Genotypic and phenotypic landscapes of 51 pharmacogenes derived from whole-genome sequencing in a Thai population.

Tytuł:: Genotypic and phenotypic landscapes of 51 pharmacogenes derived from whole-genome sequencing in a Thai population.
Autorzy:: Wankaew N; Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand.
Chariyavilaskul P; Clinical Pharmacokinetics and Pharmacogenomics Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.; Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
Chamnanphon M; Clinical Pharmacokinetics and Pharmacogenomics Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.; Department of Pathology, Faculty of Medicine, Srinakharinwirot University, Nakornnayok, Thailand.
Assawapitaksakul A; Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.
Chetruengchai W; Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.
Pongpanich M; Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.; Age-related Inflammation and Degeneration Research Unit, Chulalongkorn University, Bangkok, Thailand.
Shotelersuk V; Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.
Źródło:: PloS one [PLoS One] 2022 Feb 17; Vol. 17 (2), pp. e0263621. Date of Electronic Publication: 2022 Feb 17 (Print Publication: 2022).
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
Język:: English
Imprint Name(s):: Original Publication: San Francisco, CA : Public Library of Science
MeSH Terms:: Genetic Association Studies*
Genetic Markers*
Polymorphism, Single Nucleotide*
Asian People/*genetics
High-Throughput Nucleotide Sequencing/*methods
Pharmacogenetics/*methods
Whole Genome Sequencing/*methods
Female ; Gene Frequency ; Healthy Volunteers ; Humans ; Male ; Thailand
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Substance Nomenclature:: 0 (Genetic Markers)
Entry Date(s):: Date Created: 20220217 Date Completed: 20220228 Latest Revision: 20221207
Update Code:: 20240105
PubMed Central ID:: PMC8853512
DOI:: 10.1371/journal.pone.0263621
PMID:: 35176049
: Czasopismo naukowe

Pełny tekst

Differences in drug responses in individuals are partly due to genetic variations in pharmacogenes, which differ among populations. Here, genome sequencing of 171 unrelated Thai individuals from all regions of Thailand was used to call star alleles of 51 pharmacogenes by Stargazer, determine allele and genotype frequencies, predict phenotype and compare high-impact variant frequencies between Thai and other populations. Three control genes, EGFR, VDR, and RYR1, were used, giving consistent results. Every individual had at least three genes with variant or altered phenotype. Forty of the 51 pharmacogenes had at least one individual with variant or altered phenotype. Moreover, thirteen genes had at least 25% of individuals with variant or altered phenotype including SLCO1B3 (97.08%), CYP3A5 (88.3%), CYP2C19 (60.82%), CYP2A6 (60.2%), SULT1A1 (56.14%), G6PD (54.39%), CYP4B1 (50.00%), CYP2D6 (48.65%), CYP2F1 (46.41%), NAT2 (40.35%), SLCO2B1 (28.95%), UGT1A1 (28.07%), and SLCO1B1 (26.79%). Allele frequencies of high impact variants from our samples were most similar to East Asian. Remarkably, we identified twenty predicted high impact variants which have not previously been reported. Our results provide information that contributes to the implementation of pharmacogenetic testing in Thailand and other Southeast Asian countries, bringing a step closer to personalized medicine.
Competing Interests: The authors have declared that no competing interests exist.

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