Approach for phased sequence-based genotyping of the critical pharmacogene dihydropyrimidine dehydrogenase (DPYD)

The study aimed to develop a cost-efficient long-read sequencing method to genotype the DPYD gene, focusing on producing phased genotypes to better understand fluoropyrimidine treatment outcomes. This research addresses a critical issue in cancer treatment where current genotyping methods can detect risk variants but cannot determine the phase, or the cis/trans configuration, when multiple variants are present. The phase is important because different configurations can lead to varying levels of toxicity risk, which influences dosing recommendations.

For the sequencing, the researchers used the Oxford Nanopore Technologies (ONT) platform to sequence the full coding region of the DPYD gene. This sequencing method produced long reads that allowed for the accurate phasing of DPYD variants, overcoming the limitations of conventional genotyping methods that are unable to detect phase information.

The major findings demonstrated that this nanopore-based method could reliably phase DPYD variants, detecting 11 additional heterozygous genotypes that standard methods missed. The phased genotyping results were shown to be critical for determining appropriate dosing of fluoropyrimidine-based therapies, as individuals with multiple DPYD variants in a trans configuration face higher toxicity risks than those with variants in cis. This study highlights the importance of phased sequencing in guiding safer and more effective chemotherapy treatments.