Nanopore sequencing of the pharmacogene CYP2D6 allows simultaneous haplotyping and detection of duplications

The main aim of this study was to explore the application of Oxford Nanopore sequencing technology to analyse the CYP2D6 gene, which plays a key role in drug metabolism. The researchers sought to overcome challenges associated with accurately genotyping CYP2D6, particularly in detecting gene duplications and phasing variants to determine haplotypes. CYP2D6 genotyping is complicated by the presence of similar pseudogenes like CYP2D7, and structural variations such as gene duplications and deletions.

Oxford Nanopore’s GridION sequencer was employed to sequence 32 samples, using long PCR amplicons that spanned the entire CYP2D6 gene. Providing long reads, this sequencing method allowed the researchers to phase variants and identify structural variations like gene duplications, without interference from the homologous CYP2D7 pseudogene.

The major findings demonstrated that nanopore sequencing enabled the accurate haplotyping of 52 CYP2D6 alleles, including 12 novel or newly identified subvariants. The study also successfully identified gene duplications in multiple samples by detecting a skewed allele ratio, confirming that nanopore sequencing can simultaneously provide haplotype information and detect structural variations. This work highlights the potential of nanopore sequencing for comprehensive CYP2D6 genotyping, including the detection of both sequence and structural variants, which can impact drug response and therapy personalisation.