Background: CYP2D6 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 (CYP2D6 and CYP2C19) 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 (CYP2D6 having >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. Methods: Ninety-two samples with a variety of CYP2D6 and CYP2C19 genotypes according to prior AmpliChip CYP450 and TaqMan CYP2C19*17 data 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 for CYP2C19. Variant pattern to haplotype translation was automated. Results: The inter-platform concordance for CYP2C19 was high (up to 100% for available data). For CYP2D6, the IonS5-PharmacoScan concordance was 94% for a range of variants tested apart from those with at least one extra copy of a CYP2D6 gene (occurring at a frequency of 3.8%, 33/853), or those with substantial sequence derived from pseudogene, known as hybrids (3%, 26/853). Conclusions: Inter-platform concordance for CYP2C19 was high, and, moreover, the Ion S5 and PharmacoScan data were 100% concordant with that from a TaqMan CYP2C19*2 assay. We have also demonstrated feasibility of using an NGS platform for genotyping CYP2D6 and CYP2C19, with automated data interpretation methodology. This points the way to a method of making CYP2D6 and CYP2C19 genotyping more readily accessible.

中文翻译：

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CYP2D6和CYP2C19基因分型技术的交叉验证

背景：CYP2D6和CYP2C19是细胞色素P450酶，参与多种治疗类别的许多药物的代谢。编码它们的基因（CYP2D6和CYP2C19）的变体模式（称为单倍型）与酶活性之间的关联已得到很好的描述。该基因实际上占药物标签中21％的生物标志物。尽管如此，基因分型并不常见，部分归因于其具有挑战性的性质（CYP2D6具有> 100个单倍型，包括具有相邻假基因序列的单倍型和基因重复）。我们交叉验证了用于识别这些基因中彼此相对的单倍型的不同方法。方法：从基于基因组的抑郁症治疗药物（GENDEP）中选择了92份根据先前AmpliChip CYP450和TaqMan CYP2C19 * 17数据而具有各种CYP2D6和CYP2C19基因型的样本。通过TaqMan拷贝数变异（CNV）和单核苷酸变异（SNV）分析，基于下一代测序的Ion S5 AmpliSeq药物基因组学小组，PharmacoScan，长距离聚合酶链反应（L-PCR）进行基因分型，然后进行扩增子分析，和CYP2C19的Agena。单倍型翻译的变异模式是自动化的。结果：CYP2C19的平台间一致性很高（可用数据高达100％）。对于CYP2D6，除了具有至少一个CYP2D6基因的额外拷贝（以3.8％的频率出现，33/853）的测试变异范围外，IonS5-PharmacoScan的一致性为94％，或具有源自假基因的实质序列的序列，称为杂种（3％，26/853）。结论：CYP2C19的平台间一致性很高，而且，Ion S5和PharmacoScan数据与TaqMan CYP2C19 * 2测定的数据一致。我们还展示了使用NGS平台通过自动数据解释方法对CYP2D6和CYP2C19进行基因分型的可行性。这为使CYP2D6和CYP2C19基因分型更容易获得的方法指明了方向。我们还展示了使用NGS平台通过自动数据解释方法对CYP2D6和CYP2C19进行基因分型的可行性。这为使CYP2D6和CYP2C19基因分型更容易获得的方法指明了方向。我们还展示了使用NGS平台通过自动数据解释方法对CYP2D6和CYP2C19进行基因分型的可行性。这为使CYP2D6和CYP2C19基因分型更容易获得的方法指明了方向。