Clinically actionable genotypes among 10,000 patients with preemptive pharmacogenomic testing

Since September 2010, more than 10,000 patients have undergone preemptive, panel‐based pharmacogenomic testing through the Vanderbilt Pharmacogenomic Resource for Enhanced Decisions in Care and Treatment program. Analysis of the genetic data from the first 9,589 individuals reveals that the frequency of genetic variants is concordant with published allele frequencies. Based on five currently implemented drug–gene interactions, the multiplexed test identified one or more actionable variants in 91% of the genotyped patients and in 96% of African American patients. Using medication exposure data from electronic medical records, we compared a theoretical “reactive,” prescription‐triggered, serial single‐gene testing strategy with our preemptive, multiplexed genotyping approach. Reactive genotyping would have generated 14,656 genetic tests. These data highlight three advantages of preemptive genotyping: (i) the vast majority of patients carry at least one pharmacogenetic variant; (ii) data are available at the point of care; and (iii) there is a substantial reduction in testing burden compared with a reactive strategy.

[1]  M. Saif Dihydropyrimidine dehydrogenase gene (DPYD) polymorphism among Caucasian and non-Caucasian patients with 5-FU- and capecitabine-related toxicity using full sequencing of DPYD. , 2013, Cancer genomics & proteomics.

[2]  J. Ablin,et al.  Warfarin therapy in a patient homozygous for the CYP2C9 3 allele. , 2002, The Israel Medical Association journal : IMAJ.

[3]  T. Klein,et al.  Clinical Pharmacogenetics Implementation Consortium Guidelines for HLA‐B Genotype and Abacavir Dosing , 2012, Clinical pharmacology and therapeutics.

[4]  T E Klein,et al.  Clinical Pharmacogenetics Implementation Consortium Guidelines for Thiopurine Methyltransferase Genotype and Thiopurine Dosing: 2013 Update , 2013, Clinical pharmacology and therapeutics.

[5]  J. Mega,et al.  Clinical Pharmacogenetics Implementation Consortium Guidelines for CYP2C19 Genotype and Clopidogrel Therapy: 2013 Update , 2013, Clinical pharmacology and therapeutics.

[6]  Melissa A. Basford,et al.  Optimizing Drug Outcomes Through Pharmacogenetics: A Case for Preemptive Genotyping , 2012, Clinical pharmacology and therapeutics.

[7]  T. Meade,et al.  CYP2C9*3 allelic variant and bleeding complications , 1999, The Lancet.

[8]  A. Nafziger,et al.  Evaluation of inhibitory drug interactions during drug development: Genetic polymorphisms must be considered , 2005, Clinical pharmacology and therapeutics.

[9]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[10]  Matthias Griese,et al.  A CFTR potentiator in patients with cystic fibrosis and the G551D mutation. , 2011, The New England journal of medicine.

[11]  Teri E. Klein,et al.  Clinical Pharmacogenetics Implementation Consortium Guidelines for Dihydropyrimidine Dehydrogenase Genotype and Fluoropyrimidine Dosing , 2013, Clinical pharmacology and therapeutics.

[12]  angesichts der Corona-Pandemie,et al.  UPDATE , 1973, The Lancet.

[13]  D. Hospenthal,et al.  Prevalence of glucose-6-phosphate dehydrogenase deficiency in U.S. Army personnel. , 2006, Military medicine.

[14]  Russ B Altman,et al.  PharmGKB summary: very important pharmacogene information for G6PD , 2012, Pharmacogenetics and genomics.

[15]  G. Feldman,et al.  Preconception and prenatal cystic fibrosis carrier screening of African Americans reveals unanticipated frequencies for specific mutations , 2004, Genetics in Medicine.

[16]  Son Doan,et al.  Application of information technology: MedEx: a medication information extraction system for clinical narratives , 2010, J. Am. Medical Informatics Assoc..

[17]  F. Duelm,et al.  Prevalence of glucose-6-phosphate dehydrogenase deficiency in U.S. military , 2007 .

[18]  F. Collins,et al.  A vision for the future of genomics research , 2003, Nature.

[19]  Alex P. Reiner,et al.  Genetic ancestry in lung-function predictions. , 2010, The New England journal of medicine.

[20]  R. Sinha,et al.  UGT1A1 and UGT1A9 functional variants, meat intake, and colon cancer, among Caucasians and African-Americans. , 2008, Mutation research.

[21]  W. Trager,et al.  Genetic association between sensitivity to warfarin and expression of CYP2C9*3. , 1997, Pharmacogenetics.

[22]  L Gong,et al.  The Clinical Pharmacogenomics Implementation Consortium: CPIC Guideline for SLCO1B1 and Simvastatin‐Induced Myopathy , 2012, Clinical pharmacology and therapeutics.

[23]  M. Pencina,et al.  Dosing clopidogrel based on CYP2C19 genotype and the effect on platelet reactivity in patients with stable cardiovascular disease. , 2011, JAMA.

[24]  Jacques Fellay,et al.  Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance , 2009, Nature.

[25]  K. Sangkuhl,et al.  Supplement to: Clinical Pharmacogenetics Implementation Consortium Guideline for CYP2D6 and CYP2C19 Genotypes and Dosing of Tricyclic Antidepressants , 2013 .

[26]  R. Diasio,et al.  Increased Prevalence of Dihydropyrimidine Dehydrogenase Deficiency in African-Americans Compared with Caucasians , 2006, Clinical Cancer Research.

[27]  T E Klein,et al.  Clinical Pharmacogenetics Implementation Consortium (CPIC) Guidelines for Codeine Therapy in the Context of Cytochrome P450 2D6 (CYP2D6) Genotype , 2012, Clinical pharmacology and therapeutics.

[28]  T E Klein,et al.  Clinical Pharmacogenetics Implementation Consortium Guidelines for Thiopurine Methyltransferase Genotype and Thiopurine Dosing , 2011, Clinical pharmacology and therapy.

[29]  K. Sangkuhl,et al.  Clinical Pharmacogenetics Implementation Consortium Guidelines for Cytochrome P450–2C19 (CYP2C19) Genotype and Clopidogrel Therapy , 2011, Clinical pharmacology and therapeutics.

[30]  D. Oh,et al.  Effect of OATP1B1 (SLCO1B1) variant alleles on the pharmacokinetics of pitavastatin in healthy volunteers , 2005, Clinical pharmacology and therapeutics.

[31]  L. Gong,et al.  Clinical Pharmacogenetics Implementation Consortium (CPIC) Guidelines for IFNL3 (IL28B) Genotype and PEG Interferon‐α–Based Regimens , 2014, Clinical pharmacology and therapy.

[32]  H. McLeod,et al.  Characterization of the human dihydropyrimidine dehydrogenase gene. , 1998, Genomics.

[33]  M. Whirl‐Carrillo,et al.  Clinical Pharmacogenetics Implementation Consortium Guidelines for CYP2C9 and VKORC1 Genotypes and Warfarin Dosing , 2011, Clinical pharmacology and therapeutics.

[34]  Xiang Liu,et al.  Association of UGT1A1*28 polymorphisms with irinotecan-induced toxicities in colorectal cancer: a meta-analysis in Caucasians , 2013, The Pharmacogenomics Journal.

[35]  Melissa A. Basford,et al.  Predicting warfarin dosage in European-Americans and African-Americans using DNA samples linked to an electronic health record. , 2012, Pharmacogenomics.

[36]  Caroline A. Lee,et al.  Rosuvastatin pharmacokinetics and pharmacogenetics in white and Asian subjects residing in the same environment , 2005, Clinical pharmacology and therapeutics.

[37]  C. Thorn,et al.  Clinical Pharmacogenetics Implementation Consortium Guidelines for Human Leukocyte Antigen‐B Genotype and Allopurinol Dosing , 2013, Clinical pharmacology and therapeutics.

[38]  J. Kelsoe,et al.  Clinical Pharmacogenetics Implementation Consortium Guidelines for HLA‐B Genotype and Carbamazepine Dosing , 2012, Clinical pharmacology and therapeutics.

[39]  J J Swen,et al.  Clinical Pharmacogenetics Implementation Consortium Guideline for CYP2D6 and CYP2C19 Genotypes and Dosing of Tricyclic Antidepressants , 2013, Clinical pharmacology and therapeutics.

[40]  E. Clayton,et al.  Operational Implementation of Prospective Genotyping for Personalized Medicine: The Design of the Vanderbilt PREDICT Project , 2012, Clinical pharmacology and therapeutics.

[41]  Carol Coupland,et al.  Individualising the risks of statins in men and women in England and Wales: population-based cohort study , 2010, Heart.