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, S. 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, I. J. Kullo, G. P. Jarvik, E. B. Larson, C. A. McCarty, M. S. Williams, J. C. Denny, L. J. Rasmussen-Torvik, D. M. Roden

Research output: Contribution to journalArticlepeer-review

86 Scopus citations

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

Bibliographical note

Funding Information:
The eMERGE Network was initiated and funded by NHGRI through the following grants: U01HG006828 (Cincinnati Children's Hospital Medical Center/Boston Children's Hospital); U01HG006830 (Children's Hospital of Philadelphia); U01HG006389 (Essential Institute of Rural Health, Marshfield Clinic Research Foundation and Pennsylvania State University); U01HG006382 (Geisinger Clinic); U01HG006375 (Group Health Cooperative/University of Washington); U01HG006379 (Mayo Clinic); U01HG006380 (Icahn School of Medicine at Mount Sinai); U01HG006388 (Northwestern University); U01HG006378 (Vanderbilt University Medical Center); and U01HG006385 (Vanderbilt University Medical Center serving as the Coordinating Center). The PGRNSeq dataset (eMERGE PGx), please also add U01HG004438 (CIDR) serving as a Sequencing Center. This work was also supported in part by the Mayo Clinic Center for Individualized Medicine, National Institutes of Health grants U19 GM61388 (the Pharmacogenomics Research Network), R01 GM28157, U01 HG005137, R01 CA138461, and R01 AG034676 (the Rochester Epidemiology Project).

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