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Tang F, Xiao Y, Zhou C, Zhang H, Wang J, Zeng Y. NGS-based targeted sequencing identified six novel variants in patients with Duchenne/Becker muscular dystrophy from southwestern China. BMC Med Genomics 2023; 16:121. [PMID: 37254189 DOI: 10.1186/s12920-023-01556-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND At present, Multiplex ligation-dependent probe amplification (MLPA) and exome sequencing are common gene detection methods in patients with Duchenne muscular dystrophy or Becker muscular dystrophy (DMD/BMD), but they can not cover the whole-genome sequence of the DMD gene. In this study, the whole genome capture of the DMD gene and next-generation sequencing (NGS) technology were used to detect the patients with DMD/BMD in Southwest China, to clarify the application value of this technology and further study the gene variant spectrum. METHODS From 2017 to 2020, 51 unrelated patients with DMD/BMD in southwestern China were clinically diagnosed at West China Second University Hospital of Sichuan University (Chengdu, China). The whole-genome of the DMD gene was captured from the peripheral blood of all patients, and next-generation sequencing was performed. Large copy number variants (CNVs) in the exon regions of the DMD gene were verified through MLPA, and small variations (such as single nucleotide variation and < 50 bp fragment insertions/deletions) were validated using Sanger sequencing. RESULTS Among the 51 patients, 49 (96.1% [49/51]) had pathogenic or likely pathogenic variants in the DMD gene. Among the 49 positive samples, 17 patients (34.7% [17/49]) had CNVs in the exon regions and 32 patients (65.3% [32/49]) had small variations. A total of six novel variants were identified: c.10916_10917del, c.1790T>A, c.1842del, c.5015del, c.5791_5792insCA, and exons 38-50 duplication. CONCLUSIONS Pathogenic or likely pathogenic variants of the DMD gene were detected in 49 patients (96.1% [49/51]), of which 6 variants (12.2% [6/49]) had not been previously reported. This study confirmed the value of NGS-based targeted sequencing for the DMD gene expanding the spectrum of variants in DMD, which may provide effective genetic counseling and prenatal diagnosis for families.
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Affiliation(s)
- Feng Tang
- Department of Medical Genetics, West China Second University Hospital of Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yuanyuan Xiao
- Department of Medical Genetics, West China Second University Hospital of Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Cong Zhou
- Department of Medical Genetics, West China Second University Hospital of Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Haixia Zhang
- Department of Medical Genetics, West China Second University Hospital of Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Jing Wang
- Department of Medical Genetics, West China Second University Hospital of Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yang Zeng
- Department of Medical Genetics, West China Second University Hospital of Sichuan University, Chengdu, People's Republic of China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
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Asari M, Okuda K, Hoshina C, Omura T, Tasaki Y, Shiono H, Matsubara K, Shimizu K. Multicolor-based discrimination of 21 short tandem repeats and amelogenin using four fluorescent universal primers. Anal Biochem 2015; 494:16-22. [PMID: 26505528 DOI: 10.1016/j.ab.2015.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 10/06/2015] [Accepted: 10/14/2015] [Indexed: 01/20/2023]
Abstract
The aim of this study was to develop a cost-effective genotyping method using high-quality DNA for human identification. A total of 21 short tandem repeats (STRs) and amelogenin were selected, and fluorescent fragments at 22 loci were simultaneously amplified in a single-tube reaction using locus-specific primers with 24-base universal tails and four fluorescent universal primers. Several nucleotide substitutions in universal tails and fluorescent universal primers enabled the detection of specific fluorescent fragments from the 22 loci. Multiplex polymerase chain reaction (PCR) produced intense FAM-, VIC-, NED-, and PET-labeled fragments ranging from 90 to 400 bp, and these fragments were discriminated using standard capillary electrophoretic analysis. The selected 22 loci were also analyzed using two commercial kits (the AmpFLSTR Identifiler Kit and the PowerPlex ESX 17 System), and results for two loci (D19S433 and D16S539) were discordant between these kits due to mutations at the primer binding sites. All genotypes from the 100 samples were determined using 2.5 ng of DNA by our method, and the expected alleles were completely recovered. Multiplex 22-locus genotyping using four fluorescent universal primers effectively reduces the costs to less than 20% of genotyping using commercial kits, and our method would be useful to detect silent alleles from commercial kit analysis.
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Affiliation(s)
- Masaru Asari
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan.
| | - Katsuhiro Okuda
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Chisato Hoshina
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Tomohiro Omura
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto 606-8507, Japan
| | - Yoshikazu Tasaki
- Department of Hospital Pharmacy and Pharmacology, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Hiroshi Shiono
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Kazuo Matsubara
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto 606-8507, Japan
| | - Keiko Shimizu
- Department of Legal Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan
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Chen CA, Wang CC, Jong YJ, Wu SM. Label-Free Fluorescent Copper Nanoclusters for Genotyping of Deletion and Duplication of Duchenne Muscular Dystrophy. Anal Chem 2015; 87:6228-32. [DOI: 10.1021/acs.analchem.5b00918] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | | | - Yuh-Jyh Jong
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- College of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Shou-Mei Wu
- Department of Chemistry, College of Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
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Syu JR, Wang CC, Jong YJ, Wu SM. Genotyping of exons 1 to 20 in Duchenne muscular dystrophy by universal multiplex PCR and short-end capillary electrophoresis. Electrophoresis 2014; 35:3387-94. [DOI: 10.1002/elps.201400172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/25/2014] [Accepted: 08/05/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Jing-Rou Syu
- School of Pharmacy; College of Pharmacy; Kaohsiung Medical University; Kaohsiung Taiwan
| | - Chun-Chi Wang
- School of Pharmacy; College of Pharmacy; Kaohsiung Medical University; Kaohsiung Taiwan
| | - Yuh-Jyh Jong
- Graduate Institute of Medicine; Kaohsiung Medical University; Kaohsiung Taiwan
- Department of Pediatrics; Kaohsiung Medical University Hospital; Kaohsiung Taiwan
- College of Biological Science and Technology; National Chiao Tung University; Hsinchu Taiwan
| | - Shou-Mei Wu
- School of Pharmacy; College of Pharmacy; Kaohsiung Medical University; Kaohsiung Taiwan
- Department of Chemistry; College of Sciences; National Sun Yat-Sen University; Kaohsiung Taiwan
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