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Personalized Medicine Volume 12, 2015 - Issue 2
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Research Article

Performance of Exome Sequencing for Pharmacogenomics

Eric R Londin1 Department of Pathology, Anatomy & Cellular Biology, Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19146, USACorrespondence[email protected]
View further author information
,
Peter Clark2 Department of Pathology & Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USAView further author information
,
Marialuisa Sponziello3 Department of Internal Medicine & Medical Specialties, University of Rome “Sapienza”, Rome, ItalyView further author information
,
Larry J Kricka4 Department of Pathology & Laboratory Medicine, University of Pennsylvania Medical Center, Philadelphia, PA 19104, USAView further author information
,
Paolo Fortina5 Cancer Genomics Laboratory, Department of Cancer Biology, Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19146, USA;6 Department of Molecular Medicine, University of Rome “Sapienza”, Rome, ItalyView further author information
&
Jason Y Park7 Department of Pathology, University of Texas Southwestern Medical Center & Children’s Medical Center, Dallas, TX 75235, USA;8 Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USAView further author information
Pages 109-115 | Published online: 23 Mar 2015

References

  • Pharmg kb ( 2014 ). The Pharmacogenomics Knowledgebase . www.pharmgkb.org .
  • Carlson CS , ReiderMJ , NickersonDA , EberleMA , KruglyakL . Comment on ‘Discrepancies in dbSNP confirmations rates and allele frequency distributions from varying genotyping error rates and patterns’ . Bioinformatics21 ( 2 ), 141 – 143 ( 2005 ).
  • Daly AK , KingBP . Pharmacogenetics of oral anticoagulants . Pharmacogenetics13 ( 5 ), 247 – 252 ( 2003 ).
  • Amplichip. CYP450 Test ( 2014 ). http://molecular.roche.com/assays/Pages/AmpliChipCYP450Test.aspx .
  • Affymetrix. DMET Plus Solution ( 2014 ). www.affymetrix.com/estore/browse/level_three_category_and_children.jsp?category=35791&categoryIdClicked=35791&expand=true&parent=35923 .
  • Rumble SM , LacrouteP , DalcaAV , FiumeM , SidowA , BrudnoM . SHRiMP: accurate mapping of short color-space reads . PLoS Comput. Biol.5 ( 5 ), e1000386 ( 2009 ).
  • Martin M . Cutadapt removes adapter sequences from high-throughput sequencing reads . EMBnet. journal17 , 10 – 12 ( 2011 ).
  • Li H , HandsakerB , WysokerAet al. The sequence alignment/map format and SAMtools . Bioinformatics25 ( 16 ), 2078 – 2079 ( 2009 ).
  • Burmester JK , SedovaM , ShaperoMH , MansfieldE . DMET microarray technology for pharmacogenomics-based personalized medicine . Methods Mol. Biol.632 , 99 – 124 ( 2010 ).
  • Deeken JF , CormierT , PriceDKet al. A pharmacogenetic study of docetaxel and thalidomide in patients with castration-resistant prostate cancer using the DMET genotyping platform . Pharmacogenomics J.10 ( 3 ), 191 – 199 ( 2010 ).
  • Sissung TM , EnglishBC , VenzonD , FiggWD , DeekenJF . Clinical pharmacology and pharmacogenetics in a genomics era: the DMET platform . Pharmacogenomics11 ( 1 ), 89 – 103 ( 2010 ).
  • Johnson JA , GongL , Whirl-CarrilloMet al. Clinical Pharmacogenetics Implementation Consortium Guidelines for CYP2C9 and VKORC1 genotypes and warfarin dosing . Clin. Pharmacol. Ther.90 ( 4 ), 625 – 629 ( 2011 ).
  • Asan , XuY , JiangHet al. Comprehensive comparison of three commercial human whole-exome capture platforms . Genome Biol.12 ( 9 ), R95 ( 2011 ).
  • Meynert AM , BicknellLS , HurlesME , JacksonAP , TaylorMS . Quantifying single nucleotide variant detection sensitivity in exome sequencing . BMC Bioinformatics14 , 195 ( 2013 ).
  • Yang Y , MuznyDM , ReidJGet al. Clinical whole-exome sequencing for the diagnosis of Mendelian disorders . N. Engl. J. Med.369 ( 16 ), 1502 – 1511 ( 2013 ).
  • NHLBI . Exome Sequencing Project (ESP) ( 2014 ). http://evs.gs.washington.edu/EVS/ .
  • De Gregori M , GarbinG , De GregoriSet al. Genetic variability at COMT but not at OPRM1 and UGT2B7 loci modulates morphine analgesic response in acute postoperative pain . Eur. J. Clin. Pharmacol.69 ( 9 ), 1651 – 1658 ( 2013 ).
  • Agundez JA , Garcia-MartinE , Alonso-NavarroH , Jimenez-JimenezFJ . Anti-Parkinson’s disease drugs and pharmacogenetic considerations . Expert Opin. Drug Metab. Toxicol.9 ( 7 ), 859 – 874 ( 2013 ).
  • Jung JA , LimHS . Association between CYP2D6 genotypes and the clinical outcomes of adjuvant tamoxifen for breast cancer: a meta-analysis . Pharmacogenomics15 ( 1 ), 49 – 60 ( 2014 ).
  • Martinez De Duenas E , Ochoa ArandaE , Blancas Lopez-BarajasIet al. Adjusting the dose of tamoxifen in patients with early breast cancer and CYP2D6 poor metabolizer phenotype . Breast23 ( 4 ), 400 – 406 ( 2014 ).
  • Langaee TY , ZhuHJ , WangXet al. The influence of the CYP2C19*10 allele on clopidogrel activation and CYP2C19*2 genotyping . Pharmacogenet. Genomics24 ( 8 ), 381 – 386 ( 2014 ).
  • Tatarunas V , JankauskieneL , KupstyteNet al. The role of clinical parameters and of CYP2C19 G681 and CYP4F2 G1347A polymorphisms on platelet reactivity during dual antiplatelet therapy . Blood Coagul. Fibrinolysis25 ( 4 ), 369 – 374 ( 2014 ).
  • Canestaro WJ , AustinMA , ThummelKE . Genetic factors affecting statin concentrations and subsequent myopathy: a HuGENet systematic review . Genet. Med.16 ( 11 ), 810 – 819 ( 2014 ).
  • De Keyser CE , PetersBJ , BeckerMLet al. The SLCO1B1 c.521T>C polymorphism is associated with dose decrease or switching during statin therapy in the Rotterdam Study . Pharmacogenet. Genomics24 ( 1 ), 43 – 51 ( 2014 ).
  • Rasmussen-Torvik LJ , StallingsSC , GordonASet al. Design and anticipated outcomes of the eMERGE-PGx project: a multicenter pilot for preemptive pharmacogenomics in electronic health record systems . Clin. Pharmacol. Ther.96 ( 4 ), 482 – 489 ( 2014 ).
  • ENCODE Project Consortium . An integrated encyclopedia of DNA elements in the human genome . Nature489 ( 7414 ), 57 – 74 ( 2012 ).

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