| Summary: | 碩士 === 國立臺灣大學 === 基因體暨蛋白體醫學研究所 === 107 === Inherited genetic variations of cytochrome P450 (CYP) genes play an important role in drug dosing, responses and efficacy in each individual toward a wide variety of clinically used medications. Moreover, CYP genes show marked interethnic variability with inter-population differences in allele frequency. With the development of next-generation sequencing, pharmacogenomics testing has greatly benefited patients by enabling personalization of medication management, pursuing better efficacy and decreased risk of side effects. Thus, it is important to genotype star alleles and phase ambiguous haplotypes of CYP genes and other major pharmacogenes, and also identify the allele frequencies in Taiwanese population with implications for precision medicine. In this study, we first upgraded National Taiwan University Hospital (NTUH) pharmacogenomics (PGx) testing platform using capture-based target region enrichment followed by next-generation sequencing (NGS), a common methodology based on its low cost, deep depth of coverage, long length of reads than whole genome sequencing. Our updated NTUH PGx panel covers 250 major pharmacogenomics genes including pharmacokinetics genes and pharmacodynamics genes, such as ABCB1, CACNA1S, CFTR, various CYPs, DRYP, EGFR, RYR1, TPMT, UGT1A1 and VKORC1. The above list of genes is compiled from information provided by five important resources, FDA, CPIC, PharmGKB, PGRN, PharmVar. We also set up an NGS analysis pipeline with two genotyping toolkits, Aldy and Stargazer, for genotyping star alleles of major CYP genes from whole genome sequencing data and targeted gene sequencing data. Furthermore, we designed PCR primers for validation of NGS result to distinguish similar star allele CYP2D6*10, *36 and *36+*10, which have higher frequency in Asian. Then we applied NGS analysis pipeline and PCR assays to 78 individuals, including 8 samples from The International HapMap Project and 6 reference materials from The Genome in a Bottle Consortium as technique validations; 30 samples from Taiwan Biobank (TWB) and 33 patients with adverse drug reactions recruited from NTUH. At the same time, we sent 36 samples to commercial service, Agena Bioscience MassARRAY® System using iPLEX ADME CYP2D6 Panel, for validation. As result, we confirmed that the genotypes inferred by Aldy are more accurate than Stargazer. Next, we utilized 554 samples of TWB WGS data for calculating the allele frequency in Taiwanese. In conclusion, we revealed the distribution of allele frequencies of major CYP genes in Taiwanese and provide the information in aid of clinical therapy and academic research in future.
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