Yusmiati Liau from the University of Otago in New Zealand spoke at London Calling 2019 about “Nanopore sequencing of the CYP2D6 pharmacogene.” Liau explained that pharmacogenetics is used to learn about genes that affect responses to drugs. There is a standard nomenclature for pharmacogenetics. The PHarmVar database was used as an example. The CY2PD6 gene has been used for genotyping efforts with Sanger sequencing. However, its complex structure makes it challenging to interpret. Misgenotyping and, consequently, misphenotyping do occur. The team obtained seven reference samples from Coriell and 26 clinical samples from an adverse drug reaction cohort. The team amplified the region of the CY2PD6 gene and used the LSK-110 kit with PCR expansion. The group had to optimize the target region to obtain coverage of the region for genotyping. The results did suggest false positive variants. The group used Nanopolish and attempted to improve the genotyping. Variants could be phased and detected with this Nanopore method. Importantly, the group detected novel variants and duplicated alleles. One limitation was false negative variants. Overall, accurate detection of variants for multiple samples was achieved with the nanopore sequencing approach the team developed. The team did careful validation and optimization of the process that was helpful to learn about.
