Development and analytical validation of a targeted short‐read next generation sequencing‐based pharmacogenetic panel for comprehensive variant detection

BACKGROUND AND PURPOSE: Genomic profiling of patients for genetic variants that modify the effect of specific medications has many benefits, including the possibility of avoiding toxicities and ensuring an adequate effect of the medication. Our intention was to develop a comprehensive, high-quality pharmacogenetic test panel for clinical use with a less expensive technique than high-coverage whole-genome sequencing. EXPERIMENTAL APPROACH: We designed a targeted pan-pharmacogenomics (pan-PGx) panel based on Twist probe capture by applying Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines and aggregated data from PharmVar, PharmGKB and IPD-IMGT/HLA. Sequencing was performed using Illumina short-read sequencing. In-house computer scripts combined with freely available software, particularly PharmCAT, were used for the analysis. Validation was largely performed with Genetic Testing Reference Materials Coordination Program (GeT-RM) DNA from Coriell when applicable, otherwise with DNA from clinically well-documented material. KEY RESULTS: The validation showed that the method is both accurate and well-suited for large-scale clinical testing of pharmacogenes. Calls of single-nucleotide variants, InDels, and structural/hybrid genes and copy number variants in all major pharmacogenes could be translated into dose recommendations, making the test appropriate for clinical use. CONCLUSION AND IMPLICATIONS: This assay is suitable for clinical use and pharmacogenomic-guided drug treatments.