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Ngo TTD, Lea RA, Maksemous N, Eccles DA, Smith RA, Dunn PJ, Thao VC, Ha TMT, Bùi CB, Haupt LM, Scott R, Griffiths LR. The MinION as a cost-effective technology for diagnostic screening of the SCN1A gene in epilepsy patients. Epilepsy Res 2021; 172:106593. [PMID: 33721710 DOI: 10.1016/j.eplepsyres.2021.106593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/09/2021] [Accepted: 02/19/2021] [Indexed: 11/18/2022]
Abstract
The MinION is a portable DNA sequencer that allows real time sequencing at low capital cost investment. We assessed accuracy and cost-effectivess of the MinION for genetic diagnostic testing of known SCN1A mutations that cause Dravet Syndrome (DS). DNA samples (n = 7) from DS patients previously shown to carry SCN1A mutations via Ion Torrent and Sanger sequencing were sequenced using the MinION. SCN1A amplicons for 8 exons were sequenced using the MinION with 1D chemistry on an R9.4 flow cell. All known missense mutations were detected in all samples showing 100 % concordance with results from other methods. However, the MinION failed to detect the insertions/deletions (INDELs) present in these patients. Nevertheless, these results indicate that MinION is a cost-effective platform for use as an initial screening step in the detection of nucleotide substitution mutations in in SCN1A, especially in under-resourced laboratories or hospitals. Further improvements are required to reliably detect INDELS in this gene.
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Affiliation(s)
- Thi Tuyet Dieu Ngo
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia; Department of Physiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Viet Nam
| | - Rodney A Lea
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia; Hunter Medical Research Institute, School of Biomedical Sciences, Newcastle, Australia.
| | - Neven Maksemous
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - David A Eccles
- The Malaghan Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Robert A Smith
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Paul J Dunn
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Van Cao Thao
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Thi Minh Thi Ha
- Department of Medical Genetics, Hue University of Medicine and Pharmacy, Hue University, Hue, Viet Nam
| | - Chi Bao Bùi
- School of Medicine, Vietnam National University, Ho Chi Min City, Viet Nam
| | - Larisa M Haupt
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Rodney Scott
- Hunter Medical Research Institute, School of Biomedical Sciences, Newcastle, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
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