Assessment of a pharmacogenomic marker panel in a polypharmacy population identified from electronic medical records

• Published in: Pharmacogenomics Vol. 14; no. 7; pp. 735 - 744
• Main Authors: Oetjens, Matthew T, Denny, Joshua C, Ritchie, Marylyn D, Gillani, Niloufar B, Richardson, Danielle M, Restrepo, Nicole A, Pulley, Jill M, Dilks, Holli H, Basford, Melissa A, Bowton, Erica, Masys, Dan R, Wilke, Russell A, Roden, Dan M, Crawford, Dana C
• Format: Journal Article
• Language: English
• Published: England Future Medicine Ltd 01.05.2013
• Subjects: ADME; Adult; Aged; Aged, 80 and over; Analysis; biorepository; BioVU; CYP2D6 protein; Cytochrome P-450; Cytochrome P-450 CYP2D6 - genetics; DNA Copy Number Variations; Electronic Health Records; European Continental Ancestry Group - genetics; Female; Gene Frequency; Genetic Markers - genetics; Genome-Wide Association Study - methods; Genotype; genotyping; Humans; Illumina; Male; medicine rare variants; Middle Aged; personalized medicine; Pharmacogenetics; Physiological aspects; Polymorphism, Single Nucleotide; Polypharmacy; Population genetics; precision; Young Adult; United States
• ISSN: 1462-2416; 1744-8042
• DOI: 10.2217/pgs.13.64

The ADME Core Panel assays 184 variants across 34 pharmacogenes, many of which are difficult to accurately genotype with standard multiplexing methods. We genotyped 326 frequently medicated individuals of European descent in Vanderbilt s biorepository linked to de-identified electronic medical records, BioVU, on the ADME Core Panel to assess quality and performance of the assay. We compared quality control metrics and determined the extent of direct and indirect marker overlap between the ADME Core Panel and the Illumina Omni1-Quad. We found the quality of the ADME Core Panel data to be high, with exceptions in select copy number variants and markers in certain genes (notably ). Most of the common variants on the ADME panel are genotyped by the Omni1, but absent rare variants and copy number variants could not be accurately tagged by single markers. Our frequently medicated study population did not convincingly differ in allele frequency from reference populations, suggesting that heterogeneous clinical samples (with respect to medications) have similar allele frequency distributions in pharmacogenetics genes compared with reference populations. Original submitted 25 October 2012; Revision submitted 20 March 2013