Haplotyping pharmacogenes using TLA combined with Illumina or nanopore sequencing

The main aim of this study was to evaluate the effectiveness of Targeted Locus Amplification (TLA) for haplotyping pharmacogenes, using either short-read NGS or Oxford Nanopore sequencing platforms. The study focused on sequencing four pharmacogenes (CYP2D6, CYP2C19, CYP1A2, and BRCA1) to assess how well these technologies can phase variants and generate complete haplotypes. The motivation was to overcome the limitations of current pharmacogenetic genotyping assays, which often fail to provide complete haplotype information and can miss important variant interactions.

Oxford Nanopore sequencing, specifically the MinION device, was used in this study alongside short-read sequencing to compare the performance of both platforms. The TLA technique was combined with sequencing to generate long DNA fragments for haplotyping.

The study found that the nanopore sequencing platform provided better phasing accuracy for complex pharmacogenes like CYP2D6 due to its long-read capabilities, particularly in regions with high sequence homology to pseudogenes like CYP2D7. The results showed that for CYP2D6, nanopore sequencing achieved correct phasing and variant calling, while short-read sequencing struggled with phasing due to shorter reads.