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Characterization of pharmacogenomic variants in a Brazilian admixed cohort of elderly individuals based on whole-genome sequencing data

Affiliation
School of Public Health ,University of São Paulo ,São Paulo ,Brazil
Bertholim-Nasciben, Luciana;
Affiliation
Human Genome and Stem Cell Research Center ,University of São Paulo ,São Paulo ,Brazil
Scliar, Marilia O.;
Affiliation
Department of Anthropology ,University of Toronto at Mississauga ,Mississauga ,ON ,Canada
Debortoli, Guilherme;
Affiliation
The Centre for Applied Genomics ,The Hospital for Sick Children ,Toronto ,ON ,Canada
Thiruvahindrapuram, Bhooma;
Affiliation
The Centre for Applied Genomics ,The Hospital for Sick Children ,Toronto ,ON ,Canada
Scherer, Stephen W.;
Affiliation
Medical-Surgical Nursing Department ,School of Nursing ,University of São Paulo ,São Paulo ,Brazil
Duarte, Yeda A. O.;
Affiliation
Human Genome and Stem Cell Research Center ,University of São Paulo ,São Paulo ,Brazil
Zatz, Mayana;
Affiliation
Divisão de Pesquisa Clínica e Desenvolvimento Tecnológico ,Instituto Nacional de Câncer ,Rio de Janeiro ,Brazil
Suarez-Kurtz, Guilherme;
Affiliation
Department of Anthropology ,University of Toronto at Mississauga ,Mississauga ,ON ,Canada
Parra, Esteban J.;
Affiliation
Human Genome and Stem Cell Research Center ,University of São Paulo ,São Paulo ,Brazil
Naslavsky, Michel S.

Introduction: Research in the field of pharmacogenomics (PGx) aims to identify genetic variants that modulate response to drugs, through alterations in their pharmacokinetics (PK) or pharmacodynamics (PD). The distribution of PGx variants differs considerably among populations, and whole-genome sequencing (WGS) plays a major role as a comprehensive approach to detect both common and rare variants. This study evaluated the frequency of PGx markers in the context of the Brazilian population, using data from a population-based admixed cohort from Sao Paulo, Brazil, which includes variants from WGS of 1,171 unrelated, elderly individuals. Methods: The Stargazer tool was used to call star alleles and structural variants (SVs) from 38 pharmacogenes. Clinically relevant variants were investigated, and the predicted drug response phenotype was analyzed in combination with the medication record to assess individuals potentially at high-risk of gene-drug interaction. Results: In total, 352 unique star alleles or haplotypes were observed, of which 255 and 199 had a frequency < 0.05 and < 0.01, respectively. For star alleles with frequency > 5% ( n = 97), decreased, loss-of-function and unknown function accounted for 13.4%, 8.2% and 27.8% of alleles or haplotypes, respectively. Structural variants (SVs) were identified in 35 genes for at least one individual, and occurred with frequencies >5% for CYP2D6, CYP2A6, GSTM1, and UGT2B17. Overall 98.0% of the individuals carried at least one high risk genotype-predicted phenotype in pharmacogenes with PharmGKB level of evidence 1A for drug interaction. The Electronic Health Record (EHR) Priority Result Notation and the cohort medication registry were combined to assess high-risk gene-drug interactions. In general, 42.0% of the cohort used at least one PharmGKB evidence level 1A drug, and 18.9% of individuals who used PharmGKB evidence level 1A drugs had a genotype-predicted phenotype of high-risk gene-drug interaction. Conclusion: This study described the applicability of next-generation sequencing (NGS) techniques for translating PGx variants into clinically relevant phenotypes on a large scale in the Brazilian population and explores the feasibility of systematic adoption of PGx testing in Brazil.

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License Holder: Copyright © 2023 Bertholim-Nasciben, Scliar, Debortoli, Thiruvahindrapuram, Scherer, Duarte, Zatz, Suarez-Kurtz, Parra and Naslavsky.

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