Psychiatric Level 1A evidence pharmacogenomics in a Brazilian admixed cohort and global populations
Abstract
Purpose: To compare minor allele frequencies (MAFs) of psychiatric drug response variants in a Brazilian admixed cohort with global populations and other Brazilian groups. Methods: PharmGKB MAFs were gathered from publicly available genetic datasets for Brazil and worldwide. Results: Among 146 variants in CYP2D6 and CYP2C19, 41 were present in Brazil, mostly rare (MAF <1%). 11 variants showed significant MAF differences with large effect sizes compared with global populations. CYP2C19*3 (rs4986893), CYP2C19*17 (rs12248560), CYP2D6*17 (rs28371706-A) and CYP2D6*29 (rs61736512) exhibited higher frequencies in Brazil, with the latter three also differing from other Brazilian groups. Conclusion: This study highlights significant pharmacogenomic diversity in Brazil and globally, underscoring the need for more research in personalized psychiatric drug therapy.
References
- 1. Comparative efficacy and acceptability of 21 antidepressant drugs for the acute treatment of adults with major depressive disorder: a systematic review and network meta-analysis. Lancet 391(10128), 1357–1366 (2018).
- 2. . Genes, environment, and individual differences in responding to treatment for depression. Harv. Rev. Psychiatry 19(3), 109–124 (2011).
- 3. . Editorial: from trial and error to individualised pharmacogenomics-based pharmacotherapy in psychiatry. Front. Pharmacol. 12, 725565 (2021).
- 4. . Pharmacogenetics in psychiatric care, a call for uptake of available applications. Psychiatry Res. 292, 113336 (2020).
- 5. . The role of pharmacogenomics in precision psychiatry. Pharmacogenomics 24(10), 523–527 (2023).
- 6. . CPIC: Clinical Pharmacogenetics Implementation Consortium of the Pharmacogenomics Research Network. Clin. Pharmacol. Ther. 89(3), 464–7 (2011).
- 7. . Genomics of disease risk in globally diverse populations. Nat. Rev. Genet. 20(9), 520–535 (2019).
- 8. . Pharmacogenetic differentiation across Latin America. Pharmacogenomics 23(4), 225–233 (2022).
- 9. . Pharmacogenomic implications of population admixture: Brazil as a model case. Pharmacogenomics 15(2), 209–219 (2014).
- 10. . Genetic admixture in Brazil. Am. J. Med. Genet. C Semin. Med. Genet. 184(4), 928–938 (2020).
- 11. . The missing diversity in human genetic studies. Cell 177(1), 26–31 (2019).
- 12. . Genomewide association studies in pharmacogenomics. Clin. Pharmacol. Ther. 110(3), 637 (2021).
- 13. Genetic structure of pharmacogenetic biomarkers in Brazil inferred from a systematic review and population-based cohorts: a RIBEF/EPIGEN-Brazil initiative. Pharmacogenomics J. 18(6), 749–759 (2018).
- 14. Characterization of pharmacogenomic variants in a Brazilian admixed cohort of elderly individuals based on whole-genome sequencing data. Front. Pharmacol. 14, 1178715 (2023).
- 15. . Health equality, race and pharmacogenomics. Br. J. Clin. Pharmacol. 88(1), 27–33 (2022).
- 16. . Evaluation of current regulation and guidelines of pharmacogenomic drug labels: opportunities for improvements. Clin. Pharmacol. Ther. 107(5), 1240–1255 (2020).
- 17. Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil. Nat. Commun. 13(1), 1004 (2022).
- 18. Variant interpretation using population databases: Lessons from gnomAD. Hum. Mutat. 43(8), 1012–1030 (2022).
- 19. . Sample size, power and effect size revisited: simplified and practical approaches in pre-clinical, clinical and laboratory studies. Biochem. Med. (Zagreb) 31(1), 010502 (2021).
- 20. . Understanding the effect size and its measures. Biochem. Med. (Zagreb) 26(2), 150–63 (2016).
- 21. Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines for CYP2C19 and voriconazole therapy. Clin. Pharmacol. Ther. 102(1), 45–51 (2017).
- 22. A review of the important role of CYP2D6 in pharmacogenomics. Genes (Basel) 11(11), 1295 (2020).
- 23. . Sequencing the CYP2D6 gene: from variant allele discovery to clinical pharmacogenetic testing. Pharmacogenomics 18(7), 673–685 (2017).
- 24. . Improving the understanding of genetic variants in rare disease with large-scale reference populations. JAMA 322(13), 1305–1306 (2019).
- 25. Variation in 100 relevant pharmacogenes among emiratis with insights from understudied populations. Sci. Rep. 10(1), 21310 (2020).
- 26. . Actionable pharmacogenetic variation in the Slovenian genomic database. Front. Pharmacol. 10, 240 (2019).
- 27. A population study of clinically actionable genetic variation affecting drug response from the Middle East. NPJ Genom. Med. 7(1), 10 (2022).
- 28. . From pharmacogenetics to pharmaco-omics: milestones and future directions. HGG Adv. 3(2), 100100 (2022).
- 29. An optimized prediction framework to assess the functional impact of pharmacogenetic variants. Pharmacogenomics J. 19(2), 115–126 (2019).
- 30. Exome-wide assessment of the functional impact and pathogenicity of multinucleotide mutations. Genome Res. 29(7), 1047–1056 (2019).
- 31. Prediction of CYP2D6 phenotype from genotype across world populations. Genet. Med. 19(1), 69–76 (2017).
- 32. . Worldwide distribution of cytochrome P450 alleles: a meta-analysis of population-scale sequencing projects. Clin. Pharmacol. Ther. 102(4), 688–700 (2017).
- 33. Characterization of novel CYP2D6 alleles across sub-Saharan African populations. J. Pers. Med. 12(10), 1575 (2022).
- 34. CYP2D6 worldwide genetic variation shows high frequency of altered activity variants and no continental structure. Pharmacogenet. Genomics 17(2), 93–101 (2007).
- 35. . High frequency of CYP2D6 ultrarapid metabolizer genotype in the Finnish population. Basic Clin. Pharmacol. Toxicol. 119(3), 291–296 (2016).
- 36. Recommendations for clinical CYP2D6 genotyping allele selection. J. Molec. Diagn. 23(9), 1047–1064 (2021).
- 37. Recommendations for clinical CYP2C19 genotyping allele selection. J. Molec. Diagn. 20(3), 269–276 (2018).
- 38. . Pharmacogenetic differentiation across Latin America. Pharmacogenomics 23(4), 225–233 (2022).
- 39. Genomic ancestry, CYP2D6, CYP2C9, and CYP2C19 among Latin Americans. Clin. Pharmacol. Ther. 107(1), 257–268 (2020).
- 40. Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for CYP2D6, CYP2C19, CYP2B6, SLC6A4, and HTR2A genotypes and serotonin reuptake inhibitor antidepressants. Clin. Pharmacol. Ther. 114(1), 51–68 (2023).