Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network

W. S. Bush, D. R. Crosslin, A. Owusu-Obeng, J. Wallace, B. Almoguera, M. A. Basford, Suzette J Bielinski, D. S. Carrell, J. J. Connolly, D. Crawford, K. F. Doheny, C. J. Gallego, A. S. Gordon, B. Keating, J. Kirby, T. Kitchner, S. Manzi, A. R. Mejia, V. Pan, C. L. PerryJ. F. Peterson, C. A. Prows, J. Ralston, S. A. Scott, A. Scrol, M. Smith, S. C. Stallings, T. Veldhuizen, W. Wolf, S. Volpi, K. Wiley, R. Li, T. Manolio, E. Bottinger, M. H. Brilliant, D. Carey, R. L. Chisholm, C. G. Chute, J. L. Haines, H. Hakonarson, J. B. Harley, I. A. Holm, Iftikhar Jan Kullo, G. P. Jarvik, E. B. Larson, C. A. McCarty, M. S. Williams, J. C. Denny, L. J. Rasmussen-Torvik, D. M. Roden, M. D. Ritchie

Research output: Contribution to journalArticle

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Abstract

Genetic variation can affect drug response in multiple ways, although it remains unclear how rare genetic variants affect drug response. The electronic Medical Records and Genomics (eMERGE) Network, collaborating with the Pharmacogenomics Research Network, began eMERGE-PGx, a targeted sequencing study to assess genetic variation in 82 pharmacogenes critical for implementation of “precision medicine.” The February 2015 eMERGE-PGx data release includes sequence-derived data from ∼5,000 clinical subjects. We present the variant frequency spectrum categorized by variant type, ancestry, and predicted function. We found 95.12% of genes have variants with a scaled Combined Annotation-Dependent Depletion score above 20, and 96.19% of all samples had one or more Clinical Pharmacogenetics Implementation Consortium Level A actionable variants. These data highlight the distribution and scope of genetic variation in relevant pharmacogenes, identifying challenges associated with implementing clinical sequencing for drug treatment at a broader level, underscoring the importance for multifaceted research in the execution of precision medicine.

Original languageEnglish (US)
Pages (from-to)160-169
Number of pages10
JournalClinical Pharmacology and Therapeutics
DOIs
StatePublished - Aug 1 2016

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Electronic Health Records
Genomics
Precision Medicine
Pharmacogenetics
Pharmaceutical Preparations
Research
Genes
Therapeutics

ASJC Scopus subject areas

  • Pharmacology
  • Pharmacology (medical)

Cite this

Bush, W. S., Crosslin, D. R., Owusu-Obeng, A., Wallace, J., Almoguera, B., Basford, M. A., ... Ritchie, M. D. (2016). Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network. Clinical Pharmacology and Therapeutics, 160-169. https://doi.org/10.1002/cpt.350

Genetic variation among 82 pharmacogenes : The PGRNseq data from the eMERGE network. / Bush, W. S.; Crosslin, D. R.; Owusu-Obeng, A.; Wallace, J.; Almoguera, B.; Basford, M. A.; Bielinski, Suzette J; Carrell, D. S.; Connolly, J. J.; Crawford, D.; Doheny, K. F.; Gallego, C. J.; Gordon, A. S.; Keating, B.; Kirby, J.; Kitchner, T.; Manzi, S.; Mejia, A. R.; Pan, V.; Perry, C. L.; Peterson, J. F.; Prows, C. A.; Ralston, J.; Scott, S. A.; Scrol, A.; Smith, M.; Stallings, S. C.; Veldhuizen, T.; Wolf, W.; Volpi, S.; Wiley, K.; Li, R.; Manolio, T.; Bottinger, E.; Brilliant, M. H.; Carey, D.; Chisholm, R. L.; Chute, C. G.; Haines, J. L.; Hakonarson, H.; Harley, J. B.; Holm, I. A.; Kullo, Iftikhar Jan; Jarvik, G. P.; Larson, E. B.; McCarty, C. A.; Williams, M. S.; Denny, J. C.; Rasmussen-Torvik, L. J.; Roden, D. M.; Ritchie, M. D.

In: Clinical Pharmacology and Therapeutics, 01.08.2016, p. 160-169.

Research output: Contribution to journalArticle

Bush, WS, Crosslin, DR, Owusu-Obeng, A, Wallace, J, Almoguera, B, Basford, MA, Bielinski, SJ, Carrell, DS, Connolly, JJ, Crawford, D, Doheny, KF, Gallego, CJ, Gordon, AS, Keating, B, Kirby, J, Kitchner, T, Manzi, S, Mejia, AR, Pan, V, Perry, CL, Peterson, JF, Prows, CA, Ralston, J, Scott, SA, Scrol, A, Smith, M, Stallings, SC, Veldhuizen, T, Wolf, W, Volpi, S, Wiley, K, Li, R, Manolio, T, Bottinger, E, Brilliant, MH, Carey, D, Chisholm, RL, Chute, CG, Haines, JL, Hakonarson, H, Harley, JB, Holm, IA, Kullo, IJ, Jarvik, GP, Larson, EB, McCarty, CA, Williams, MS, Denny, JC, Rasmussen-Torvik, LJ, Roden, DM & Ritchie, MD 2016, 'Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network', Clinical Pharmacology and Therapeutics, pp. 160-169. https://doi.org/10.1002/cpt.350
Bush WS, Crosslin DR, Owusu-Obeng A, Wallace J, Almoguera B, Basford MA et al. Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network. Clinical Pharmacology and Therapeutics. 2016 Aug 1;160-169. https://doi.org/10.1002/cpt.350
Bush, W. S. ; Crosslin, D. R. ; Owusu-Obeng, A. ; Wallace, J. ; Almoguera, B. ; Basford, M. A. ; Bielinski, Suzette J ; Carrell, D. S. ; Connolly, J. J. ; Crawford, D. ; Doheny, K. F. ; Gallego, C. J. ; Gordon, A. S. ; Keating, B. ; Kirby, J. ; Kitchner, T. ; Manzi, S. ; Mejia, A. R. ; Pan, V. ; Perry, C. L. ; Peterson, J. F. ; Prows, C. A. ; Ralston, J. ; Scott, S. A. ; Scrol, A. ; Smith, M. ; Stallings, S. C. ; Veldhuizen, T. ; Wolf, W. ; Volpi, S. ; Wiley, K. ; Li, R. ; Manolio, T. ; Bottinger, E. ; Brilliant, M. H. ; Carey, D. ; Chisholm, R. L. ; Chute, C. G. ; Haines, J. L. ; Hakonarson, H. ; Harley, J. B. ; Holm, I. A. ; Kullo, Iftikhar Jan ; Jarvik, G. P. ; Larson, E. B. ; McCarty, C. A. ; Williams, M. S. ; Denny, J. C. ; Rasmussen-Torvik, L. J. ; Roden, D. M. ; Ritchie, M. D. / Genetic variation among 82 pharmacogenes : The PGRNseq data from the eMERGE network. In: Clinical Pharmacology and Therapeutics. 2016 ; pp. 160-169.
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abstract = "Genetic variation can affect drug response in multiple ways, although it remains unclear how rare genetic variants affect drug response. The electronic Medical Records and Genomics (eMERGE) Network, collaborating with the Pharmacogenomics Research Network, began eMERGE-PGx, a targeted sequencing study to assess genetic variation in 82 pharmacogenes critical for implementation of “precision medicine.” The February 2015 eMERGE-PGx data release includes sequence-derived data from ∼5,000 clinical subjects. We present the variant frequency spectrum categorized by variant type, ancestry, and predicted function. We found 95.12{\%} of genes have variants with a scaled Combined Annotation-Dependent Depletion score above 20, and 96.19{\%} of all samples had one or more Clinical Pharmacogenetics Implementation Consortium Level A actionable variants. These data highlight the distribution and scope of genetic variation in relevant pharmacogenes, identifying challenges associated with implementing clinical sequencing for drug treatment at a broader level, underscoring the importance for multifaceted research in the execution of precision medicine.",
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AU - Bush, W. S.

AU - Crosslin, D. R.

AU - Owusu-Obeng, A.

AU - Wallace, J.

AU - Almoguera, B.

AU - Basford, M. A.

AU - Bielinski, Suzette J

AU - Carrell, D. S.

AU - Connolly, J. J.

AU - Crawford, D.

AU - Doheny, K. F.

AU - Gallego, C. J.

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AU - Kirby, J.

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AU - Manzi, S.

AU - Mejia, A. R.

AU - Pan, V.

AU - Perry, C. L.

AU - Peterson, J. F.

AU - Prows, C. A.

AU - Ralston, J.

AU - Scott, S. A.

AU - Scrol, A.

AU - Smith, M.

AU - Stallings, S. C.

AU - Veldhuizen, T.

AU - Wolf, W.

AU - Volpi, S.

AU - Wiley, K.

AU - Li, R.

AU - Manolio, T.

AU - Bottinger, E.

AU - Brilliant, M. H.

AU - Carey, D.

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AU - Jarvik, G. P.

AU - Larson, E. B.

AU - McCarty, C. A.

AU - Williams, M. S.

AU - Denny, J. C.

AU - Rasmussen-Torvik, L. J.

AU - Roden, D. M.

AU - Ritchie, M. D.

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