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A multiplex pharmacogenetics assay using the MinION nanopore sequencing device

Publication

Date: 28th February 2019 | Source: BioRxiv

Authors: Yusmiati Liau, Simone L. Cree, Simran Maggo, Allison L. Miller, John F. Pearson, Patrick A. Gladding, Martin A. Kennedy.

Aim 
The MinION nanopore sequencing device opens the opportunity to cost-effective and point-of-care DNA sequencing. We developed a multiplex assay targeting pharmacogenetic variants related to clopidogrel and warfarin, two commonly used drugs that show response variability due to genetic polymorphisms.

Materials & Methods 
Six reference and 78 clinical DNA samples were amplified by PCR to generate 15 amplicons targeting key variants. These products were then barcoded to enable sample multiplexing. Three variant calling tools were used to compare genotyping accuracy.

Results and Conclusions 
All but three samples were successfully sequenced and genotyped. Nanopolish software achieved accuracy >90 % for all except one variant. While minor mis-genotyping issues exist, this work demonstrates that drug-specific or broad pharmacogenetic screening assays are possible on the MinION sequencing device.

Read the full text Watch Yusmiati's LC19 talk on CYP2D6 variant identification

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