Pharmacogenetic content of commercial genome-wide genotyping arrays

Pharmacogenomics. 2018 Oct;19(15):1159-1167. doi: 10.2217/pgs-2017-0129. Epub 2018 Oct 1.


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.

Keywords: ADME; GWAS; genotyping arrays; linkage disequilibrium; pharmacogenomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Drug-Related Side Effects and Adverse Reactions / genetics
  • Genome, Human / genetics*
  • Genome-Wide Association Study / methods
  • Genotype
  • Humans
  • Oligonucleotide Array Sequence Analysis / methods*
  • Pharmacogenetics / methods*
  • Polymorphism, Single Nucleotide / genetics
  • Precision Medicine / methods