Long‐Read Sequencing Enhances Pharmacogenomic Profiling by Resolving Complex Haplotypes, Novel Star Alleles, and Structural Variants

Clinical Pharmacology & Therapeutics, vol. 119, pp. 536–545

Abstract

Pharmacogenomics has shifted drug therapy from trial-and-error to personalized approaches by leveraging genetic biomarkers. However, traditional genotyping assays and short-read sequencing often fail to resolve structural complexity in pharmacogenes, leading to ambiguous haplotypes and incorrect phenotype predictions. To evaluate the potential of emerging long-read sequencing technologies in overcoming these limitations, we analyzed diplotypes and drug response phenotypes across 20 clinically actionable pharmacogenes using Oxford Nanopore or PacBio data from 100 healthy individuals in the 1,000 Genomes Project and 159 participants from the Genomics England cancer and rare disease cohorts, alongside Illumina short-read sequencing data. Long reads achieved phasing accuracies of >98% (Oxford Nanopore) and 96.5% (PacBio), with most genes covered by a single phased haploblock. Variant detection metrics were high (i.e., precision, recall, and F1 > 0.92). Genotype and phenotype concordance between short- and long-read predictions exceeded 99%. Short-read predictions contributed nearly twice as much to overall discordant cases compared to those of long reads. Notably, long reads identified 19 novel star (*) alleles and 106 novel suballeles in nine pharmacogenes, including CYP2D6, CYP2B6, CYP2C9, CYP2C19, CYP4F2, and SLCO1B1, which have been submitted to PharmVar. Additionally, long reads resolved 13 ambiguous CYP2D6 structural variants, including a potentially novel structure. Also, a homozygous TA repeat (UGT1A1*80 + *28) was identified that is associated with a poor metabolizer phenotype. Overall, we reassigned 77 genotypes across nine genes for 58 of the 100 investigated 1,000 Genomes Project subjects. These results demonstrate the superiority of long-read sequencing in phasing and resolving complex genomic regions enabling more precise pharmacogenomic profiling. As sequencing costs decline with rapid technological advances, long-read sequencing may become the method of choice in clinical pharmacogenomics, enhancing therapeutic safety and efficacy.

Authors 5

1. Sumudu Rangika Samarasinghe

   Queensland University of Technology

   Affiliation as printed

   Centre for Genomics and Personalised Health Queensland University of Technology Brisbane Queensland Australia

   Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia

2. Andrea Gaedigk

   Children’s Mercy Research Institute · University of Missouri–Kansas City

   Affiliation as printed

   Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children’s Mercy Research Institute, and School of Medicine University of Missouri‐Kansas City Kansas City Missouri USA

   Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Research Institute, and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA

3. Jesse Joachim Swen Aachen Department of Clinical Pharmacy and Toxicology Leiden University Medical Center Leiden The Netherlands Department of Clinical Pharmacy and Toxicology

   Leiden University Medical Center

   Affiliation as printed

   Department of Clinical Pharmacy and Toxicology Leiden University Medical Center Leiden The Netherlands

   Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands

4. Henk‐Jan Guchelaar Aachen Department of Clinical Pharmacy and Toxicology Leiden University Medical Center Leiden The Netherlands Department of Clinical Pharmacy and Toxicology

   Leiden University Medical Center

   Affiliation as printed

   Department of Clinical Pharmacy and Toxicology Leiden University Medical Center Leiden The Netherlands

   Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands

5. Shivashankar Hiriyur Nagaraj corresponding

   Translational Research Institute · Queensland University of Technology

   Affiliation as printed

   Centre for Genomics and Personalised Health Queensland University of Technology Brisbane Queensland Australia

   Translational Research Institute Queensland University of Technology Brisbane Queensland Australia

   Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia

   Translational Research Institute, Queensland University of Technology, Brisbane, Queensland, Australia