Analysis of Genetic Variation in CYP450 Genes for Clinical Implementation

Abstract

Background: Genetic determinants of drug response remain stable throughout life and offer great promise to patient-tailored drug therapy. The adoption of pharmacogenetic (PGx) testing in patient care requires accurate, cost effective and rapid genotyping with clear guidance on the use of the results. Hence, we evaluated a 32 SNPs panel for implementing PGx testing in clinical laboratories.

Methods: We designed a 32-SNP panel for PGx testing in clinical laboratories. The variants were selected using the clinical annotations of the Pharmacogenomics Knowledgebase (PharmGKB) and include polymorphisms of CYP2C9, CYP2C19, CYP2D6, CYP3A5 and VKORC1 genes. The CYP2D6 gene allele quantification was determined simultaneously with TaqMan copy number assays targeting intron 2 and exon 9 regions. The genotyping results showed high call rate accuracy according to concordance with genotypes identified by independent analyses on Sequenome massarray and droplet digital PCR. Furthermore, 506 genomic samples across three major ethnic groups of Singapore (Malay, Indian and Chinese) were analysed on our workflow.

Results: We found that 98% of our study subjects carry one or more CPIC actionable variants. The major alleles detected include CYP2C9*3, CYP2C19*2, CYP2D6*10, CYP2D6*36, CYP2D6*41, CYP3A5*3 and VKORC1*2. These translate into a high percentage of intermediate (IM) and poor metabolizer (PM) phenotypes for these genes in our population.

Conclusion: Genotyping may be useful to identify patients who are prone to drug toxicity with standard doses of drug therapy in our population. The simplicity and robustness of this PGx panel is highly suitable for use in a clinical laboratory.

Fig 1. Frequency of metabolizer groups in 3 major ethnic groups of Singapore population.

(A) CYP2C9 (B) CYP2C19 and (C) CYP2D6.

Fig 2. The frequencies of actionable diplotypes for each drug-gene rule.

The definition of actionable diplotypes is defined as follows: (i) warfarin, CYP2C9 *2 or *3 heterozygote or homozygote with VKORC1 GA or AA genotype and CYP2C9*1 with VKORC1 AA genotype; (ii) clopidogrel, CYP2C19*2, *3 and *6; (iii) codeine, CYP2D6 poor and intermediate metabolizers; (iv) tacrolimus, CYP3A5*1 heterozygote or homozygote.