UMPlex™: a targeted next-generation sequencing primer design workflow
Abstract We have developed a tailored next-generation sequencing (tNGS) panel, employing our innovative UMPlex™ primer design workflow, to enhance pathogen identification in clinical diagnostics. Through iterative experimentation and rigorous validation, we refined the primer design by excluding tho...
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| Format: | Article |
| Language: | English |
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BMC
2025-07-01
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| Series: | Virology Journal |
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| Online Access: | https://doi.org/10.1186/s12985-025-02831-6 |
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| author | Dachuan Lin Xiaomin Zhang Dan Wang Tongyingzi Liu Tong Li Yingluan Zhang Lihua Li Yi Huang Yongchao Guo Renli Zhang Xinchun Chen Tiejian Feng |
| author_facet | Dachuan Lin Xiaomin Zhang Dan Wang Tongyingzi Liu Tong Li Yingluan Zhang Lihua Li Yi Huang Yongchao Guo Renli Zhang Xinchun Chen Tiejian Feng |
| author_sort | Dachuan Lin |
| collection | DOAJ |
| description | Abstract We have developed a tailored next-generation sequencing (tNGS) panel, employing our innovative UMPlex™ primer design workflow, to enhance pathogen identification in clinical diagnostics. Through iterative experimentation and rigorous validation, we refined the primer design by excluding those with insufficient specificity or efficiency. To mitigate amplification challenges arising from pathogenic mutations, we implemented a strategy of using a minimum of two primer pairs per pathogen, ensuring redundancy and robust detection. Validation using clinical samples showcased high specificity and efficacy, with 11 cultured pathogens isolated exclusively. In a study involving 107 positive respiratory samples, tNGS outperformed the TaqMan Array, detecting a higher number of pathogens in patients with influenza-like symptoms of unknown etiology. Additionally, tNGS yielded higher read counts for potentially pathogenic microorganisms and produced results consistent with metagenomic NGS, despite generating a reduced data volume. This approach not only improves detection rates but also offers a flexible tool for both clinical diagnostics and surveillance, particularly in the context of influenza-like illnesses. |
| format | Article |
| id | doaj-art-dbf16f618f604ded88adedf0efcc997d |
| institution | DOAJ |
| issn | 1743-422X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj-art-dbf16f618f604ded88adedf0efcc997d2025-08-20T03:03:23ZengBMCVirology Journal1743-422X2025-07-0122111210.1186/s12985-025-02831-6UMPlex™: a targeted next-generation sequencing primer design workflowDachuan Lin0Xiaomin Zhang1Dan Wang2Tongyingzi Liu3Tong Li4Yingluan Zhang5Lihua Li6Yi Huang7Yongchao Guo8Renli Zhang9Xinchun Chen10Tiejian Feng11Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University & Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical UniversityShenzhen Center for Disease Control and PreventionShenzhen Uni-Medica Technology Co., Ltd.Shenzhen Center for Disease Control and PreventionShenzhen Center for Disease Control and PreventionShenzhen Center for Disease Control and PreventionHainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University & Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical UniversityHainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University & Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical UniversityShenzhen Uni-Medica Technology Co., Ltd.Shenzhen Center for Disease Control and PreventionGuangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University Medical SchoolShenzhen Center for Disease Control and PreventionAbstract We have developed a tailored next-generation sequencing (tNGS) panel, employing our innovative UMPlex™ primer design workflow, to enhance pathogen identification in clinical diagnostics. Through iterative experimentation and rigorous validation, we refined the primer design by excluding those with insufficient specificity or efficiency. To mitigate amplification challenges arising from pathogenic mutations, we implemented a strategy of using a minimum of two primer pairs per pathogen, ensuring redundancy and robust detection. Validation using clinical samples showcased high specificity and efficacy, with 11 cultured pathogens isolated exclusively. In a study involving 107 positive respiratory samples, tNGS outperformed the TaqMan Array, detecting a higher number of pathogens in patients with influenza-like symptoms of unknown etiology. Additionally, tNGS yielded higher read counts for potentially pathogenic microorganisms and produced results consistent with metagenomic NGS, despite generating a reduced data volume. This approach not only improves detection rates but also offers a flexible tool for both clinical diagnostics and surveillance, particularly in the context of influenza-like illnesses.https://doi.org/10.1186/s12985-025-02831-6Targeted next-generation sequencingPersonalized primer designClinical surveillanceInfluenza-like patients |
| spellingShingle | Dachuan Lin Xiaomin Zhang Dan Wang Tongyingzi Liu Tong Li Yingluan Zhang Lihua Li Yi Huang Yongchao Guo Renli Zhang Xinchun Chen Tiejian Feng UMPlex™: a targeted next-generation sequencing primer design workflow Virology Journal Targeted next-generation sequencing Personalized primer design Clinical surveillance Influenza-like patients |
| title | UMPlex™: a targeted next-generation sequencing primer design workflow |
| title_full | UMPlex™: a targeted next-generation sequencing primer design workflow |
| title_fullStr | UMPlex™: a targeted next-generation sequencing primer design workflow |
| title_full_unstemmed | UMPlex™: a targeted next-generation sequencing primer design workflow |
| title_short | UMPlex™: a targeted next-generation sequencing primer design workflow |
| title_sort | umplex™ a targeted next generation sequencing primer design workflow |
| topic | Targeted next-generation sequencing Personalized primer design Clinical surveillance Influenza-like patients |
| url | https://doi.org/10.1186/s12985-025-02831-6 |
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