Louis-Philippe Lemieux Perreault1,2, Nabil Zaïd1,2,3, Michel Cameron1,2,4, Ian Mongrain1,2, Marie-Pierre Dubé1,2,5. 1. Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, 5000 Belanger Street, Montreal, H1T 1C8, Canada. 2. Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada. 3. Université Mohammed V - Faculté des Sciences, Avenue des Nations Unies, Agdal, Rabat Morocco. 4. BiogeniQ, 4105-G Boulevard Matte, Brossard, J4Y 2P4, Canada. 5. Université de Montréal, Faculty of Medicine, 2900 Boulevard Edouard-Montpetit, Montreal, H3T 1J4, Canada.
Abstract
AIM: We have evaluated the pharmacogenetic content of commercial human genome-wide genotyping arrays, as it is a critical determinant to enabling pharmacogenomic discoveries. METHODS: Using bioinformatics approaches, we assessed 27,811 genetic variants in 3146 genes for their presence in 18 Illumina and 15 Affymetrix genome-wide arrays. RESULTS: The pharmacogenetic content of the arrays varied greatly. The combination of the Affymetrix precision medicine array and PharmacoScan arrays (Affymetrix) had the highest coverage for a set of clinically actionable absorption, distribution, metabolism and excretion (ADME) variants, single nucleotide ADME variants and ADME insertions/deletions, with a physical coverage of 125/130 (96.2%), 9924/24,138 (41.1%) and 2252/3994 (56.4%), respectively. CONCLUSION: The combination of the Affymetrix precision medicine array and PharmacoScan arrays provided both genome-wide and pharmacogene coverage, which is crucial in the discovering of new variants responsible for drug adverse effects. These results will help in the design of pharmacogenomic studies and will enable a critical review of results from past studies.
AIM: We have evaluated the pharmacogenetic content of commercial human genome-wide genotyping arrays, as it is a critical determinant to enabling pharmacogenomic discoveries. METHODS: Using bioinformatics approaches, we assessed 27,811 genetic variants in 3146 genes for their presence in 18 Illumina and 15 Affymetrix genome-wide arrays. RESULTS: The pharmacogenetic content of the arrays varied greatly. The combination of the Affymetrix precision medicine array and PharmacoScan arrays (Affymetrix) had the highest coverage for a set of clinically actionable absorption, distribution, metabolism and excretion (ADME) variants, single nucleotide ADME variants and ADME insertions/deletions, with a physical coverage of 125/130 (96.2%), 9924/24,138 (41.1%) and 2252/3994 (56.4%), respectively. CONCLUSION: The combination of the Affymetrix precision medicine array and PharmacoScan arrays provided both genome-wide and pharmacogene coverage, which is crucial in the discovering of new variants responsible for drug adverse effects. These results will help in the design of pharmacogenomic studies and will enable a critical review of results from past studies.