Comparative evaluation of genotyping and low-pass sequencing for pharmacogenetic variant and phenotype inference
TL;DR
Overall, LP-WGS provides broader variant coverage and improved resolution for selected pharmacogenes but did not resolve all clinically important loci, and these findings support further evaluation of LP-WGS as a scalable PGx screening approach, especially where long-term genomic data reuse is a priority.
Abstract
Background. Pharmacogenetic (PGx) testing can guide drug prescribing but remains limited by the genomic assay used. Genotyping arrays are widely implemented yet limited to predefined variants, whereas low-pass whole-genome sequencing (LP-WGS) is not constrained by fixed probe design and may provide broader PGx variant availability after imputation. Methods. We compared Illumina Global Screening Array (GSA) v3 with ~1x LP-WGS for PGx profiling in 500 hospital biobank participants with electronic health record evidence of exposure to pharmacogenetically actionable drugs and reported adverse drug reactions. Concordance was evaluated genome-wide, at 20 actionable pharmacogenes for PharmCAT-derived star alleles and metabolizer phenotypes, and for HLA alleles. Results. Genome-wide concordance between imputed array and LP-WGS data was high (median 99.63%; interquartile range, 99.59%-99.64%). For pharmacogenetically relevant variants, LP-WGS captured a larger fraction, particularly rare alleles absent from the array data, whilst maintaining high concordance at shared sites. Predicted phenotype concordance exceeded 98% for most genes, although gene-specific differences in phenotype classification were observed. LP-WGS reduced missing phenotype assignments for selected loci, particularly CYP2C19 and NAT2, by improving resolution of star-allele structure. However, in structurally complex or incompletely characterized genes such as CYP2C9 and CYP2D6, broader variant recovery increased indeterminate classifications rather than consistently improving clinical interpretability. For HLA loci, concordance varied by imputation strategy, with SNP2HLA performing marginally better utilizing the GSA array compared to the LP-WGS approach. Conclusions. Overall, LP-WGS provides broader variant coverage and improved resolution for selected pharmacogenes but did not resolve all clinically important loci. These findings support further evaluation of LP-WGS as a scalable PGx screening approach, especially where long-term genomic data reuse is a priority.