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Shang X, Peng Z, Ye Y, Asan, Zhang X, Chen Y, Zhu B, Cai W, Chen S, Cai R, Guo X, Zhang C, Zhou Y, Huang S, Liu Y, Chen B, Yan S, Chen Y, Ding H, Yin X, Wu L, He J, Huang D, He S, Yan T, Fan X, Zhou Y, Wei X, Zhao S, Cai D, Guo F, Zhang Q, Li Y, Zhang X, Lu H, Huang H, Guo J, Zhu F, Yuan Y, Zhang L, Liu N, Li Z, Jiang H, Zhang Q, Zhang Y, Juhari WKW, Hanafi S, Zhou W, Xiong F, Yang H, Wang J, Zilfalil BA, Qi M, Yang Y, Yin Y, Mao M, Xu X. Rapid Targeted Next-Generation Sequencing Platform for Molecular Screening and Clinical Genotyping in Subjects with Hemoglobinopathies. EBioMedicine 2017; 23:150-159. [PMID: 28865746 PMCID: PMC5605365 DOI: 10.1016/j.ebiom.2017.08.015] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/15/2017] [Accepted: 08/15/2017] [Indexed: 12/17/2022] Open
Abstract
Hemoglobinopathies are among the most common autosomal-recessive disorders worldwide. A comprehensive next-generation sequencing (NGS) test would greatly facilitate screening and diagnosis of these disorders. An NGS panel targeting the coding regions of hemoglobin genes and four modifier genes was designed. We validated the assay by using 2522 subjects affected with hemoglobinopathies and applied it to carrier testing in a cohort of 10,111 couples who were also screened through traditional methods. In the clinical genotyping analysis of 1182 β-thalassemia subjects, we identified a group of additional variants that can be used for accurate diagnosis. In the molecular screening analysis of the 10,111 couples, we detected 4180 individuals in total who carried 4840 mutant alleles, and identified 186 couples at risk of having affected offspring. 12.1% of the pathogenic or likely pathogenic variants identified by our NGS assay, which were undetectable by traditional methods. Compared with the traditional methods, our assay identified an additional at-risk 35 couples. We describe a comprehensive NGS-based test that offers advantages over the traditional screening/molecular testing methods. To our knowledge, this is among the first large-scale population study to systematically evaluate the application of an NGS technique in carrier screening and molecular diagnosis of hemoglobinopathies.
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Affiliation(s)
- Xuan Shang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Zhiyu Peng
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China
| | - Yuhua Ye
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Asan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Xinhua Zhang
- Department of Hematology, 303rd Hospital of the People's Liberation Army, Nanning, Guangxi, China
| | - Yan Chen
- The Second Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou, China
| | - Baosheng Zhu
- Genetic Diagnosis Center, First People's Hospital of Yunnan Province, Medical School of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Wangwei Cai
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, Hainan, China
| | - Shaoke Chen
- Department of Genetic and Metabolic Laboratory, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, Guangxi, China
| | - Ren Cai
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Xiaoling Guo
- Maternity and Child Health Care Hospital of Foshan City, Foshan, Guangdong, China
| | - Chonglin Zhang
- Guilin Women and Children health care hospital, Guilin, Guangxi, China
| | - Yuqiu Zhou
- Department of Clinical Laboratory, Zhuhai Municipal Maternal and Child Healthcare Hospital, Zhuhai Institute of Medical Genetics, Zhuhai, Guangdong, China
| | - Shuodan Huang
- Maternal and Child Health Hospital in Meizhou, Meizhou, Guangdong, China
| | - Yanhui Liu
- Department of Prenatal Diagnosis Center, Dong Guan Maternal and Child Health Hospital, Dongguan, Guangdong, China
| | - Biyan Chen
- Baise Women and Children Care Hospital, Baise, Guangxi, China
| | - Shanhuo Yan
- Genetic Laboratory, Qinzhou Maternaland Child Health Hospital, Qingzhou, Guangxi, China
| | - Yajun Chen
- Women and Children's Health Hospital of Shaoguan, Shaoguan, Guangdong, China
| | - Hongmei Ding
- Department of Gynecology and Obstetrics, The People's Hospital of Yunfu City, Yunfu, Guangdong, China
| | - Xiaolin Yin
- Department of Hematology, 303rd Hospital of the People's Liberation Army, Nanning, Guangxi, China
| | - Liusong Wu
- The Second Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou, China
| | - Jing He
- Genetic Diagnosis Center, First People's Hospital of Yunnan Province, Medical School of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Dongai Huang
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, Hainan, China
| | - Sheng He
- Department of Genetic and Metabolic Laboratory, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, Guangxi, China
| | - Tizhen Yan
- Department of Medical Genetics, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Xin Fan
- Department of Genetic and Metabolic Laboratory, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, Guangxi, China
| | - Yuehong Zhou
- Pingguo Women and Children Care Hospital, Baise, Guangxi, China
| | - Xiaofeng Wei
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Sumin Zhao
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Decheng Cai
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Fengyu Guo
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Qianqian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Yun Li
- BGI Clinical Laboratories-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Xuelian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Haorong Lu
- BGI Clinical Laboratories-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Huajie Huang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Junfu Guo
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Fei Zhu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Yuan Yuan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China; Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Li Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Na Liu
- BGI Clinical Laboratories-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Zhiming Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Hui Jiang
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China
| | - Qiang Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Yijia Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | | | - Sarifah Hanafi
- Department of Paediatric, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Wanjun Zhou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Fu Xiong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China
| | - Huanming Yang
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China; James D. Watson Institute of Genome Sciences, Hangzhou, Zhejiang, China
| | - Jian Wang
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China; James D. Watson Institute of Genome Sciences, Hangzhou, Zhejiang, China
| | - Bin Alwi Zilfalil
- Department of Paediatric, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Ming Qi
- School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Center for Genetic & Genomic Medicine, Zhejiang University Medical School 1st Affiliated Hospital, James Watson Institute of Genome Sciences, Hangzhou, Zhejiang, China
| | - Yaping Yang
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
| | - Ye Yin
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China
| | - Mao Mao
- BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, China.
| | - Xiangmin Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Key Laboratory of Biological Chip, Guangzhou, Guangdong, China.
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