Aims: This study was designed to develop a high-resolution melting (HRM) analysis-based cardiovascular (CV) pharmacogenetics (PGx) genotyping panel for the Canon DNA Genetic Analyzer multiplex genotyping platform and cross-validate its performance with the TaqMan®-based OpenArray® method.
Methods: The CV PGx genotyping panel containing 17 single nucleotide polymorphisms (SNPs) selected from 5 genes (CYP2C9, CYP2C19, CYP4F2, SLCO1B1, and VKORC1) and the CYP2C cluster was used to compare genotyping results between analysis methods. Genomic DNA from 223 clinical samples was used to genotype the 17 SNPs on the Canon DNA Genetic Analyzer and TaqMan OpenArray Quant Studio Real-Time PCR (polymerase chain reaction) System.
Results: The concordance between the Canon DNA analyzer and TaqMan-based OpenArray genotyping results for the 17 SNPs ranged from 99.10% to 100% where SNPs (rs4244285, rs12248560, rs4986893, rs72552267, rs28399504, rs4149056, rs28371686, rs9332131, rs72558189, rs9923231, rs12777823), (rs41291556, rs1799853, rs7900194, rs28371685, rs2108622), and (rs1057910) showed 100%, 99.60%, and 99.10% concordance, respectively.
Conclusion: These results show that the HRM analysis-based CV PGx genotyping panel performed well when compared with TaqMan-based OpenArray. The multiple genetic variant testing capability, efficient turnaround time and reproducibility of both assays formats suggest that the PGx panel with the DNA analyzer or other real-time PCR instruments with HRM assay analysis capability can be used for PGx testing in both research and clinical practice settings.
Keywords: cardiovascular pharmacogenetics genotyping panel; high-resolution melting analysis; microfluidic; rapid serial PCR.