title: Pharmacogenomics: accessing important alleles by imputation from commercial genome-wide SNP arrays.
abstract: Personalized medicine is becoming a medical reality, as important genotype-phenotype relationships are being unraveled. The availability of pharmacogenomic data is a key element of individualized care. In this study, we explored genotype imputation as a means to infer important pharmacogenomic alleles from a regular commercially available genome-wide SNP array. Using these arrays as a starting point can reduce testing costs, increasing access to these pharmacogenomic data and still retain a larger amount of genome-wide information. IMPUTE2 and MaCH-Admix were used to perform genotype imputation with a dense reference panel from 1000 Genomes data. We were able to correctly infer genotypes for the warfarin-related loci VKORC1 and CYP2C9 alleles 2, 3, 5, and 11 and also clopidogrel-related CYP2C19 alleles 2 and 17 for a small sample of Brazilian individuals, as well as for HapMap samples. The success of an imputation approach in admixed samples using publicly available reference panels can encourage further imputation initiatives in those populations.
authors.affiliation: Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil.
authors.forename: R
authors.initials: R
authors.lastname: Liboredo
authors.affiliation: Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil spena@dcc.ufmg.br.
authors.forename: S D J
authors.initials: SD
authors.lastname: Pena
mesh_terms: D000483:Alleles; D001938:Brazil; D019295:Computational Biology; D065729:Cytochrome P-450 CYP2C9 / Q000235:genetics; D030561:Databases, Nucleic Acid; D005260:Female; D056726:Genetic Association Studies; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D008297:Male; D010597:Pharmacogenetics; D020641:Polymorphism, Single Nucleotide; D012984:Software; D064417:Vitamin K Epoxide Reductases / Q000235:genetics
chemical_list: D065729:Cytochrome P-450 CYP2C9; C578523:VKORC1 protein, human; D064417:Vitamin K Epoxide Reductases