Targeted adaptive sampling enables clinical pharmacogenomics testing and genome-wide genotyping

Area of Science:

• Genomics
• Pharmacogenomics
• Molecular Biology

Background:

• Current pharmacogenomics (PGx) technologies face limitations in resolving complex genetic regions, detecting structural variants, and accurately phasing alleles.
• Accurate genetic variant detection is crucial for personalized medicine, impacting drug efficacy and safety.

Purpose of the Study:

• To develop and validate an end-to-end pharmacogenomics (PGx) workflow using Targeted Adaptive Sampling-Long Read Sequencing (TAS-LRS).
• To assess the performance of TAS-LRS for accurate, haplotype-resolved testing of pharmacogenes and genome-wide genotyping.

Main Methods:

• An integrated workflow combining a streamlined laboratory protocol with a specialized bioinformatics pipeline, including a novel CYP2D6 caller.
• Utilized 1,000 ng of DNA with three-sample multiplexing on a PromethION flow cell for targeted and off-target sequencing.
• Validated the assay on 17 reference and clinical samples.

Main Results:

• Achieved consistent on-target (25x) and off-target (3x) coverage, enabling accurate testing of 35 pharmacogenes.
• Demonstrated high concordance for small variants (99.9%) and structural variants (>95%), with phased diplotypes and metabolizer phenotypes reaching 97.7% and 98.0% concordance.
• Off-target reads facilitated accurate genome-wide imputation, outperforming microarrays.

Conclusions:

• TAS-LRS provides a feasible and scalable solution for clinical pharmacogenomics (PGx) testing.
• This long-read sequencing approach combines targeted and genome-wide utility, enhancing accuracy and resolution.
• The developed workflow represents a significant advancement for personalized medicine and drug response prediction.