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

Matthew T. Oetjens, Joshua C. Denny, Marylyn Deriggi Ritchie, Niloufar B. Gillani, Danielle M. Richardson, Nicole A. Restrepo, Jill M. Pulley, Holli H. Dilks, Melissa A. Basford, Erica Bowton, Dan R. Masys, Russell A. Wilke, Dan M. Roden, Dana C. Crawford

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Background: The ADME Core Panel assays 184 variants across 34 pharmacogenes, many of which are difficult to accurately genotype with standard multiplexing methods. Methods: We genotyped 326 frequently medicated individuals of European descent in Vanderbilts 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. Results: 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 CYP2D6). 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. Conclusion: 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 201.

Original languageEnglish (US)
Pages (from-to)735-744
Number of pages10
JournalPharmacogenomics
Volume14
Issue number7
DOIs
StatePublished - May 1 2013

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Polypharmacy
Electronic Health Records
Pharmacogenetics
Gene Frequency
Population
Cytochrome P-450 CYP2D6
Quality Control
Genes
Genotype

All Science Journal Classification (ASJC) codes

  • Molecular Medicine
  • Genetics
  • Pharmacology

Cite this

Oetjens, M. T., Denny, J. C., Ritchie, M. D., Gillani, N. B., Richardson, D. M., Restrepo, N. A., ... Crawford, D. C. (2013). Assessment of a pharmacogenomic marker panel in a polypharmacy population identified from electronic medical records. Pharmacogenomics, 14(7), 735-744. https://doi.org/10.2217/pgs.13.64
Oetjens, Matthew T. ; Denny, Joshua C. ; Ritchie, Marylyn Deriggi ; 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. / Assessment of a pharmacogenomic marker panel in a polypharmacy population identified from electronic medical records. In: Pharmacogenomics. 2013 ; Vol. 14, No. 7. pp. 735-744.
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Oetjens, MT, Denny, JC, Ritchie, MD, Gillani, NB, Richardson, DM, Restrepo, NA, Pulley, JM, Dilks, HH, Basford, MA, Bowton, E, Masys, DR, Wilke, RA, Roden, DM & Crawford, DC 2013, 'Assessment of a pharmacogenomic marker panel in a polypharmacy population identified from electronic medical records', Pharmacogenomics, vol. 14, no. 7, pp. 735-744. https://doi.org/10.2217/pgs.13.64

Assessment of a pharmacogenomic marker panel in a polypharmacy population identified from electronic medical records. / Oetjens, Matthew T.; Denny, Joshua C.; Ritchie, Marylyn Deriggi; 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.

In: Pharmacogenomics, Vol. 14, No. 7, 01.05.2013, p. 735-744.

Research output: Contribution to journalArticle

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AU - Denny, Joshua C.

AU - Ritchie, Marylyn Deriggi

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AU - Richardson, Danielle M.

AU - Restrepo, Nicole A.

AU - Pulley, Jill M.

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AU - Basford, Melissa A.

AU - Bowton, Erica

AU - Masys, Dan R.

AU - Wilke, Russell A.

AU - Roden, Dan M.

AU - Crawford, Dana C.

PY - 2013/5/1

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N2 - Background: The ADME Core Panel assays 184 variants across 34 pharmacogenes, many of which are difficult to accurately genotype with standard multiplexing methods. Methods: We genotyped 326 frequently medicated individuals of European descent in Vanderbilts 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. Results: 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 CYP2D6). 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. Conclusion: 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 201.

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Oetjens MT, Denny JC, Ritchie MD, Gillani NB, Richardson DM, Restrepo NA et al. Assessment of a pharmacogenomic marker panel in a polypharmacy population identified from electronic medical records. Pharmacogenomics. 2013 May 1;14(7):735-744. https://doi.org/10.2217/pgs.13.64