Low-cost generation of clinical-grade layperson-friendly pharmacogenetic passports using oligonucleotide arrays

Abstract

Pharmacogenomic (PGx) information is essential for precision medicine, enabling drug prescriptions to be personalized according to an individual's genetic background. Almost all individuals will carry a genetic marker that affects their drug response, so the ideal drug prescription for these individuals will differ from the population-level guidelines. Currently, PGx information is often not available at first prescription, reducing its effectiveness. Pharmacogenetic information is most often obtained using special assays, making it expensive and time-consuming to generate. We therefore hypothesized that we could also use genome-wide oligonucleotide genotyping arrays to generate comprehensive PGx information (PGx passports), thereby decreasing the cost and time required for PGx testing, and lowering the barrier to generating PGx information prior to first prescription. Taking advantage of existing genetic data generated in two biobanks, we developed and validated Asterix, a low-cost clinical-grade PGx passport pipeline for 12 PGx genes. In these biobanks we performed and clinically validated genetic variant calling and statistical phasing and imputation. In addition, we developed and validated a novel CYP2D6 copy number variant calling tool, foregoing the need to use separate PCR-based copy number detection. Ultimately, we returned 1227 PGx passports to biobank participants via a layperson-friendly app, improving knowledge of PGx among citizens. Our study demonstrates the feasibility of a low-cost clinical-grade PGx passport pipeline that could be readily implemented in clinical settings to enhance personalized healthcare, ensuring that patients receive the most effective and safe drug therapy based on their unique genetic makeup.