From gene to dose: Long-read sequencing and -allele tools to refine phenotype predictions of CYP2C19

• Published in: Frontiers in pharmacology Vol. 14; p. 1076574
• Main Authors: Graansma, Lonneke J, Zhai, Qinglian, Busscher, Loes, Menafra, Roberta, van den Berg, Redmar R, Kloet, Susan L, van der Lee, Maaike
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 01.03.2023
• Subjects: bioinformatics; CYP2C19; long-read sequencing; personalized medicine; pharmacogenomics; Pharmacology; pharmacogenomics; CYP2C19; long-read sequencing; bioinformatics; personalized medicine
• ISSN: 1663-9812; 1663-9812
• DOI: 10.3389/fphar.2023.1076574

Inter-individual differences in drug response based on genetic variations can lead to drug toxicity and treatment inefficacy. A large part of this variability is caused by genetic variants in pharmacogenes. Unfortunately, the Single Nucleotide Variant arrays currently used in clinical pharmacogenomic (PGx) testing are unable to detect all genetic variability in these genes. Long-read sequencing, on the other hand, has been shown to be able to resolve complex (pharmaco) genes. In this study we aimed to assess the value of long-read sequencing for research and clinical PGx focusing on the important and highly polymorphic gene. With a capture-based long-read sequencing panel we were able to characterize the entire region and assign variants to their allele of origin (phasing), resulting in the identification of 813 unique variants in 37 samples. To assess the clinical utility of this data we have compared the performance of three different *-allele tools (Aldy, PharmCat and PharmaKU) which are specifically designed to assign haplotypes to pharmacogenes based on all input variants. We conclude that long-read sequencing can improve our ability to characterize the locus, help to identify novel haplotypes and that *-allele tools are a useful asset in phenotype prediction. Ultimately, this approach could help to better predict an individual's drug response and improve therapy outcomes. However, the added value in clinical PGx might currently be limited.