Targeted haplotyping in pharmacogenomics using Oxford Nanopore Technologies' adaptive sampling

Area of Science:

• Genomics and Bioinformatics
• Clinical Pharmacology
• Molecular Diagnostics

Background:

• Pharmacogenomics (PGx) links genetic variations to drug responses for personalized dosing.
• Current PGx platforms (microarray, PCR, short-read sequencing) have limitations in identifying structural variants and phasing haplotypes for star-allele assignment.
• Accurate star-allele assignment is crucial for precise PGx interpretation.

Purpose of the Study:

• To evaluate Oxford Nanopore Technologies' adaptive sampling for targeted PGx gene enrichment.
• To assess the accuracy of variant and star-allele calling using nanopore sequencing in PGx.
• To determine the feasibility of multiplexing samples for increased throughput in clinical PGx settings.

Main Methods:

• Enrichment of 1,036 pharmacogenomically relevant genes using adaptive sampling on Oxford Nanopore Technologies platform.
• Variant and star-allele calling on five Genome in a Bottle reference samples.
• Evaluation of performance with multiplexed samples on a PromethION flow cell.

Main Results:

• High concordance with existing truth sets for variant and star-allele calling.
• Achieved 99.35% recall and 99.84% precision for targeted variants.
• Demonstrated multiplexing of up to three samples without significant performance degradation.

Conclusions:

• Nanopore sequencing with adaptive sampling is accurate for PGx variant and star-allele identification.
• This method overcomes limitations of current platforms, enabling detection of structural variants and unambiguous phasing.
• The approach is suitable for clinical PGx applications, advancing personalized medicine.