Requirements for Comprehensive Pharmacogenetic Genotyping Platforms

References

• Spear BB , Heath-ChiozziM , HuffJ . Clinical application of pharmacogenetics . Trends Mol. Med.7 , 201 – 204 ( 2001 ).
   PubMed Web of Science ®Google Scholar
• Harper AR , TopolEJ . Pharmacogenomics in clinical practice and drug development . Nat. Biotechnol.30 , 1117 – 1124 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Sim SC , KacevskaM , Ingelman-SundbergM . Pharmacogenomics of drug-metabolizing enzymes: a recent update on clinical implications and endogenous effects . Pharmacogenomics J.13 , 1 – 11 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Pirmohamed M . Adverse drug reactions as cause of admission to hospital: prospective analysis of 18,820 patients . BMJ329 , 15 – 19 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Davies EC , GreenCF , TaylorSet al. Adverse drug reactions in hospital in-patients: a prospective analysis of 3695 patient-episodes . PLoS ONE4 , e4439 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Gallagher RM , MasonJR , BirdKAet al. Adverse drug reactions causing admission to a paediatric hospital . PLoS ONE7 , e50127 – e50128 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Thiesen S , ConroyEJ , BellisJRet al. Incidence, characteristics and risk factors of adverse drug reactions in hospitalized children – a prospective observational cohort study of 6,601 admissions . BMC medicine11 , 237 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Relling MV , EvansWE . Pharmacogenomics in the clinic . Nature526 , 343 – 350 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Johnson JA , GongL , Whirl-CarrilloMet al. Clinical pharmacogenetics implementation consortium guidelines for CYP2C9 and VKORC1 genotypes and warfarin dosing . Clinical Pharmacol. Ther.90 , 625 – 629 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Crews KR , GaedigkA , DunnenbergerHMet al. Clinical pharmacogenetics implementation consortium guidelines for cytochrome p450 2d6 genotype and codeine therapy: 2014 update . Clin. Pharmacol. Ther.95 , 376 – 382 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Wilke RA , RamseyLB , JohnsonSGet al. The clinical pharmacogenomics implementation consortium: cpic guideline for SLCO1B1 and simvastatin-induced myopathy . Clin. Pharmacol. Ther.92 , 112 – 117 ( 2009 ).
   Google Scholar
• Pratt VM , ZehnbauerB , WilsonJAet al. Characterization of 107 genomic dna reference materials for CYP2D6, CYP2C19, CYP2C9, VKORC1, and UGT1A1 . J. Mol. Diagn.12 , 835 – 846 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• 1000 Genomes Project Consortium . An integrated map of genetic variation from 1,092 human genomes . Nature491 , 56 – 65 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Tennessen JA , BighamAW , O'ConnorTDet al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes . Science337 , 64 – 69 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Nelson MR , WegmannD , EhmMGet al. An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people . Science337 , 100 – 104 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Li Y , VinckenboschN , TianGet al. Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants . Nat. Genetics42 , 969 – 972 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Marth GT , YuF , IndapARet al. The functional spectrum of low-frequency coding variation . Genome Biology12 , R84 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Fujikura K , Ingelman-SundbergM , LauschkeVM . Genetic variation in the human cytochrome P450 supergene family . Pharmacogenet. Genomics25 , 584 – 594 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Gordon AS , TaborHK , JohnsonADet al. Quantifying rare, deleterious variation in 12 human cytochrome P450 drug-metabolism genes in a large-scale exome dataset . Hum. Mol. Genetics23 , 1957 – 1963 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Kozyra M , Ingelman-SundbergM , LauschkeVM . Rare genetic variants in cellular transporters, metabolic enzymes and nuclear receptors can be important determinants of inter-individual differences in drug response . Genet Med. doi:10.1038/gim.2016.33 ( 2016 ) ( Epub ahead of print ).
   PubMed Web of Science ®Google Scholar
• Wetterstrand KA . DNA sequencing costs: data from the NHGRI Genome Sequencing Program (GSP) . www.genome.gov/sequencingcosts .
   Google Scholar
• Sboner A , MuX , GreenbaumD , AuerbachRK , GersteinMB . The real cost of sequencing: higher than you think!Genome Biol.12 , 125 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Rasmussen-Torvik LJ , StallingsSC , GordonASet al. Design and anticipated outcomes of the eMERGE-PGx Project: a multicenter pilot for pre-emptive pharmacogenomics in electronic health record systems . Clin. Pharmacol. Ther.96 , 482 – 489 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Gordon AS , FultonRS , QinXet al. PGRNseq: a targeted capture sequencing panel for pharmacogenetic research and implementation . Pharmacogenet. Genom.26 ( 4 ), 161 – 168 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Bielinski SJ , OlsonJE , PathakJet al. Pre-emptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol . Mayo Clinic Proceedings89 , 25 – 33 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Browning SR , BrowningBL . Haplotype phasing: existing methods and new developments . Nat. Rev. Mol. Cell. Biol.12 , 703 – 714 ( 2011 ).
   Google Scholar
• Rao Y , HoffmannE , ZiaMet al. Duplications and defects in the CYP2A6 gene: identification, genotyping, and in vivo effects on smoking . Mol. Pharmacol.58 , 747 – 755 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• McDonagh EM , WassenaarC , DavidSPet al. PharmGKB summary: very important pharmacogene information for cytochrome P-450, family 2, subfamily A, polypeptide 6 . Pharmacogenet. Genomics22 , 695 – 708 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Gaedigk A . Complexities of CYP2D6 gene analysis and interpretation . Int. Rev. Psychiatry25 , 534 – 553 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Qiao W , YangY , SebraRet al. Long-read single-molecule real-time (SMRT) full gene sequencing of cytochrome P450-2D6 (CYP2D6) . Hum. Mutation , 37 , 315 – 323 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Ammar R , PatonTA , TortiD , ShlienA , BaderGD . Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes . F1000 Research4 , 17 ( 2015 ).
   PubMedGoogle Scholar
• Lauschke VM , Ingelman-SundbergM . Precision medicine and rare genetic variants . Trends Pharmacol. Sci.37 , 85 – 86 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Drysdale CM , McGrawDW , StackCBet al. Complex promoter and coding region beta 2-adrenergic receptor haplotypes alter receptor expression and predict in vivo responsiveness . Proc. Natl Acad. Sci.97 , 10483 – 10488 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Scott SA , MartisS , PeterIet al. Identification of CYP2C19*4B: pharmacogenetic implications for drug metabolism including clopidogrel responsiveness . Pharmacogenom. J.12 , 297 – 305 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Liu M , WatsonLT & ZhangL . Predicting the combined effect of multiple genetic variants . Hum. Genomics9 ( 1 ), 18 ( 2015 ).
   PubMedGoogle Scholar
• Cong L , RanFA , CoxDet al. Multiplex genome engineering using CRISPR/Cas systems . Science339 , 819 – 823 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Kleinstiver BP , PrewMS , TsaiSQet al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities . Nature523 , 481 – 485 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Koike-Yusa H , LiY , TanE-P , Velasco-HerreraMDC , YusaK . Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library . Nat. Biotechnol.32 , 267 – 273 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Zhou Y , ZhuS , CaiCet al. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells . Nature509 , 487 – 491 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Shalem O , SanjanaNE , HartenianEet al. Genome-scale CRISPR–Cas9 knockout screening in human cells . Science343 , 84 – 87 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Wang T , BirsoyK , HughesNWet al. Identification and characterization of essential genes in the human genome . Science350 , 1096 – 1101 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Poste G . Bring on the biomarkers . Nature469 , 156 – 157 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Sanderson S , ZimmernR , KroeseMet al. How can the evaluation of genetic tests be enhanced? Lessons learned from the ACCE framework and evaluating genetic tests in the United Kingdom . Genetics Med.7 , 495 – 500 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Chung W-H , HungSI , HongHSet al. Medical genetics: a marker for Stevens–Johnson syndrome . Nature428 , 486 – 486 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Scott SA . Personalizing medicine with clinical pharmacogenetics . Genetics Med.13 , 987 – 995 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Kalman LV , AgúndezJ , AppellMLet al. Pharmacogenetic allele nomenclature: International Workgroup recommendations for test result reporting . Clin. Pharmacol. Ther.99 , 172 – 185 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Hess GP , FonsecaE , ScottR , FagernessJ . Pharmacogenomic and pharmacogenetic-guided therapy as a tool in precision medicine: current state and factors impacting acceptance by stakeholders . Genetics Res.97 , e13 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• PharmGKB . www.pharmgkb.org/page/cpicTermProject .
   Google Scholar
• Ma JD , LeeKC , KuoGM . Clinical application of pharmacogenomics . J Pharm. Prac.25 , 417 – 427 ( 2012 ).
   PubMedGoogle Scholar
• Cohen J , WilsonA , ManzolilloK . Clinical and economic challenges facing pharmacogenomics . Pharmacogenomics J.13 , 378 – 388 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Kohane IS , MasysDR , AltmanRB . The incidentalome: a threat to genomic medicine . JAMA296 , 212 – 215 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Elias S , AnnasGJ . Generic Consent for Genetic Screening . N. Eng. J. Med.330 , 1611 – 1613 ( 1994 ).
   PubMed Web of Science ®Google Scholar
• Ubiquitous Pharmacogenomics (U-PGx) . http://upgx.eu .
   Google Scholar
• Forbes SA , BeareD , GunasekaranPet al. COSMIC: exploring the world & knowledge of somatic mutations in human cancer . Nucleic Acids Res.43 , D805 – D811 ( 2015 ).
   PubMed Web of Science ®Google Scholar