Targeting and comprehensive characterization of pharmacogenes using Oxford Nanopore Technologies’ adaptive sampling
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Pharmacogenomics (PGx) is the study of how a person’s genome affects drug response. Adaptive sampling (AS) is a fast, flexible, and precise method to enrich for regions of interest by depleting off-target regions during sequencing itself, with no enrichment required during sample preparation.
Here, we demonstrate enrichment via adaptive sampling of a PGx gene panel with >278 unique pharmacogenetic targets sourced from the FDA, PharmGKB, and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
Samples were analyzed using the wf-human-variation Epi2Me Labs pipeline from Oxford Nanopore Technologies, which called small variants with Clair3, structural variants with Sniffles2, and phased reads with whatshap. We show that coverage is sufficiently high for high accuracy star (*) allele calls on five samples multiplexed on a single flow cell.
