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A multiplex pharmacogenetics assay using the MinION nanopore sequencing device.
Yusmiati Liau1, Simone L Cree1, Simran Maggo1
1Department of Pathology and Biomedical Science, University of Otago, Christchurch.
Pharmacogenetics and Genomics
|October 1, 2019
Summary
This study demonstrates the feasibility of using the MinION nanopore device for cost-effective pharmacogenetic testing. The developed multiplex assay accurately identifies genetic variants influencing drug response, paving the way for point-of-care genetic screening.
Area of Science:
- Genomics
- Pharmacogenetics
- Molecular Diagnostics
Background:
- The MinION nanopore sequencing device offers potential for affordable, on-site DNA analysis.
- Pharmacogenetic variations significantly impact patient response to crucial medications like clopidogrel and warfarin.
- Developing accessible genetic screening methods is vital for personalized medicine.
Purpose of the Study:
- To establish a multiplex assay for pharmacogenetic variant detection using the MinION platform.
- To assess the accuracy and feasibility of nanopore sequencing for genotyping key drug-response genes.
- To demonstrate proof of principle for point-of-care pharmacogenetic screening.
Main Methods:
- Developed a multiplex PCR assay targeting 27 pharmacogenetic variants across 15 amplicons.
- Barcoded DNA samples for multiplex sequencing on the MinION device.
- Compared genotyping accuracy of four variant calling tools: marginCaller, VarScan 2, nanopolish, and Clairvoyante.
Main Results:
- Successfully sequenced and genotyped 81 out of 84 samples.
- Achieved >95% accuracy for most variants using the nanopolish tool.
- Successfully detected a known single base deletion (CYP2C9*6).
Conclusions:
- The MinION platform is suitable for developing drug-specific or broad pharmacogenetic screening assays.
- Minor misgenotyping issues were observed, but the approach is promising for clinical application.
- This study validates the use of small PCR amplicons with nanopore sequencing for pharmacogenetic analysis.
