorithms have the following drawbacks: (1) they only focus on a certain aspect of genetic data or local feature data of osteosarcoma patients, and the extracted feature information is not considered as a whole; (2) they do not equalize the sample data between categories; (3) the generalization ability of the model is weak, and it is difficult to perform the task of classifying the survival status of osteosarcoma patients better. In this context, this paper designs a survival status prediction model for osteosarcoma patients based on E-CNN-SVM and multisource data fusion, taking into full consideration the characteristics of the small number of samples, high dimensionality, and interclass imbalance of osteosarcoma patients' genetic data. The model fuses four gene sequencing data highly correlated with bone tumors using the random forest algorithm in a dimensionality reduction and then equalizes the data using a hybrid sampling method combining the SMOTE algorithm and the TomekLink algorithm; secondly, the CNN model with the incentive module is used to further extract features from the data for more accurate extraction of characteristic information; finally, the data are passed to the SVM model to further improve the stability and classification performance of the model. The model has been demonstrated to be more effective in improving the accuracy of the classification of patients with osteosarcoma.
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[Research advances in the clinical genetics of leukodystrophy in children]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2022; 24:711-716. [PMID: 35762440 PMCID: PMC9250391 DOI: 10.7499/j.issn.1008-8830.2202020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Leukodystrophy (LD) is a group of genetic heterogeneous diseases characterized by primary abnormalities in glial cells and myelin sheath, and it is a common nervous system disease in children and has significant genotype-phenotype correlation. In recent years, the improvement in high-throughput sequencing has changed the diagnostic and therapeutic mode of LD, and elaborative phenotype analysis, such as the collection of natural history and multimodal neuroimaging evaluation during development, also provides important information for subsequent genetic diagnosis. This article reviews LD from the perspective of clinical genetics, in order to improve the awareness of this disease among pediatricians in China.
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An Assessment of Traditional and Genomic Screening in Newborns and their Applicability for Africa. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.101050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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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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