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Liu Y, Zhang Y, Wang J, Song S, Wang H, Meng Q, Zhan Y, Xu Y, Sun L. Multicolor melting curve analysis discloses high carrier frequency of hearing loss-associated variants among neonates in Jiangsu province. Mol Genet Genomic Med 2024; 12:e2384. [PMID: 38407562 PMCID: PMC10847707 DOI: 10.1002/mgg3.2384] [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: 11/06/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND Genetic disorders ascribe to half of cases of congenital hearing loss. Hearing screening is significant in detecting hearing loss (HL) but weak at diagnosis, which can be complemented by genetic screening. METHODS To find a feasible method to accomplish genetic screening and evaluate its advantage when combined with hearing screening, between 1 January 2022, and 10 December 2023, we performed an observational cohort study based on 2488 neonates from the Han population at three hospitals in Jiangsu province. Genetic screening for 20 variants in four common HL-associated genes by multicolor melting curve analysis (MMCA) and hearing screening were offered concurrently to all participants. RESULTS In total, 170 (6.8%) of 2488 eligible neonates were detected at least one variant and among them, the proportion of referral was higher (p < 0.05). Genetic screening combined with hearing screening was associated with a 25.0% increase (2 of 8) in discovering cases of diagnosed hearing loss that were missed by hearing screening. CONCLUSION This study suggests that genetic screening combined with hearing screening by MMCA is effective at finding potential HL cases and practical to be validated in other places.
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Affiliation(s)
- Yi Liu
- Department of Obstetrics & GynecologyThe First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsuChina
| | - Yuanyuan Zhang
- Department of Obstetrics & GynecologyThe First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsuChina
| | - Jue Wang
- Department of Obstetrics & GynecologyThe First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsuChina
| | - Shengnan Song
- Department of Obstetrics & GynecologyThe First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsuChina
| | - Huiyan Wang
- Department of Obstetrics & GynecologyChangzhou Maternity and Child Health Care HospitalChangzhouJiangsuChina
| | - Qian Meng
- Department of Obstetrics & GynecologyLianyungang Maternity and Child Health HospitalLianyungangJiangsuChina
| | - Yuan Zhan
- Department of Obstetrics & GynecologyThe First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsuChina
| | - Yetao Xu
- Department of Obstetrics & GynecologyThe First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsuChina
| | - Lizhou Sun
- Department of Obstetrics & GynecologyThe First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsuChina
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Danilchenko VY, Zytsar MV, Maslova EA, Posukh OL. Selection of Diagnostically Significant Regions of the SLC26A4 Gene Involved in Hearing Loss. Int J Mol Sci 2022; 23:ijms232113453. [PMID: 36362242 PMCID: PMC9655724 DOI: 10.3390/ijms232113453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/23/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Screening pathogenic variants in the SLC26A4 gene is an important part of molecular genetic testing for hearing loss (HL) since they are one of the common causes of hereditary HL in many populations. However, a large size of the SLC26A4 gene (20 coding exons) predetermines the difficulties of its complete mutational analysis, especially in large samples of patients. In addition, the regional or ethno-specific prevalence of SLC26A4 pathogenic variants has not yet been fully elucidated, except variants c.919-2A>G and c.2168A>G (p.His723Arg), which have been proven to be most common in Asian populations. We explored the distribution of currently known pathogenic and likely pathogenic (PLP) variants across the SLC26A4 gene sequence presented in the Deafness Variation Database for the selection of potential diagnostically important parts of this gene. As a result of this bioinformatic analysis, we found that molecular testing ten SLC26A4 exons (4, 6, 10, 11, 13−17 and 19) with flanking intronic regions can provide a diagnostic rate of 61.9% for all PLP variants in the SLC26A4 gene. The primary sequencing of these SLC26A4 regions may be applied as an initial effective diagnostic testing in samples of patients of unknown ethnicity or as a subsequent step after the targeted testing of already-known ethno- or region-specific pathogenic SLC26A4 variants.
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Affiliation(s)
- Valeriia Yu. Danilchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Marina V. Zytsar
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Ekaterina A. Maslova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Olga L. Posukh
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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Yang H, Luo H, Zhang G, Zhang J, Peng Z, Xiang J. A multiplex PCR amplicon sequencing assay to screen genetic hearing loss variants in newborns. BMC Med Genomics 2021; 14:61. [PMID: 33639928 PMCID: PMC7913202 DOI: 10.1186/s12920-021-00906-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/16/2021] [Indexed: 12/30/2022] Open
Abstract
Background Congenital hearing loss is one of the most common birth defects. Early identification and management play a crucial role in improving patients’ communication and language acquisition. Previous studies demonstrated that genetic screening complements newborn hearing screening in clinical settings. Methods We developed a multiplex PCR amplicon sequencing assay to sequence the full coding region of the GJB2 gene, the most pathogenic variants of the SLC26A4 gene, and hotspot variants in the MT-RNR1 gene. The sensitivity, specificity, and reliability were validated via samples with known genotypes. Finally, a pilot study was performed on 300 anonymous dried blood samples. Results Of 103 samples with known genotypes, the multiplex PCR amplicon sequencing assay accurately identified all the variants, demonstrating a 100% sensitivity and specificity. The consistency is high in the analysis of the test–retest reliability and internal consistency reliability. In the pilot study, 12.3% (37/300) of the newborns were found to carry at least one pathogenic variant, including 24, 10, and 3 from the GJB2, SLC26A4, and MT-RNR1 gene, respectively. With an allele frequency of 2.2%, the NM_004004.6(GJB2):c.109G>A was the most prevalent variant in the study population. Conclusion The multiplex PCR amplicon sequencing assay is an accurate and reliable test to detect hearing loss variants in the GJB2, SLC26A4, and MT-RNR1 genes. It can be used to screen genetic hearing loss in newborns.
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Affiliation(s)
- Haiyan Yang
- BGI College, Zhengzhou University, Zhengzhou, 450001, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China.,BGI Education Center, University of Chinese Academy of Sciences, BGI Park, No.21 Hongan 3rd Street, Yantian District, Shenzhen, 518083, China
| | - Hongyu Luo
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Guiwei Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Junqing Zhang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jiale Xiang
- BGI Education Center, University of Chinese Academy of Sciences, BGI Park, No.21 Hongan 3rd Street, Yantian District, Shenzhen, 518083, China. .,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
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Isaka Y, Nishio SY, Hishinuma E, Hiratsuka M, Usami SI. Improvement of a Rapid and Highly Sensitive Method for the Diagnosis of the Mitochondrial m.1555A>G Mutation Based on a Single-Stranded Tag Hybridization Chromatographic Printed-Array Strip. Genet Test Mol Biomarkers 2021; 25:79-83. [PMID: 33372830 PMCID: PMC7821431 DOI: 10.1089/gtmb.2020.0105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aims: Pathogenic variants in mitochondrial DNA are known to be associated with sensorineural hearing loss (SNHL) and aminoglycoside-induced HL. Among them, the m.1555A>G mutation is the most common. Thus, a rapid and easy companion diagnostic method for this mutation would be desirable to prevent HL caused by aminoglycoside therapy. In this study, we report an improved protocol for the single-stranded tag hybridization chromatographic printed-array strip (STH-PAS) method for identifying the m.1555A>G mutation. Methods: To evaluate the accuracy of a novel diagnostic for the m.1555A>G mutation we analyzed 378 DNA samples with or without the m.1555A>G mutation, as determined by Invader assay, and calculated the sensitivity, specificity, and false negative and false positive ratios of this new method. Results: The newly developed protocol was robust; we, obtained the same results using multiple DNA concentrations, differing annealing temperatures, and different polymerase chain reaction thermal cyclers. The diagnostic sensitivity based on the STH-PAS method was 0.99, and the specificity was 1.00. The false negative and false positive ratios were 0 and 0.01, respectively. Conclusion: We improved the genotyping method for m.1555A>G mutations. This assays will be useful as a rapid companion diagnostic before aminoglycoside use.
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Affiliation(s)
- Yuichi Isaka
- Department of Hearing Implant Sciences and Shinshu University School of Medicine, Matsumoto, Japan
| | - Shin-ya Nishio
- Department of Hearing Implant Sciences and Shinshu University School of Medicine, Matsumoto, Japan
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Eiji Hishinuma
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine and Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masahiro Hiratsuka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine and Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shin-ichi Usami
- Department of Hearing Implant Sciences and Shinshu University School of Medicine, Matsumoto, Japan
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
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Liu P, Lu L, Xu M, Zhong H, Jia R, Su L, Cao L, Dong Z, Dong N, Zhou L, Xu J. A novel multiplex PCR for virus detection by melting curve analysis. J Virol Methods 2018; 262:56-60. [PMID: 30267725 PMCID: PMC7113878 DOI: 10.1016/j.jviromet.2018.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 12/23/2022]
Abstract
Taqman probe based melting curve analysis can detect and distinguish six respiratory viruses simultaneously. The multiplex PCR established here has a good analytical sensitivity and specificity. The accordance rate between the multiplex PCR and direct fluorescent antibody testing was high. Taqman probe based melting curve analysis is well suited to multiple virus detection.
Background Rapid and accurate laboratory diagnoses of viral infections are crucial for the management and treatment of patients with viral infections. Conventional methods for virus detection are labourious, time consuming, and only a single virus can be analysed in one assay. Objectives The objective of this study was to develop a novel real-time PCR method for multiple virus detection by melting curve analysis using Taqman probes in a single reaction. Study design As a model, six respiratory viruses were detected in one tube using three fluorophores. The specificity was assessed by cross-reaction tests with other common respiratory pathogens. The analytical sensitivity was assessed by testing the limit of detection of the assay using artificial plasmids as the positive template. The clinical evaluation of the established assay was evaluated for the detection of respiratory viruses in clinical samples, and the results were compared with direct fluorescent antibody testing (DFA). Results The six respiratory viruses were clearly distinguished by their respective melting temperature values in the corresponding fluorescence detection channels. No cross reactions were observed by cross reaction tests. The detection limits of this assay were 2 to 2 × 103 copies per reaction for each virus. The clinical evaluation of this assay was demonstrated by analysing 352 clinical samples, and 67(19.0%) samples were positive for at least one virus. The accordance rate between the established PCR and DFA testing was high, and ranged from 94.57% to 100%. Conclusions Taqman probe-based melting curve analysis is well suited for detection of multiple viruses in clinical and research laboratories because of its high throughput, reliability, and cost savings.
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Affiliation(s)
- Pengcheng Liu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Lijuan Lu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Menghua Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Huaqing Zhong
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Ran Jia
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Liyun Su
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Lingfeng Cao
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Zuoquan Dong
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Niuniu Dong
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Linfu Zhou
- Medical Biotechnology Laboratory, Zhejiang University, Hangzhou, China.
| | - Jin Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China.
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Anazawa T, Yamazaki M. An ultra-small, multi-point, and multi-color photo-detection system with high sensitivity and high dynamic range. LAB ON A CHIP 2017; 17:4231-4242. [PMID: 29115316 DOI: 10.1039/c7lc01070b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although multi-point, multi-color fluorescence-detection systems are widely used in various sciences, they would find wider applications if they are miniaturized. Accordingly, an ultra-small, four-emission-point and four-color fluorescence-detection system was developed. Its size (space between emission points and a detection plane) is 15 × 10 × 12 mm, which is three-orders-of-magnitude smaller than that of a conventional system. Fluorescence from four emission points with an interval of 1 mm on the same plane was respectively collimated by four lenses and split into four color fluxes by four dichroic mirrors. Then, a total of sixteen parallel color fluxes were directly input into an image sensor and simultaneously detected. The emission-point plane and the detection plane (the image-sensor surface) were parallel and separated by a distance of only 12 mm. The developed system was applied to four-capillary array electrophoresis and successfully achieved Sanger DNA sequencing. Moreover, compared with a conventional system, the developed system had equivalent high fluorescence-detection sensitivity (lower detection limit of 17 pM dROX) and 1.6-orders-of-magnitude higher dynamic range (4.3 orders of magnitude).
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