Using HiFi Reads for Improved and Accurate Haplotyping and Phasing of Pharmacogenomic Alleles

Pharmacogenomics (PGx) utilizes genomic information to assess an individual’s response to certain medications and can be used to predict adverse drug reactions or decreased efficacy. While numerous assays and genetic tests have been developed to interrogate pharmacogenes, several limitations exist, including lack of phasing information, and poor detection in complex regions with structural variants, pseudogenes, or gene conversions. In this talk, Dr. Nina Gonzaludo, describes amplicon and targeted enrichment capture SMRT Sequencing workflows that generate HiFi reads for high resolution of PGx alleles. To fully resolve CYP2D6, a highly polymorphic gene in a region with extensive homology, she discusses an amplicon strategy that resulted in ≥99.9% accuracy per sequencing run and >99% demultiplexed on target reads to CYP2D6. Additionally, results show improved haplotyping accuracy over orthogonal technologies in a set of 22 reference samples. Separately, she discusses preliminary results from a panel enrichment strategy for high resolution genotyping and phasing of 43 clinically significant pharmacogenes. These approaches can be leveraged as cost-effective and highly accurate methods for advancing PGx research and discovery.