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DOI: 10.1101/2023.03.13.23287157

Rare Variants in Pharmacogenes Influence Clozapine Metabolism in Individuals with Schizophrenia

D. B.Kappel E. B. Rees E. Fenner ...+6 A. F. Pardinas
Clozapine is the only licensed medication for treatment-resistant schizophrenia (TRS). Few predictors for variation in response to clozapine have been identified, but clozapine metabolism is known to influence therapeutic response and the occurrence of adverse side effects. Here, we expand on genome-wide studies of clozapine metabolism, previously focused on common genetic variation, by analysing whole-exome sequencing data from 2062 individuals with schizophrenia taking clozapine in the UK. Our main aim is to investigate whether rare genomic variation in genes and gene sets involved in the clozapine metabolism pathway influences plasma concentrations of clozapine metabolites, assessed through the longitudinal analysis of 6585 pharmacokinetic assays. We observed a statistically significant association between the burden of rare damaging coding variants (MAF [≤]1%) in gene sets broadly related to drug pharmacokinetics and lower clozapine ({beta}= -0.054, SE= 0.019, P-value= 0.005) and norclozapine ({beta}= -0.043, SE= 0.018, P-value= 0.015) concentrations in plasma. Gene-based analysis identified rare variants in CYP1A2, which encodes the enzyme responsible for converting clozapine to norclozapine, as having the strongest effects of any gene on clozapine metabolism ({beta}= 0.324, SE= 0.124, P= 0.009). However, the effects of rare variants in this gene were in the opposite direction to the associations shown in the gene set analyses. Our findings support the hypothesis that rare genetic variants in known drug-metabolising enzymes and transporters can markedly influence clozapine plasma concentrations. These results also converge with common variant evidence, particularly in relation to CYP1A2, suggesting the need for further evaluations of the pharmacogenomic makeup of this gene. Overall, our results suggest that pharmacogenomic efforts trying to predict clozapine metabolism and personalise drug therapy could benefit from including rare damaging variants in pharmacogenes beyond those already identified and catalogued as PGx star alleles.