Cross-validation of technologies for genotypingCYP2D6andCYP2C19

Abstract

AbstractBackgroundCYP2D6 and CYP2C19 are cytochrome P450 enzymes involved in the metabolism of many medications from multiple therapeutic classes. Associations between patterns of variants (known as haplotypes) in the genes encoding them (CYP2D6andCYP2C19) and enzyme activities are well described. The genes in fact comprise 21% of biomarkers in drug labels. Despite this, genotyping is not common, partly attributable to its challenging nature (CYP2D6having >100 haplotypes, including those with sequence from an adjacent pseudogene, and gene duplications). We cross-validated different methodologies for identifying haplotypes in these genes against each other.MethodsNinety-two samples with a variety ofCYP2D6andCYP2C19genotypes according to prior AmpliChip CYP450 and TaqManCYP2C19*17data were selected from the Genome-based therapeutic drugs for depression (GENDEP) study. Genotyping was performed with TaqMan copy number variant (CNV) and single nucleotide variant (SNV) analysis, the next generation sequencing-based Ion S5 AmpliSeq Pharmacogenomics Panel, PharmacoScan, long-range polymerase chain reaction (L-PCR) followed by amplicon analysis, and Agena forCYP2C19. Variant pattern to haplotype translation was automated.ResultsThe inter-platform concordance forCYP2C19was high (up to 100% for available data). ForCYP2D6, the IonS5-PharmacoScan concordance was 94% for a range of variants tested apart from those with at least one extra copy of aCYP2D6gene (occurring at a frequency of 3.8%, 33/853), or those with substantial sequence derived from pseudogene, known as hybrids (3%, 26/853).ConclusionsInter-platform concordance forCYP2C19was high, and, moreover, the Ion S5 and PharmacoScan data were 100% concordant with that from a TaqManCYP2C19*2assay. We have also demonstrated feasibility of using an NGS platform for genotypingCYP2D6andCYP2C19, with automated data interpretation methodology. This points the way to a method of makingCYP2D6andCYP2C19genotyping more readily accessible.