51
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Sahana S, Sivadas A, Mangla M, Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B, Batra A, Sharma S, Siwach S, Jadhao AG, Palande NV, Jha GN, Ashrafi N, Mishra PK, Vidhya AK, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, Devi P, Rajagopal RE, Ramya JE, Devi PN, Bajaj A, Gupta V, Mathew S, Goswami S, Prakash S, Joshi K, Kumla M, Sreedevi S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, Binukumar BK, Sivasubbu S, Scaria V. Pharmacogenomic landscape of COVID-19 therapies from Indian population genomes. Pharmacogenomics 2021; 22:603-618. [PMID: 34142560 PMCID: PMC8216321 DOI: 10.2217/pgs-2021-0028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Aim: Numerous drugs are being widely prescribed for COVID-19 treatment without any direct evidence for the drug safety/efficacy in patients across diverse ethnic populations. Materials & methods: We analyzed whole genomes of 1029 Indian individuals (IndiGen) to understand the extent of drug–gene (pharmacogenetic), drug–drug and drug–drug–gene interactions associated with COVID-19 therapy in the Indian population. Results: We identified 30 clinically significant pharmacogenetic variants and 73 predicted deleterious pharmacogenetic variants. COVID-19-associated pharmacogenes were substantially overlapped with those of metabolic disorder therapeutics. CYP3A4, ABCB1 and ALB are the most shared pharmacogenes. Fifteen COVID-19 therapeutics were predicted as likely drug–drug interaction candidates when used with four CYP inhibitor drugs. Conclusion: Our findings provide actionable insights for future validation studies and improved clinical decisions for COVID-19 therapy in Indians.
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Affiliation(s)
- S Sahana
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Ambily Sivadas
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Mohit Mangla
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Abhinav Jain
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Kavita Pandhare
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Anushree Mishra
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Disha Sharma
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Mohamed Imran
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vigneshwar Senthivel
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mercy Rophina
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Bani Jolly
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Arushi Batra
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sumit Sharma
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Sanjay Siwach
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Arun G Jadhao
- Department of Zoology, RTM Nagpur University, Nagpur, Maharashtra, 440033, India
| | - Nikhil V Palande
- Department of Zoology, Shri Mathuradas Mohota College of Science, Nagpur, Maharashtra, 440009, India
| | - Ganga Nath Jha
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Nishat Ashrafi
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Prashant Kumar Mishra
- Department of Biotechnology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - A K Vidhya
- Department of Biochemistry, Dr. Kongu Science & Art College, Erode, Tamil Nadu, 638107, India
| | - Suman Jain
- Thalassemia & Sickle cell Society, Hyderabad, Telangana, 500052, India
| | - Debasis Dash
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | | | - Andrew Vanlallawma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Ranjan Jyoti Sarma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | | | | | - Radha Mahadevan
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Sunitha Kandasamy
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Pabitha Devi
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | | | - J Ezhil Ramya
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - P Nirmala Devi
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Anjali Bajaj
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vishu Gupta
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Samatha Mathew
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sangam Goswami
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Savinitha Prakash
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Kandarp Joshi
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Meya Kumla
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - S Sreedevi
- Department of Microbiology, St. Pious X Degree & PG College for Women, Hyderabad, Telangana, 500076, India
| | - Devarshi Gajjar
- Department of Microbiology, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India
| | - Ronibala Soraisham
- Department of Dermatology, Venereology & Leprology, Regional Institute of Medical Sciences, Imphal, Manipur, 795004, India
| | - Rohit Yadav
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Yumnam Silla Devi
- CSIR- North East Institute of Science & Technology, Jorhat, Assam, 785006, India
| | - Aayush Gupta
- Department of Dermatology, Dr. D.Y. Patil Medical College, Pune, Maharashtra, 411018, India
| | - Mitali Mukerji
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sivaprakash Ramalingam
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - B K Binukumar
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
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Pratt VM, Cavallari LH, Del Tredici AL, Gaedigk A, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, van Schaik RHN, Whirl-Carrillo M, Weck KE. Recommendations for Clinical CYP2D6 Genotyping Allele Selection: A Joint Consensus Recommendation of the Association for Molecular Pathology, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, and the European Society for Pharmacogenomics and Personalized Therapy. J Mol Diagn 2021; 23:1047-1064. [PMID: 34118403 DOI: 10.1016/j.jmoldx.2021.05.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/11/2021] [Accepted: 05/25/2021] [Indexed: 01/14/2023] Open
Abstract
The goals of the Association for Molecular Pathology Clinical Practice Committee's Pharmacogenomics (PGx) Working Group are to define the key attributes of pharmacogenetic alleles recommended for clinical testing, and to determine a minimal set of variants that should be included in clinical PGx genotyping assays. This document series provides recommendations on a minimal panel of variant alleles (Tier 1) and an extended panel of variant alleles (Tier 2) that will aid clinical laboratories in designing assays for PGx testing. When developing these recommendations, the Association for Molecular Pathology PGx Working Group considered the functional impact of the variant alleles, allele frequencies in multiethnic populations, the availability of reference materials, as well as other technical considerations with regard to PGx testing. The ultimate goal of this Working Group is to promote standardization of PGx gene/allele testing across clinical laboratories. This document is focused on clinical CYP2D6 PGx testing that may be applied to all cytochrome P450 2D6-metabolized medications. These recommendations are not meant to be interpreted as prescriptive but to provide a reference guide for clinical laboratories that may be either implementing PGx testing or reviewing and updating their existing platform.
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Affiliation(s)
- Victoria M Pratt
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Larisa H Cavallari
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida
| | - Andria L Del Tredici
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Millennium Health, LLC, San Diego, California
| | - Andrea Gaedigk
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Houda Hachad
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; private precision medicine consultancy, Seattle, Washington
| | - Yuan Ji
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Lisa V Kalman
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Reynold C Ly
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ann M Moyer
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stuart A Scott
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Stanford University, Stanford, California; Clinical Genomics Program, Stanford Health Care, Palo Alto, California
| | - R H N van Schaik
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Chemistry/IFCC Expert center Pharmacogenetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands; European Society of Pharmacogenomics and Personalized Therapy
| | - Michelle Whirl-Carrillo
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Biomedical Data Science, Stanford University, Stanford, California
| | - Karen E Weck
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine and Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
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53
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Wendt FR, Koller D, Pathak GA, Jacoby D, Miller EJ, Polimanti R. Biobank Scale Pharmacogenomics Informs the Genetic Underpinnings of Simvastatin Use. Clin Pharmacol Ther 2021; 110:777-785. [PMID: 33837531 DOI: 10.1002/cpt.2260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/01/2021] [Indexed: 12/31/2022]
Abstract
Studying drug-metabolizing enzymes, encoded by pharmacogenes, may inform biological mechanisms underlying the diseases for which a medication is prescribed. Until recently, pharmacogenes could not be studied at biobank scale. In 7,649 unrelated African-ancestry (AFR) and 326,214 unrelated European-ancestry (EUR) participants from the UK Biobank, we associated pharmacogene haplotypes from 50 genes with 265 (EUR) and 17 (AFR) medication use phenotypes using generalized linear models. In EUR, N-acetyltransferase 2 (NAT2) metabolizer phenotype and activity score were associated with simvastatin use. The dose of NAT2*1 was associated with simvastatin use when compared with NAT2*5 (the most common haplotype). This association was robust to effects of low-density lipoprotein cholesterol (LDL-C) concentration (NAT2*1 odds ratio (OR) = 1.07, 95% CI: 1.05-1.09, P = 1.14 × 10-8 ) and polygenic risk for LDL-C concentration (NAT2*1 OR = 1.09, 95% CI: 1.04-1.14, P = 2.26 × 10-4 ). Interactive effects between NAT2*1 and simvastatin use on LDL-C concentration (OR = 0.957, 95% CI: 0.916-0.998, P = 0.045) were replicated in the electronic Medical Records and Genomics Pharmacogenetic Sequencing Pilot (eMERGE-PGx) cohort (OR = 0.987, 95% CI: 0.976-0.998, P = 0.029). We used biobank-scale data to uncover and replicate an association between NAT2 locus variation and better response to statin therapy. Testing NAT2 alleles may be useful for making clinical decisions regarding the potential benefit (e.g., absolute risk reduction) in LDL-C concentration prior to statin treatment.
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Affiliation(s)
- Frank R Wendt
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
| | - Dora Koller
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
| | - Gita A Pathak
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
| | - Daniel Jacoby
- Section of Cardiovascular Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Edward J Miller
- Section of Cardiovascular Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Renato Polimanti
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
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54
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Luo S, Jiang R, Grzymski JJ, Lee W, Lu JT, Washington NL. Comprehensive Allele Genotyping in Critical Pharmacogenes Reduces Residual Clinical Risk in Diverse Populations. Clin Pharmacol Ther 2021; 110:759-767. [PMID: 33930192 PMCID: PMC8453755 DOI: 10.1002/cpt.2279] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022]
Abstract
Genomic‐guided pharmaceutical prescribing is increasingly recognized as an important clinical application of genetics. Accurate genotyping of pharmacogenomic (PGx) genes can be difficult, owing to their complex genetic architecture involving combinations of single‐nucleotide polymorphisms and structural variation. Here, we introduce the Helix PGx database, an open‐source star allele, genotype, and resulting metabolic phenotype frequency database for CYP2C9, CYP2C19, CYP2D6, and CYP4F2, based on short‐read sequencing of >86,000 unrelated individuals enrolled in the Helix DNA Discovery Project. The database is annotated using a pipeline that is clinically validated against a broad range of alleles and designed to call CYP2D6 structural variants with high (98%) accuracy. We find that CYP2D6 has greater allelic diversity than the other genes, manifest in both a long tail of low‐frequency star alleles, as well as a disproportionate fraction (36%) of all novel predicted loss‐of‐function variants identified. Across genes, we observe that many rare alleles (<0.1% frequency) in the overall cohort have 10 times higher frequency in one or more subgroups with non‐European genetic ancestry. Extending these PGx genotypes to predicted metabolic phenotypes, we demonstrate that >90% of the cohort harbors a high‐risk variant in one of the four pharmacogenes. Based on the recorded prescriptions for >30,000 individuals in the Healthy Nevada Project, combined with predicted PGx metabolic phenotypes, we anticipate that standard‐of‐care screening of these 4 pharmacogenes could impact nearly half of the general population.
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Affiliation(s)
| | | | - Joseph J Grzymski
- Desert Research Institute, Reno, Nevada, USA.,Renown Institute of Health Innovation, Reno, Nevada, USA
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55
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PharmaKU: A Web-Based Tool Aimed at Improving Outreach and Clinical Utility of Pharmacogenomics. J Pers Med 2021; 11:jpm11030210. [PMID: 33809530 PMCID: PMC7998233 DOI: 10.3390/jpm11030210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022] Open
Abstract
With the tremendous advancements in genome sequencing technology in the field of pharmacogenomics, data have to be made accessible to be more efficiently utilized by broader clinical disciplines. Physicians who require the drug–genome interactome information, have been challenged by the complicated pharmacogenomic star-based classification system. We present here an end-to-end web-based pharmacogenomics tool, PharmaKU, which has a comprehensive easy-to-use interface. PharmaKU can help to overcome several hurdles posed by previous pharmacogenomics tools, including input in hg38 format only, while hg19/GRCh37 is now the most popular reference genome assembly among clinicians and geneticists, as well as the lack of clinical recommendations and other pertinent dosage-related information. This tool extracts genetic variants from nine well-annotated pharmacogenes (for which diplotype to phenotype information is available) from whole genome variant files and uses Stargazer software to assign diplotypes and apply prescribing recommendations from pharmacogenomic resources. The tool is wrapped with a user-friendly web interface, which allows for choosing hg19 or hg38 as the reference genome version and reports results as a comprehensive PDF document. PharmaKU is anticipated to enable bench to bedside implementation of pharmacogenomics knowledge by bringing precision medicine closer to a clinical reality.
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56
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Desta Z, El-Boraie A, Gong L, Somogyi AA, Lauschke VM, Dandara C, Klein K, Miller NA, Klein TE, Tyndale RF, Whirl-Carrillo M, Gaedigk A. PharmVar GeneFocus: CYP2B6. Clin Pharmacol Ther 2021; 110:82-97. [PMID: 33448339 DOI: 10.1002/cpt.2166] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogs star (*) allele nomenclature for the polymorphic human CYP2B6 gene. Genetic variation within the CYP2B6 gene locus impacts the metabolism or bioactivation of clinically important drugs. Of particular importance are efficacy and safety concerns regarding: efavirenz, which is used for the treatment of HIV type-1 infection; methadone, a mainstay in the treatment of opioid use disorder and as an analgesic; ketamine, used as an antidepressant and analgesic; and bupropion, which is prescribed to treat depression and for smoking cessation. This GeneFocus provides a comprehensive overview and summary of CYP2B6 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
- Zeruesenay Desta
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ahmed El-Boraie
- Centre for Addiction and Mental Health and Departments of Pharmacology & Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Andrew A Somogyi
- Discipline of Pharmacology, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology & Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kathrin Klein
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Neil A Miller
- Genomic Medicine Center, Children's Mercy, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Rachel F Tyndale
- Centre for Addiction and Mental Health and Departments of Pharmacology & Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | | | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
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57
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Twesigomwe D, Drögemöller BI, Wright GEB, Siddiqui A, da Rocha J, Lombard Z, Hazelhurst S. StellarPGx: A Nextflow Pipeline for Calling Star Alleles in Cytochrome P450 Genes. Clin Pharmacol Ther 2021; 110:741-749. [PMID: 33492672 DOI: 10.1002/cpt.2173] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/05/2021] [Indexed: 11/12/2022]
Abstract
Bioinformatics pipelines for calling star alleles (haplotypes) in cytochrome P450 (CYP) genes are important for the implementation of precision medicine. Genotyping CYP genes using high throughput sequencing data is complicated, e.g., by being highly polymorphic, not to mention the structural variations especially in CYP2D6, CYP2A6, and CYP2B6. Genome graph-based variant detection approaches have been shown to be reliable for genotyping HLA alleles. However, their application to enhancing star allele calling in CYP genes has not been extensively explored. We present StellarPGx, a Nextflow pipeline for accurately genotyping CYP genes by combining genome graph-based variant detection, read coverage information from the original reference-based alignments, and combinatorial diplotype assignments. The implementation of StellarPGx using Nextflow facilitates its portability, reproducibility, and scalability on various user platforms. StellarPGx is currently able to genotype 12 important pharmacogenes belonging to the CYP1, 2, and 3 families. For purposes of validation, we use CYP2D6 as a model gene owing to its high degree of polymorphisms (over 130 star alleles defined to date, including complex structural variants) and clinical importance. We applied StellarPGx and three existing callers to 109 whole genome sequenced samples for which the Genetic Testing Reference Material Coordination Program (GeT-RM) has recently provided consensus truth CYP2D6 diplotypes. StellarPGx had the highest CYP2D6 diplotype concordance (99%) with GeT-RM compared with Cyrius (98%), Aldy (82%), and Stargazer (84%). This exemplifies the high accuracy of StellarPGx and highlights its importance for both research and clinical pharmacogenomics applications. The StellarPGx pipeline is open-source and available from https://github.com/SBIMB/StellarPGx.
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Affiliation(s)
- David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Britt I Drögemöller
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Galen E B Wright
- Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Winnipeg Health Sciences Centre and Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Pharmacology and Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Azra Siddiqui
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Jorge da Rocha
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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58
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Botton MR, Whirl-Carrillo M, Del Tredici AL, Sangkuhl K, Cavallari LH, Agúndez JAG, Duconge J, Lee MTM, Woodahl EL, Claudio-Campos K, Daly AK, Klein TE, Pratt VM, Scott SA, Gaedigk A. PharmVar GeneFocus: CYP2C19. Clin Pharmacol Ther 2021; 109:352-366. [PMID: 32602114 PMCID: PMC7769975 DOI: 10.1002/cpt.1973] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/15/2020] [Indexed: 12/17/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C19 gene. CYP2C19 genetic variation impacts the metabolism of many drugs and has been associated with both efficacy and safety issues for several commonly prescribed medications. This GeneFocus provides a comprehensive overview and summary of CYP2C19 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
| | | | | | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - José A G Agúndez
- UNEx, ARADyAL, Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, Cáceres, Spain
| | - Jorge Duconge
- School of Pharmacy, University of Puerto Rico, San Juan, Puerto Rico
| | | | - Erica L Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
| | | | - Ann K Daly
- Newcastle University, Newcastle upon Tyne, UK
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Victoria M Pratt
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy, Kansas City, Missouri, USA
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59
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Taliun D, Harris DN, Kessler MD, Carlson J, Szpiech ZA, Torres R, Taliun SAG, Corvelo A, Gogarten SM, Kang HM, Pitsillides AN, LeFaive J, Lee SB, Tian X, Browning BL, Das S, Emde AK, Clarke WE, Loesch DP, Shetty AC, Blackwell TW, Smith AV, Wong Q, Liu X, Conomos MP, Bobo DM, Aguet F, Albert C, Alonso A, Ardlie KG, Arking DE, Aslibekyan S, Auer PL, Barnard J, Barr RG, Barwick L, Becker LC, Beer RL, Benjamin EJ, Bielak LF, Blangero J, Boehnke M, Bowden DW, Brody JA, Burchard EG, Cade BE, Casella JF, Chalazan B, Chasman DI, Chen YDI, Cho MH, Choi SH, Chung MK, Clish CB, Correa A, Curran JE, Custer B, Darbar D, Daya M, de Andrade M, DeMeo DL, Dutcher SK, Ellinor PT, Emery LS, Eng C, Fatkin D, Fingerlin T, Forer L, Fornage M, Franceschini N, Fuchsberger C, Fullerton SM, Germer S, Gladwin MT, Gottlieb DJ, Guo X, Hall ME, He J, Heard-Costa NL, Heckbert SR, Irvin MR, Johnsen JM, Johnson AD, Kaplan R, Kardia SLR, Kelly T, Kelly S, Kenny EE, Kiel DP, Klemmer R, Konkle BA, Kooperberg C, Köttgen A, Lange LA, Lasky-Su J, Levy D, Lin X, Lin KH, Liu C, Loos RJF, Garman L, Gerszten R, Lubitz SA, Lunetta KL, Mak ACY, Manichaikul A, Manning AK, Mathias RA, McManus DD, McGarvey ST, Meigs JB, Meyers DA, Mikulla JL, Minear MA, Mitchell BD, Mohanty S, Montasser ME, Montgomery C, Morrison AC, Murabito JM, Natale A, Natarajan P, Nelson SC, North KE, O'Connell JR, Palmer ND, Pankratz N, Peloso GM, Peyser PA, Pleiness J, Post WS, Psaty BM, Rao DC, Redline S, Reiner AP, Roden D, Rotter JI, Ruczinski I, Sarnowski C, Schoenherr S, Schwartz DA, Seo JS, Seshadri S, Sheehan VA, Sheu WH, Shoemaker MB, Smith NL, Smith JA, Sotoodehnia N, Stilp AM, Tang W, Taylor KD, Telen M, Thornton TA, Tracy RP, Van Den Berg DJ, Vasan RS, Viaud-Martinez KA, Vrieze S, Weeks DE, Weir BS, Weiss ST, Weng LC, Willer CJ, Zhang Y, Zhao X, Arnett DK, Ashley-Koch AE, Barnes KC, Boerwinkle E, Gabriel S, Gibbs R, Rice KM, Rich SS, Silverman EK, Qasba P, Gan W, Papanicolaou GJ, Nickerson DA, Browning SR, Zody MC, Zöllner S, Wilson JG, Cupples LA, Laurie CC, Jaquish CE, Hernandez RD, O'Connor TD, Abecasis GR. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature 2021; 590:290-299. [PMID: 33568819 PMCID: PMC7875770 DOI: 10.1038/s41586-021-03205-y] [Citation(s) in RCA: 965] [Impact Index Per Article: 321.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 01/07/2021] [Indexed: 02/08/2023]
Abstract
The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases. The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data. The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and Phenotypes)1. In the first 53,831 TOPMed samples, we detected more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome. Additional previously undescribed variants were detected through assembly of unmapped reads and customized analysis in highly variable loci. Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals). These rare variants provide insights into mutational processes and recent human evolutionary history. The extensive catalogue of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and noncoding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and reach of genome-wide association studies to include variants down to a frequency of approximately 0.01%.
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Affiliation(s)
- Daniel Taliun
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Daniel N Harris
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael D Kessler
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jedidiah Carlson
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, USA
| | - Raul Torres
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Sarah A Gagliano Taliun
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | | | | | - Hyun Min Kang
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | | | - Jonathon LeFaive
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Seung-Been Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xiaowen Tian
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Brian L Browning
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Sayantan Das
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | | | | | - Douglas P Loesch
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Thomas W Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Albert V Smith
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Xiaoming Liu
- USF Genomics, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Dean M Bobo
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - François Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin Milwaukee, Milwaukee, WI, USA
| | | | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
- Department of Epidemiology, Columbia University Medical Center, New York, NY, USA
| | | | | | - Rebecca L Beer
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emelia J Benjamin
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Lawrence F Bielak
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Michael Boehnke
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A Brody
- Department of Medicine, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Brian E Cade
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - James F Casella
- Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA
- Division of Pediatric Hematology, Johns Hopkins University, Baltimore, MD, USA
| | - Brandon Chalazan
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Mina K Chung
- Department of Cardiovascular Medicine, Heart & Vascular Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Clary B Clish
- Metabolomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Population Health Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Joanne E Curran
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Dawood Darbar
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Susan K Dutcher
- McDonnell Genome Institute, Washington University, St Louis, MO, USA
- Department of Genetics, Washington University, St Louis, MO, USA
| | - Patrick T Ellinor
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Leslie S Emery
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Diane Fatkin
- Molecular Cardiology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Kensington, New South Wales, Australia
- Cardiology Department, St Vincent's Hospital, Darlinghurst, New South Wales, Australia
| | - Tasha Fingerlin
- National Jewish Health, Center for Genes, Environment and Health, Denver, CO, USA
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Myriam Fornage
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Christian Fuchsberger
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Stephanie M Fullerton
- Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Mark T Gladwin
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel J Gottlieb
- VA Boston Healthcare System, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Michael E Hall
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jiang He
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
- Tulane University Translational Science Institute, Tulane University, New Orleans, LA, USA
| | - Nancy L Heard-Costa
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jill M Johnsen
- Department of Medicine, University of Washington, Seattle, WA, USA
- Bloodworks Northwest Research Institute, Seattle, WA, USA
| | - Andrew D Johnson
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA, USA
| | - Robert Kaplan
- Albert Einstein College of Medicine, New York, NY, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Tanika Kelly
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
| | - Shannon Kelly
- Department of Epidemiology, Vitalant Research Institute, San Francisco, CA, USA
- Department of Pediatrics, UCSF Benioff Children's Hospital, Oakland, CA, USA
- Division of Pediatric Hematology, UCSF Benioff Children's Hospital, Oakland, CA, USA
| | - Eimear E Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Douglas P Kiel
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Robert Klemmer
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Barbara A Konkle
- Department of Medicine, University of Washington, Seattle, WA, USA
- Bloodworks Northwest Research Institute, Seattle, WA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Leslie A Lange
- Department of Medicine, University of Colorado at Denver, Aurora, CO, USA
| | - Jessica Lasky-Su
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Levy
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA, USA
| | - Xihong Lin
- Biostatistics and Statistics, Harvard University, Boston, MA, USA
| | - Keng-Han Lin
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lori Garman
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | | | | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Angel C Y Mak
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Alisa K Manning
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, USA
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David D McManus
- Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Stephen T McGarvey
- International Health Institute, Brown University, Providence, RI, USA
- Department of Epidemiology, Brown University, Providence, RI, USA
- Department of Anthropology, Brown University, Providence, RI, USA
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Harvard Medical School, The Broad Institute of MIT and Harvard, Boston, MA, USA
| | | | - Julie L Mikulla
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mollie A Minear
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Braxton D Mitchell
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Sanghamitra Mohanty
- Texas Cardiac Arrhythmia Institute, St David's Medical Center, Austin, TX, USA
- Department of Internal Medicine, Dell Medical School, Austin, TX, USA
| | - May E Montasser
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Courtney Montgomery
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joanne M Murabito
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Andrea Natale
- Texas Cardiac Arrhythmia Institute, St David's Medical Center, Austin, TX, USA
| | - Pradeep Natarajan
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey R O'Connell
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jacob Pleiness
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Wendy S Post
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Bruce M Psaty
- Department of Medicine, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - D C Rao
- Division of Biostatistics, Washington University in St Louis, St Louis, MO, USA
| | - Susan Redline
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dan Roden
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Chloé Sarnowski
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Sebastian Schoenherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Jeong-Sun Seo
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Macrogen Inc, Seoul, Republic of Korea
- Gong Wu Genomic Medicine Institute, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Sudha Seshadri
- Framingham Heart Study, Framingham, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center at San Antonio, San Antonio, TX, USA
| | - Vivien A Sheehan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Wayne H Sheu
- Taichung Veterans General Hospital Taiwan, Taichung City, Taiwan
| | | | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | | | - Russell P Tracy
- Department of Pathology & Laboratory Medicine, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - David J Van Den Berg
- Center for Genetic Epidemiology, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ramachandran S Vasan
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | | | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Daniel E Weeks
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Scott T Weiss
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | | | - Cristen J Willer
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine-Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Yingze Zhang
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xutong Zhao
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Donna K Arnett
- Department of Epidemiology, University of Kentucky, Lexington, KY, USA
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eric Boerwinkle
- University of Texas Health Science Center at Houston, Houston, TX, USA
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Stacey Gabriel
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Pankaj Qasba
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Weiniu Gan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - George J Papanicolaou
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Northwest Genomics Center, Seattle, WA, USA
- Brotman Baty Institute, Seattle, WA, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Framingham Heart Study, Framingham, MA, USA.
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA.
| | - Cashell E Jaquish
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Gonçalo R Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA.
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Cyrius: accurate CYP2D6 genotyping using whole-genome sequencing data. THE PHARMACOGENOMICS JOURNAL 2021; 21:251-261. [PMID: 33462347 PMCID: PMC7997805 DOI: 10.1038/s41397-020-00205-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/13/2020] [Accepted: 12/04/2020] [Indexed: 12/03/2022]
Abstract
Responsible for the metabolism of ~21% of clinically used drugs, CYP2D6 is a critical component of personalized medicine initiatives. Genotyping CYP2D6 is challenging due to sequence similarity with its pseudogene paralog CYP2D7 and a high number and variety of common structural variants (SVs). Here we describe a novel bioinformatics method, Cyrius, that accurately genotypes CYP2D6 using whole-genome sequencing (WGS) data. We show that Cyrius has superior performance (96.5% concordance with truth genotypes) compared to existing methods (84–86.8%). After implementing the improvements identified from the comparison against the truth data, Cyrius’s accuracy has since been improved to 99.3%. Using Cyrius, we built a haplotype frequency database from 2504 ethnically diverse samples and estimate that SV-containing star alleles are more frequent than previously reported. Cyrius will be an important tool to incorporate pharmacogenomics in WGS-based precision medicine initiatives.
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Tafazoli A, Wawrusiewicz-Kurylonek N, Posmyk R, Miltyk W. Pharmacogenomics, How to Deal with Different Types of Variants in Next Generation Sequencing Data in the Personalized Medicine Area. J Clin Med 2020; 10:jcm10010034. [PMID: 33374421 PMCID: PMC7796098 DOI: 10.3390/jcm10010034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
Pharmacogenomics (PGx) is the knowledge of diverse drug responses and effects in people, based on their genomic profiles. Such information is considered as one of the main directions to reach personalized medicine in future clinical practices. Since the start of applying next generation sequencing (NGS) methods in drug related clinical investigations, many common medicines found their genetic data for the related metabolizing/shipping proteins in the human body. Yet, the employing of technology is accompanied by big obtained data, which most of them have no clear guidelines for consideration in routine treatment decisions for patients. This review article talks about different types of NGS derived PGx variants in clinical studies and try to display the current and newly developed approaches to deal with pharmacogenetic data with/without clear guidelines for considering in clinical settings.
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Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, 15-089 Białystok, Poland;
- Clinical Research Centre, Medical University of Białystok, 15-276 Bialystok, Poland
| | | | - Renata Posmyk
- Department of Clinical Genetics, Medical University of Białystok, 15-089 Białystok, Poland; (N.W.-K.); (R.P.)
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, 15-089 Białystok, Poland;
- Correspondence: ; Tel.: +48-857485845
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Al-Mahayri ZN, Patrinos GP, Wattanapokayakit S, Iemwimangsa N, Fukunaga K, Mushiroda T, Chantratita W, Ali BR. Variation in 100 relevant pharmacogenes among emiratis with insights from understudied populations. Sci Rep 2020; 10:21310. [PMID: 33277594 PMCID: PMC7718919 DOI: 10.1038/s41598-020-78231-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023] Open
Abstract
Genetic variations have an established impact on the pharmacological response. Investigating this variation resulted in a compilation of variants in "pharmacogenes". The emergence of next-generation sequencing facilitated large-scale pharmacogenomic studies and exhibited the extensive variability of pharmacogenes. Some rare and population-specific variants proved to be actionable, suggesting the significance of population pharmacogenomic research. A profound gap exists in the knowledge of pharmacogenomic variants enriched in some populations, including the United Arab Emirates (UAE). The current study aims to explore the landscape of variations in relevant pharmacogenes among healthy Emiratis. Through the resequencing of 100 pharmacogenes for 100 healthy Emiratis, we identified 1243 variants, of which 63% are rare (minor allele frequency ≤ 0.01), and 30% were unique. Filtering the variants according to Pharmacogenomics Knowledge Base (PharmGKB) annotations identified 27 diplotypes and 26 variants with an evident clinical relevance. Comparison with global data illustrated a significant deviation of allele frequencies in the UAE population. Understudied populations display a distinct allelic architecture and various rare and unique variants. We underscored pharmacogenes with the highest variation frequencies and provided investigators with a list of candidate genes for future studies. Population pharmacogenomic studies are imperative during the pursuit of global pharmacogenomics implementation.
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Affiliation(s)
- Zeina N Al-Mahayri
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates
| | - George P Patrinos
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates.,Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, Patras, Greece.,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Sukanya Wattanapokayakit
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Nareenart Iemwimangsa
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Koya Fukunaga
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates. .,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates. .,Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
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63
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McInnes G, Dalton R, Sangkuhl K, Whirl-Carrillo M, Lee SB, Tsao PS, Gaedigk A, Altman RB, Woodahl EL. Transfer learning enables prediction of CYP2D6 haplotype function. PLoS Comput Biol 2020; 16:e1008399. [PMID: 33137098 PMCID: PMC7660895 DOI: 10.1371/journal.pcbi.1008399] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 11/12/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022] Open
Abstract
Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic gene whose protein product metabolizes more than 20% of clinically used drugs. Genetic variations in CYP2D6 are responsible for interindividual heterogeneity in drug response that can lead to drug toxicity and ineffective treatment, making CYP2D6 one of the most important pharmacogenes. Prediction of CYP2D6 phenotype relies on curation of literature-derived functional studies to assign a functional status to CYP2D6 haplotypes. As the number of large-scale sequencing efforts grows, new haplotypes continue to be discovered, and assignment of function is challenging to maintain. To address this challenge, we have trained a convolutional neural network to predict functional status of CYP2D6 haplotypes, called Hubble.2D6. Hubble.2D6 predicts haplotype function from sequence data and was trained using two pre-training steps with a combination of real and simulated data. We find that Hubble.2D6 predicts CYP2D6 haplotype functional status with 88% accuracy in a held-out test set and explains 47.5% of the variance in in vitro functional data among star alleles with unknown function. Hubble.2D6 may be a useful tool for assigning function to haplotypes with uncurated function, and used for screening individuals who are at risk of being poor metabolizers.
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Affiliation(s)
- Gregory McInnes
- Biomedical Informatics Training Program, Stanford University, Stanford, California, United States of America
| | - Rachel Dalton
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, United States of America
- Department of Biomedical and Translational Research, University of Florida, Gainesville, Florida, United States of America
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
| | - Michelle Whirl-Carrillo
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
| | - Seung-been Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Philip S. Tsao
- VA Palo Alto Epidemiology Research and Information Center for Genomics, VAPAHCS, Palo Alto, California, United States of America
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children’s Mercy Kansas City, Kansas City, Missouri, United States of America
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
| | - Russ B. Altman
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
- Departments of Bioengineering, Genetics, and Medicine, Stanford University, Stanford, California, United States of America
| | - Erica L. Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, United States of America
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64
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Taylor C, Crosby I, Yip V, Maguire P, Pirmohamed M, Turner RM. A Review of the Important Role of CYP2D6 in Pharmacogenomics. Genes (Basel) 2020; 11:E1295. [PMID: 33143137 PMCID: PMC7692531 DOI: 10.3390/genes11111295] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/25/2020] [Accepted: 10/28/2020] [Indexed: 12/14/2022] Open
Abstract
Cytochrome P450 2D6 (CYP2D6) is a critical pharmacogene involved in the metabolism of ~20% of commonly used drugs across a broad spectrum of medical disciplines including psychiatry, pain management, oncology and cardiology. Nevertheless, CYP2D6 is highly polymorphic with single-nucleotide polymorphisms, small insertions/deletions and larger structural variants including multiplications, deletions, tandem arrangements, and hybridisations with non-functional CYP2D7 pseudogenes. The frequency of these variants differs across populations, and they significantly influence the drug-metabolising enzymatic function of CYP2D6. Importantly, altered CYP2D6 function has been associated with both adverse drug reactions and reduced drug efficacy, and there is growing recognition of the clinical and economic burdens associated with suboptimal drug utilisation. To date, pharmacogenomic clinical guidelines for at least 48 CYP2D6-substrate drugs have been developed by prominent pharmacogenomics societies, which contain therapeutic recommendations based on CYP2D6-predicted categories of metaboliser phenotype. Novel algorithms to interpret CYP2D6 function from sequencing data that consider structural variants, and machine learning approaches to characterise the functional impact of novel variants, are being developed. However, CYP2D6 genotyping is yet to be implemented broadly into clinical practice, and so further effort and initiatives are required to overcome the implementation challenges and deliver the potential benefits to the bedside.
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Affiliation(s)
- Christopher Taylor
- Wolfson Centre for Personalised Medicine, University of Liverpool, Liverpool L69 3BX, UK; (V.Y.); (M.P.); (R.M.T.)
- MC Diagnostics, St Asaph Business Park, Saint Asaph LL17 0LJ, UK; (I.C.); (P.M.)
| | - Ian Crosby
- MC Diagnostics, St Asaph Business Park, Saint Asaph LL17 0LJ, UK; (I.C.); (P.M.)
| | - Vincent Yip
- Wolfson Centre for Personalised Medicine, University of Liverpool, Liverpool L69 3BX, UK; (V.Y.); (M.P.); (R.M.T.)
| | - Peter Maguire
- MC Diagnostics, St Asaph Business Park, Saint Asaph LL17 0LJ, UK; (I.C.); (P.M.)
| | - Munir Pirmohamed
- Wolfson Centre for Personalised Medicine, University of Liverpool, Liverpool L69 3BX, UK; (V.Y.); (M.P.); (R.M.T.)
| | - Richard M. Turner
- Wolfson Centre for Personalised Medicine, University of Liverpool, Liverpool L69 3BX, UK; (V.Y.); (M.P.); (R.M.T.)
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A systematic comparison of pharmacogene star allele calling bioinformatics algorithms: a focus on CYP2D6 genotyping. NPJ Genom Med 2020; 5:30. [PMID: 32789024 PMCID: PMC7398905 DOI: 10.1038/s41525-020-0135-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/20/2020] [Indexed: 02/07/2023] Open
Abstract
Genetic variation in genes encoding cytochrome P450 enzymes has important clinical implications for drug metabolism. Bioinformatics algorithms for genotyping these highly polymorphic genes using high-throughput sequence data and automating phenotype prediction have recently been developed. The CYP2D6 gene is often used as a model during the validation of these algorithms due to its clinical importance, high polymorphism, and structural variations. However, the validation process is often limited to common star alleles due to scarcity of reference datasets. In addition, there has been no comprehensive benchmark of these algorithms to date. We performed a systematic comparison of three star allele calling algorithms using 4618 simulations as well as 75 whole-genome sequence samples from the GeT-RM project. Overall, we found that Aldy and Astrolabe are better suited to call both common and rare diplotypes compared to Stargazer, which is affected by population structure. Aldy was the best performing algorithm in calling CYP2D6 structural variants followed by Stargazer, whereas Astrolabe had limitations especially in calling hybrid rearrangements. We found that ensemble genotyping, characterised by taking a consensus of genotypes called by all three algorithms, has higher haplotype concordance but it is prone to ambiguities whenever complete discrepancies between the tools arise. Further, we evaluated the effects of sequencing coverage and indel misalignment on genotyping accuracy. Our account of the strengths and limitations of these algorithms is extremely important to clinicians and researchers in the pharmacogenomics and precision medicine communities looking to haplotype CYP2D6 and other pharmacogenes using high-throughput sequencing data.
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Claw KG, Beans JA, Lee SB, Avey JP, Stapleton PA, Scherer SE, El-Boraie A, Tyndale RF, Nickerson DA, Dillard DA, Thummel KE, Robinson RF. Pharmacogenomics of Nicotine Metabolism: Novel CYP2A6 and CYP2B6 Genetic Variation Patterns in Alaska Native and American Indian Populations. Nicotine Tob Res 2020; 22:910-918. [PMID: 31241144 PMCID: PMC7249913 DOI: 10.1093/ntr/ntz105] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/21/2019] [Indexed: 11/12/2022]
Abstract
INTRODUCTION Alaska Native and American Indian (AN/AI) populations have higher tobacco use prevalence than other ethnic/racial groups. Pharmacogenetic testing to tailor tobacco cessation treatment may improve cessation rates. This study characterized polymorphic variations among AN/AI people in genes associated with metabolism of nicotine and drugs used for tobacco cessation. METHODS Recruitment of AN/AI individuals represented six subgroups, five geographic subgroups throughout Alaska and a subgroup comprised of AIs from the lower 48 states living in Alaska. We sequenced the CYP2A6 and CYP2B6 genes to identify known and novel gain, reduced, and loss-of-function alleles, including structural variation (eg, gene deletions, duplications, and hybridizations). RESULTS Variant allele frequencies differed substantially between AN/AI subgroups. The gene deletion CYP2A6*4 and reduced function CYP2A6*9 alleles were found at high frequency in Northern/Western subgroups and in Lower 48/Interior subgroups, respectively. The reduced function CYP2B6*6 allele was observed in all subgroups and a novel, predicted reduced function CYP2B6 variant was found at relatively high frequency in the Southeastern subgroup. CONCLUSIONS Diverse CYP2A6 and CYP2B6 variation among the subgroups highlight the need for comprehensive pharmacogenetic testing to guide tobacco cessation therapy for AN/AI populations. IMPLICATIONS Nicotine metabolism is largely determined by CYP2A6 genotype, and variation in CYP2A6 activity has altered the treatment success in other populations. These findings suggest pharmacogenetic-guided smoking cessation drug treatment could provide benefit to this unique population seeking tobacco cessation therapy.
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Affiliation(s)
- Katrina G Claw
- Department of Pharmaceutics, University of Washington, Seattle, WA
| | - Julie A Beans
- Research Department, Southcentral Foundation, Anchorage, AK
| | - Seung-Been Lee
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Jaedon P Avey
- Research Department, Southcentral Foundation, Anchorage, AK
| | - Patricia A Stapleton
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA
| | - Steven E Scherer
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Ahmed El-Boraie
- Departments of Pharmacology and Toxicology, and Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Rachel F Tyndale
- Departments of Pharmacology and Toxicology, and Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
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CYP2D6 haplotypes with enhancer single-nucleotide polymorphism rs5758550 and rs16947 (*2 allele): implications for CYP2D6 genotyping panels. Pharmacogenet Genomics 2020; 29:39-47. [PMID: 30520769 DOI: 10.1097/fpc.0000000000000363] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
INTRODUCTION CYP2D6 metabolizes ∼25% of all clinically used drugs, with numerous genetic polymorphisms affecting enzyme activity and drug response. Clinical utility of current CYP2D6 genotyping is partially compromised the unresolved complex haplotype structure of the CYP2D6 locus. We have identified a distal enhancer single-nucleotide polymorphism rs5758550 that robustly increases CYP2D6 expression, whereas rs16947 (CYP2D6*2), previously considered inert, reduces correct mRNA splicing and expression, thereby affecting presumed activity of other alleles on the *2 haplotype. OBJECTIVE This study aims to determine the structure and frequency of haplotypes containing either rs5758550 or rs16947, or both, together with other relevant CYP2D6 alleles, assigning predictive enzyme activity scores to each, and addressing ambiguities in estimating diplotypes in different populations. METHODS The structure and frequency of haplotypes containing rs5758550 and/or rs16947 in different populations were determined by using phased genotype data from 'The 1000 Genomes Project'. The assigned haplotype-phenotype relationship was tested by associating assigned CYP2D6 activity score with CYP2D6 enzyme activity in a cohort of 122 human liver microsomes. RESULTS Addition of enhancer single-nucleotide polymorphism rs5758550 and *2 to a CYP2D6 panel improves prediction of CYP2D6 activity. Moreover, the haplotype containing rs5758550 and rs16947 predict extensive CYP2D6 activity more accurately than CYP2D6*2A, a surrogate marker for extensive activity. CONCLUSION With further studies, the results support possible incorporation of rs5758550 and rs16947 into CYP2D6 biomarker panels for more accurate prediction of CYP2D6 metabolizer status.
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68
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Chen X, Sanchis-Juan A, French CE, Connell AJ, Delon I, Kingsbury Z, Chawla A, Halpern AL, Taft RJ, Bentley DR, Butchbach MER, Raymond FL, Eberle MA. Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data. Genet Med 2020; 22:945-953. [PMID: 32066871 PMCID: PMC7200598 DOI: 10.1038/s41436-020-0754-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 11/21/2022] Open
Abstract
Purpose Spinal muscular atrophy (SMA), caused by loss of the SMN1 gene, is a leading cause of early childhood death. Due to the near identical sequences of SMN1 and SMN2, analysis of this region is challenging. Population-wide SMA screening to quantify the SMN1 copy number (CN) is recommended by the American College of Medical Genetics and Genomics. Methods We developed a method that accurately identifies the CN of SMN1 and SMN2 using genome sequencing (GS) data by analyzing read depth and eight informative reference genome differences between SMN1/2. Results We characterized SMN1/2 in 12,747 genomes, identified 1568 samples with SMN1 gains or losses and 6615 samples with SMN2 gains or losses, and calculated a pan-ethnic carrier frequency of 2%, consistent with previous studies. Additionally, 99.8% of our SMN1 and 99.7% of SMN2 CN calls agreed with orthogonal methods, with a recall of 100% for SMA and 97.8% for carriers, and a precision of 100% for both SMA and carriers. Conclusion This SMN copy-number caller can be used to identify both carrier and affected status of SMA, enabling SMA testing to be offered as a comprehensive test in neonatal care and an accurate carrier screening tool in GS sequencing projects.
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Affiliation(s)
| | - Alba Sanchis-Juan
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK.,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Courtney E French
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Andrew J Connell
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Isabelle Delon
- East Midlands and East of England NHS Genomic Laboratory Hub, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | | | | | | | - Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA.,Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA.,Department of Pediatrics, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - F Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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Nofziger C, Turner AJ, Sangkuhl K, Whirl-Carrillo M, Agúndez JAG, Black JL, Dunnenberger HM, Ruano G, Kennedy MA, Phillips MS, Hachad H, Klein TE, Gaedigk A. PharmVar GeneFocus: CYP2D6. Clin Pharmacol Ther 2020; 107:154-170. [PMID: 31544239 PMCID: PMC6925641 DOI: 10.1002/cpt.1643] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 08/29/2019] [Indexed: 01/13/2023]
Abstract
The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus. CYP2D6 genetic variation impacts the metabolism of numerous drugs and, thus, can impact drug efficacy and safety. This GeneFocus provides a comprehensive overview and summary of CYP2D6 genetic variation and describes how the information provided by PharmVar is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
| | - Amy J. Turner
- Department of Pediatrics, Section of Genomic Pediatrics and Children’s Research Institute, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- RPRD Diagnostics LLC, Wauwatosa, Wisconsin, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | | | - José A. G. Agúndez
- University Institute of Molecular Pathology Biomarkers, UEx, Cáceres; ARADyAL Instituto de Salud Carlos III. Spain
| | - John L. Black
- Personalized Genomics Laboratory, Division of Laboratory Genetics and Genomics, Mayo Clinic laboratories, Mayo Clinic, Rochester MN (200 1st Street SW, Rochester MN 55902)
| | - Henry M. Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanton, IL, USA
| | - Gualberto Ruano
- Institute of Living at Hartford Hospital, Genomas Laboratory of Personalized Health, Hartford, Connecticut (67 Jefferson Street, Hartford, Connecticut 06106)
| | - Martin A. Kennedy
- Department of Pathology and Biomedical Science, University Otago, Christchurch, New Zealand
| | - Michael S. Phillips
- Sequence Bioinformatics Inc., 139 Water Street, 2 Floor, St. John’s NL, A1C 1B2, Canada
| | | | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children’s Mercy Kansas City, Kansas City and School of Medicine, University of Missouri-Kansas City, Kansas City, MO, USA
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70
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van der Lee M, Allard WG, Bollen S, Santen GWE, Ruivenkamp CAL, Hoffer MJV, Kriek M, Guchelaar HJ, Anvar SY, Swen JJ. Repurposing of Diagnostic Whole Exome Sequencing Data of 1,583 Individuals for Clinical Pharmacogenetics. Clin Pharmacol Ther 2019; 107:617-627. [PMID: 31594036 PMCID: PMC7027978 DOI: 10.1002/cpt.1665] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/12/2019] [Indexed: 12/14/2022]
Abstract
For ~ 80 drugs, widely recognized pharmacogenetics dosing guidelines are available. However, the use of these guidelines in clinical practice remains limited as only a fraction of patients is subjected to pharmacogenetic screening. We investigated the feasibility of repurposing whole exome sequencing (WES) data for a panel of 42 variants in 11 pharmacogenes to provide a pharmacogenomic profile. Existing diagnostic WES‐data from child‐parent trios totaling 1,583 individuals were used. Results were successfully extracted for 39 variants. No information could be extracted for three variants, located in CYP2C19, UGT1A1, and CYP3A5, and for CYP2D6 copy number. At least one actionable phenotype was present in 86% of the individuals. Haplotype phasing proved relevant for CYP2B6 assignments as 1.5% of the phenotypes were corrected after phasing. In conclusion, repurposing WES‐data can yield meaningful pharmacogenetic profiles for 7 of 11 important pharmacogenes, which can be used to guide drug treatment.
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Affiliation(s)
- Maaike van der Lee
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands.,Leiden Network for Personalized Therapeutics, Leiden, The Netherlands
| | - William G Allard
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sander Bollen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Kriek
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands.,Leiden Network for Personalized Therapeutics, Leiden, The Netherlands
| | - Seyed Y Anvar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands.,Leiden Network for Personalized Therapeutics, Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jesse J Swen
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands.,Leiden Network for Personalized Therapeutics, Leiden, The Netherlands
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71
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Giri J, Moyer AM, Bielinski SJ, Caraballo PJ. Concepts Driving Pharmacogenomics Implementation Into Everyday Healthcare. Pharmgenomics Pers Med 2019; 12:305-318. [PMID: 31802928 PMCID: PMC6826176 DOI: 10.2147/pgpm.s193185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
Abstract
Pharmacogenomics (PGx) is often promoted as the domain of precision medicine with the greatest potential to readily impact everyday healthcare. Rapid advances in PGx knowledge derived from extensive basic and clinical research along with decreasing costs of laboratory testing have led to an increased interest in PGx and expectations of imminent clinical translation with substantial clinical impact. However, the implementation of PGx into clinical workflows is neither simple nor straightforward, and comprehensive processes and multidisciplinary collaboration are required. Several national and international institutions have pioneered models for implementing clinical PGx, and these initial models have led to a better understanding of unresolved challenges. In this review, we have categorized and explored the most relevant of these challenges to highlight potential gaps and present possible solutions. We describe the ongoing need for basic and clinical research to drive further developments in evidence-based medicine. Integration into daily clinical workflows introduces new challenges requiring innovative solutions; specifically those related to the electronic health record and embedded clinical decision support. We describe advances in PGx testing and result reporting and describe the critical need for increased standardization in these areas across laboratories. We also explore the complexity of the PGx knowledge required for clinical practice and the need for educational strategies to ensure adequate understanding among members of current and future healthcare teams. Finally, we evaluate knowledge obtained from previous implementation efforts and discuss how to best apply these learnings to future projects. Despite these challenges, the future of precision medicine appears promising due to the rapidity of recent advances in the field and current multidisciplinary efforts to effectively translate PGx to everyday clinical practice.
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Affiliation(s)
- Jyothsna Giri
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Pedro J Caraballo
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
- Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, MN, USA
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72
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Dalton R, Lee SB, Claw KG, Prasad B, Phillips BR, Shen DD, Wong LH, Fade M, McDonald MG, Dunham MJ, Fowler DM, Rettie AE, Schuetz E, Thornton TA, Nickerson DA, Gaedigk A, Thummel KE, Woodahl EL. Interrogation of CYP2D6 Structural Variant Alleles Improves the Correlation Between CYP2D6 Genotype and CYP2D6-Mediated Metabolic Activity. Clin Transl Sci 2019; 13:147-156. [PMID: 31536170 PMCID: PMC6951848 DOI: 10.1111/cts.12695] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/08/2019] [Indexed: 01/03/2023] Open
Abstract
The cytochrome P450 2D6 (CYP2D6) gene locus is challenging to accurately genotype due to numerous single nucleotide variants and complex structural variation. Our goal was to determine whether the CYP2D6 genotype‐phenotype correlation is improved when diplotype assignments incorporate structural variation, identified by the bioinformatics tool Stargazer, with next‐generation sequencing data. Using CYP2D6 activity measured with substrates dextromethorphan and metoprolol, activity score explained 40% and 34% of variability in metabolite formation rates, respectively, when diplotype calls incorporated structural variation, increasing from 36% and 31%, respectively, when diplotypes did not incorporate structural variation. We also investigated whether the revised Clinical Pharmacogenetics Implementation Consortium (CPIC) recommendations for translating genotype to phenotype improve CYP2D6 activity predictions over the current system. Although the revised recommendations do not improve the correlation between activity score and CYP2D6 activity, perhaps because of low frequency of the CYP2D6*10 allele, the correlation with metabolizer phenotype group was significantly improved for both substrates. We also measured the function of seven rare coding variants: one (A449D) exhibited decreased (44%) and another (R474Q) increased (127%) activity compared with reference CYP2D6.1 protein. Allele‐specific analysis found that A449D is part of a novel CYP2D6*4 suballele, CYP2D6*4.028. The novel haplotype containing R474Q was designated CYP2D6*138 by PharmVar; another novel haplotype containing R365H was designated CYP2D6*139. Accuracy of CYP2D6 phenotype prediction is improved when the CYP2D6 gene locus is interrogated using next‐generation sequencing coupled with structural variation analysis. Additionally, revised CPIC genotype to phenotype translation recommendations provides an improvement in assigning CYP2D6 activity.
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Affiliation(s)
- Rachel Dalton
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
| | - Seung-Been Lee
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Katrina G Claw
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Bhagwat Prasad
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Brian R Phillips
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Danny D Shen
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Lai Hong Wong
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Mitch Fade
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Matthew G McDonald
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Maitreya J Dunham
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Douglas M Fowler
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Erin Schuetz
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Deborah A Nickerson
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, & Therapeutic Innovation, Children's Mercy Kansas City and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Erica L Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
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73
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Sangkuhl K, Whirl-Carrillo M, Whaley RM, Woon M, Lavertu A, Altman RB, Carter L, Verma A, Ritchie MD, Klein TE. Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clin Pharmacol Ther 2019; 107:203-210. [PMID: 31306493 PMCID: PMC6977333 DOI: 10.1002/cpt.1568] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 06/11/2019] [Indexed: 11/07/2022]
Abstract
Pharmacogenomics (PGx) decision support and return of results is an active area of precision medicine. One challenge of implementing PGx is extracting genomic variants and assigning haplotypes in order to apply prescribing recommendations and information from the Clinical Pharmacogenetics Implementation Consortium (CPIC), the US Food and Drug Administration (FDA), the Pharmacogenomics Knowledgebase (PharmGKB), etc. Pharmacogenomics Clinical Annotation Tool (PharmCAT) (i) extracts variants specified in guidelines from a genetic data set derived from sequencing or genotyping technologies, (ii) infers haplotypes and diplotypes, and (iii) generates a report containing genotype/diplotype-based annotations and guideline recommendations. We describe PharmCAT and a pilot validation project comparing results for 1000 Genomes Project sequences of Coriell samples with corresponding Genetic Testing Reference Materials Coordination Program (GeT-RM) sample characterization. PharmCAT was highly concordant with the GeT-RM data. PharmCAT is available in GitHub to evaluate, test, and report results back to the community. As precision medicine becomes more prevalent, our ability to consistently, accurately, and clearly define and report PGx annotations and prescribing recommendations is critical.
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Affiliation(s)
- Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Palo Alto, California, USA
| | | | - Ryan M Whaley
- Department of Biomedical Data Science, Stanford University, Palo Alto, California, USA
| | - Mark Woon
- Department of Biomedical Data Science, Stanford University, Palo Alto, California, USA
| | - Adam Lavertu
- Biomedical Informatics Training Program, Stanford University, Palo Alto, California, USA
| | - Russ B Altman
- Departments of Biomedical Data Science, Biomedical Engineering, Genetics and Medicine, Stanford University, Palo Alto, California, USA
| | - Lester Carter
- formerly Department of Genetics, Stanford University, Palo Alto, California, USA
| | - Anurag Verma
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Teri E Klein
- Department of Biomedical Data Science and Biomedical Informatics Research, School of Medicine, Stanford University, Palo Alto, California, USA
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74
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Suzuki O, Dong OM, Howard RM, Wiltshire T. Characterizing the pharmacogenome using molecular inversion probes for targeted next-generation sequencing. Pharmacogenomics 2019; 20:1005-1020. [DOI: 10.2217/pgs-2019-0057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Aim: This study assesses the technical performance and cost of a targeted next-generation sequencing (NGS) multigene pharmacogenetic (PGx) test. Materials & methods: A genetic test was developed for 21 PGx genes using molecular inversion probes to generate library fragments for NGS. Performance of this test was assessed using 53 unique reference control cell lines from the Genetic Testing Reference Materials Coordination Program (GeT-RM). Results: 93.7% of variants were successfully called and the repeatability rate was 99.9%. Reference calls were available for 78.4% of diplotype calls resulting from PGx testing, and concordance for the test was 85.7%. Cost per sample was $32–$56. Conclusion: A targeted NGS assay using molecular inversion probe technology is able to characterize the pharmacogenome efficiently.
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Affiliation(s)
- Oscar Suzuki
- Division of Pharmacotherapy & Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Center for Pharmacogenomics & Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Olivia M Dong
- Division of Pharmacotherapy & Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Center for Pharmacogenomics & Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rachel M Howard
- Division of Pharmacotherapy & Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Center for Pharmacogenomics & Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tim Wiltshire
- Division of Pharmacotherapy & Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Center for Pharmacogenomics & Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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75
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Lee SB, Wheeler MM, Thummel KE, Nickerson DA. Calling Star Alleles With Stargazer in 28 Pharmacogenes With Whole Genome Sequences. Clin Pharmacol Ther 2019; 106:1328-1337. [PMID: 31206625 PMCID: PMC6896231 DOI: 10.1002/cpt.1552] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/30/2019] [Indexed: 02/01/2023]
Abstract
Variation in the enzymatic activity of pharmacogenes is defined by star alleles (haplotypes) comprised of single-nucleotide variants, small insertion-deletions, and large structural variants. We recently developed Stargazer, a next-generation sequencing-based tool to call star alleles for the clinically important CYP2D6 gene. Here, we present the utility of extending Stargazer to call star alleles for 28 pharmacogenes using whole genome sequencing (WGS) data. We applied Stargazer to WGS data from 70 ethnically diverse samples from the Genetic Testing Reference Materials Coordination Program (GeT-RM). These reference samples were extensively characterized by GeT-RM using multiple pharmacogenetic testing assays. In all 28 genes, Stargazer recalled 100% of star alleles (N = 92) present in GeT-RM's consensus genotypes (N = 1,559). Stargazer also detected star alleles not previously reported by GeT-RM, including complex structural variants. Our results demonstrate that combining WGS data and Stargazer enables automated, accurate, and comprehensive genotyping of pharmacogenes in the human genome.
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Affiliation(s)
- Seung-Been Lee
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Marsha M Wheeler
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Kenneth E Thummel
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
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76
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Cavallari LH, Van Driest SL, Prows CA, Bishop JR, Limdi NA, Pratt VM, Ramsey LB, Smith DM, Tuteja S, Duong BQ, Hicks JK, Lee JC, Obeng AO, Beitelshees AL, Bell GC, Blake K, Crona DJ, Dressler L, Gregg RA, Hines LJ, Scott SA, Shelton RC, Weitzel KW, Johnson JA, Peterson JF, Empey PE, Skaar TC. Multi-site investigation of strategies for the clinical implementation of CYP2D6 genotyping to guide drug prescribing. Genet Med 2019; 21:2255-2263. [PMID: 30894703 PMCID: PMC6754805 DOI: 10.1038/s41436-019-0484-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/27/2019] [Indexed: 12/19/2022] Open
Abstract
Purpose: A number of institutions have clinically implemented CYP2D6 genotyping to guide drug prescribing. We compared implementation strategies of early adopters of CYP2D6 testing, barriers faced by both early adopters and institutions in the process of implementing CYP2D6 testing, and approaches taken to overcome these barriers. Methods: We surveyed eight early adopters of CYP2D6 genotyping and eight institutions in the process of adoption. Data were collected on testing approaches, return of results procedures, applications of genotype results, challenges faced, and lessons learned. Results: Among early adopters, CYP2D6 testing was most commonly ordered to assist with opioid and antidepressant prescribing. Key differences among programs included test ordering and genotyping approaches, result reporting, and clinical decision support. However, all sites tested for copy number variation and 9 common variants, and reported results in the medical record. Most sites provided automatic consultation and had designated personnel to assist with genotype-informed therapy recommendations. Primary challenges were related to stakeholder support, CYP2D6 gene complexity, phenotype assignment, and sustainability. Conclusion: There are specific challenges unique to CYP2D6 testing given the complexity of the gene and its relevance to multiple medications. Consensus lessons learned may guide those interested in pursuing similar clinical pharmacogenetic programs.
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Affiliation(s)
- Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA.
| | - Sara L Van Driest
- Departments of Pediatrics and Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cynthia A Prows
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jeffrey R Bishop
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Nita A Limdi
- Department of Neurology and Hugh Kaul Personalized Medicine Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Laura B Ramsey
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - D Max Smith
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - Sony Tuteja
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin Q Duong
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - J Kevin Hicks
- Department of Individualized Cancer Management, Moffitt Cancer Center, Tampa, FL, USA
| | - James C Lee
- Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, USA
| | - Aniwaa Owusu Obeng
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Gillian C Bell
- Personalized Medicine Program, Mission Health, Asheville, NC, USA
| | - Kathryn Blake
- Center for Pharmacogenomics and Translational Research, Nemours Children's Specialty Care, Jacksonville, FL, USA
| | - Daniel J Crona
- Division of Pharmacotherapy and Experimental Therapeutics and Center for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC, USA
| | - Lynn Dressler
- Personalized Medicine Program, Mission Health, Asheville, NC, USA
| | | | - Lindsay J Hines
- Department of Psychology, University of North Dakota, Grand Forks, ND; Sanford Brain and Spine Center and Sanford Imagenetics, Fargo, ND, USA
| | - Stuart A Scott
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY and Sema4, a Mount Sinai venture, Stamford, CT, USA
| | - Richard C Shelton
- Department of Psychiatry, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kristin Wiisanen Weitzel
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - Josh F Peterson
- Departments of Biomedical Informatics and Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip E Empey
- Department of Pharmacy and Therapeutics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Todd C Skaar
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN, USA
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77
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Gaedigk A, Sangkuhl K, Whirl-Carrillo M, Twist GP, Klein TE, Miller NA. The Evolution of PharmVar. Clin Pharmacol Ther 2018; 105:29-32. [PMID: 30536702 PMCID: PMC6312487 DOI: 10.1002/cpt.1275] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/25/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - Greyson P Twist
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA.,Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Neil A Miller
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA.,Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri, USA
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78
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Nofziger C, Paulmichl M. Accurately genotyping CYP2D6: not for the faint of heart. Pharmacogenomics 2018; 19:999-1002. [PMID: 30020016 DOI: 10.2217/pgs-2018-0105] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | - Markus Paulmichl
- Center for Health & Bioresources, Austrian Institute of Technology, Vienna, Austria.,NESMOS Department, University of Rome Sapienza, Rome, Italy
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