Cancer pharmacogenomics, challenges in implementation, and patient-focused perspectives

References

• WheelerDAWangLFrom human genome to cancer genome: the first decadeGenome Res20132371054106223817046
   PubMed Web of Science ®Google Scholar
• President Obama’s Precision Medicine Initiative [webpage on the Internet]Washington, DCThe White House2015 Available from: https://www.whitehouse.gov/the-press-office/2015/01/30/fact-sheet-president-obama-s-precision-medicine-initiativeAccessed May 5, 2016
   Google Scholar
• PatelJNApplication of genotype-guided cancer therapy in solid tumorsPharmacogenomics2014151799324329193
   PubMed Web of Science ®Google Scholar
• PatelJNMandockKMcLeodHLClinically relevant cancer biomarkers and pharmacogenetic assaysJ Oncol Pharm Pract2014201657223353710
   PubMed Web of Science ®Google Scholar
• Couzin-FrankelJBreakthrough of the year 2013. Cancer immunotherapyScience201334261651432143324357284
   PubMed Web of Science ®Google Scholar
• WangLMcLeodHLWeinshilboumRMGenomics and drug responseN Engl J Med2011364121144115321428770
   PubMed Web of Science ®Google Scholar
• GillisNKPatelJNInnocentiFClinical implementation of germ line cancer pharmacogenetic variants during the next-generation sequencing eraClin Pharmacol Ther201495326928024136381
   PubMed Web of Science ®Google Scholar
• RedigAJJannePABasket trials and the evolution of clinical trial design in an era of genomic medicineJ Clin Oncol201533997597725667288
   PubMed Web of Science ®Google Scholar
• Biomarkers Definitions Working GroupBiomarkers and surrogate end-points: preferred definitions and conceptual frameworkClin Pharmacol Ther2001693899511240971
   PubMed Web of Science ®Google Scholar
• van ‘t VeerLJDaiHvan de VijverMJGene expression profiling predicts clinical outcome of breast cancerNature2002415687153053611823860
   PubMed Web of Science ®Google Scholar
• HarrisLNIsmailaNMcShaneLMUse of Biomarkers to Guide Decisions on Adjuvant Systemic Therapy for Women With Early-Stage Invasive Breast Cancer: American Society of Clinical Oncology Clinical Practice GuidelineJ Clin Oncol201634101134115026858339
   PubMed Web of Science ®Google Scholar
• TejparSSaridakiZDelorenziMBosmanFRothADMicrosatellite instability, prognosis and drug sensitivity of stage II and III colorectal cancer: more complexity to the puzzleJ Natl Cancer Inst20111031184184421597023
   PubMedGoogle Scholar
• PopatSHubnerRHoulstonRSSystematic review of microsatellite instability and colorectal cancer prognosisJ Clin Oncol200523360961815659508
   PubMed Web of Science ®Google Scholar
• LeDTUramJNWangHPD-1 blockade in tumors with mismatch repair deficiencyJ Clin Oncol201533Suppl abstr LBA100
   Google Scholar
• ChapmanPBHauschildARobertCImproved survival with vemurafenib in melanoma with BRAF V600E mutationN Engl J Med2011364262507251621639808
   PubMed Web of Science ®Google Scholar
• TranBKopetzSTieJImpact of BRAF mutation and microsatellite instability on the pattern of metastatic spread and prognosis in metastatic colorectal cancerCancer2011117204623463221456008
   PubMed Web of Science ®Google Scholar
• KwakELBangYJCamidgeDRAnaplastic lymphoma kinase inhibition in non-small-cell lung cancerN Engl J Med2010363181693170320979469
   PubMed Web of Science ®Google Scholar
• ShawATKimDWNakagawaKCrizotinib versus chemotherapy in advanced ALK-positive lung cancerN Engl J Med2013368252385239423724913
   PubMed Web of Science ®Google Scholar
• KatayamaRShawATKhanTMMechanisms of acquired crizotinib resistance in ALK-rearranged lung CancersSci Transl Med20124120120ra117
   Web of Science ®Google Scholar
• ShawATKimDWMehraRCeritinib in ALK-rearranged non-small-cell lung cancerN Engl J Med2014370131189119724670165
   PubMed Web of Science ®Google Scholar
• ShawATGandhiLGadgeelSAlectinib in ALK-positive, crizotinib-resistant, non-small-cell lung cancer: a single-group, multicentre, phase 2 trialLancet Oncol201617223424226708155
   PubMed Web of Science ®Google Scholar
• SodaMChoiYLEnomotoMIdentification of the transforming EML4-ALK fusion gene in non-small-cell lung cancerNature2007448715356156617625570
   PubMed Web of Science ®Google Scholar
• KingCRKrausMHAaronsonSAAmplification of a novel v-erbB-related gene in a human mammary carcinomaScience198522947179749762992089
   PubMed Web of Science ®Google Scholar
• YardenYShiloBZSnapShot: EGFR signaling pathwayCell20071315101818045542
   PubMed Web of Science ®Google Scholar
• LynchTJBellDWSordellaRActivating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinibN Engl J Med2004350212129213915118073
   PubMed Web of Science ®Google Scholar
• ZhouCWuYLChenGErlotinib versus chemotherapy as first-line treatment for patients with advanced EGFR mutation-positive non-small-cell lung cancer (OPTIMAL, CTONG-0802): a multicentre, open-label, randomised, phase 3 studyLancet Oncol201112873574221783417
   PubMed Web of Science ®Google Scholar
• MillerVAHirshVCadranelJAfatinib versus placebo for patients with advanced, metastatic non-small-cell lung cancer after failure of erlotinib, gefitinib, or both, and one or two lines of chemotherapy (LUX-Lung 1): a phase 2b/3 randomised trialLancet Oncol201213552853822452896
   PubMed Web of Science ®Google Scholar
• SequistLVYangJCYamamotoNPhase III study of afatinib or cisplatin plus pemetrexed in patients with metastatic lung adenocarcinoma with EGFR mutationsJ Clin Oncol201331273327333423816960
   PubMed Web of Science ®Google Scholar
• CalifanoRMorgilloFDe MelloRAMountziosGRole of mesenchymal-epithelial transition amplification in resistance to anti-epidermal growth factor receptor agentsAnn Transl Med2015368125992380
   PubMedGoogle Scholar
• YunCHMengwasserKETomsAVThe T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATPProc Natl Acad Sci U S A200810562070207518227510
   PubMed Web of Science ®Google Scholar
• JannePAYangJCKimDWAZD9291 in EGFR inhibitor-resistant non-small-cell lung cancerN Engl J Med2015372181689169925923549
   PubMed Web of Science ®Google Scholar
• SunCWangLHuangSReversible and adaptive resistance to BRAF(V600E) inhibition in melanomaNature2014508749411812224670642
   PubMed Web of Science ®Google Scholar
• RobertCKaraszewskaBSchachterJImproved overall survival in melanoma with combined dabrafenib and trametinibN Engl J Med20153721303925399551
   PubMed Web of Science ®Google Scholar
• PatelJNFuchsCSOwzarKChenZMcLeodHLGastric cancer pharmacogenetics: progress or old tripe?Pharmacogenomics20131491053106423837480
   PubMed Web of Science ®Google Scholar
• Van KuilenburgABMeinsmaRZoetekouwLVan GennipAHHigh prevalence of the IVS14 + 1G>A mutation in the dihydropyrimidine dehydrogenase gene of patients with severe 5-fluorouracil-associated toxicityPharmacogenetics200212755555812360106
   PubMedGoogle Scholar
• LeeAMShiQPaveyEDPYD variants as predictors of 5- fluorouracil toxicity in adjuvant colon cancer treatment (NCCTG N0147)J Natl Cancer Inst201410612dju29825381393
   PubMedGoogle Scholar
• MeulendijksDHenricksLMSonkeGSClinical relevance of DPYD variants c.1679T>G, c.1236G>A/HapB3, and c.1601G>A as predictors of severe fluoropyrimidine-associated toxicity: a systematic review and meta-analysis of individual patient dataLancet Oncol201516161639165026603945
   PubMed Web of Science ®Google Scholar
• DeenenMJMeulendijksDCatsAUpfront Genotyping of DPYD*2A to Individualize Fluoropyrimidine Therapy: A Safety and Cost AnalysisJ Clin Oncol201634322723426573078
   PubMed Web of Science ®Google Scholar
• CaudleKEThornCFKleinTEClinical Pharmacogenetics Implementation Consortium guidelines for dihydropyrimidine dehydrogenase genotype and fluoropyrimidine dosingClin Pharmacol Ther201394664064523988873
   PubMed Web of Science ®Google Scholar
• MathijssenRHvan AlphenRJVerweijJClinical pharmacokinetics and metabolism of irinotecan (CPT-11)Clin Cancer Res2001782182219411489791
   PubMed Web of Science ®Google Scholar
• InnocentiFRatainMJIrinotecan treatment in cancer patients with UGT1A1 polymorphismsOncology (Williston Park)2003175 Suppl 5525512800608
   PubMedGoogle Scholar
• PatelJNCancer pharmacogenomics: implications on ethnic diversity and drug responsePharmacogenet Genomics201525522323025751395
   PubMed Web of Science ®Google Scholar
• HoskinsJMGoldbergRMQuPIbrahimJGMcLeodHLUGT1A1*28 genotype and irinotecan-induced neutropenia: dose mattersJ Natl Cancer Inst200799171290129517728214
   PubMedGoogle Scholar
• SwenJJNijenhuisMde BoerAPharmacogenetics: from bench to byte – an update of guidelinesClin Pharmacol Ther201189566267321412232
   PubMed Web of Science ®Google Scholar
• ToffoliGCecchinEGaspariniGGenotype-driven phase I study of irinotecan administered in combination with fluorouracil/leucovorin in patients with metastatic colorectal cancerJ Clin Oncol201028586687120038727
   PubMed Web of Science ®Google Scholar
• MarcuelloEPaezDPareLA genotype-directed phase I-IV dose-finding study of irinotecan in combination with fluorouracil/leucovorin as first-line treatment in advanced colorectal cancerBr J Cancer20111051535721654688
   PubMed Web of Science ®Google Scholar
• NowellPCHungerfordDAChromosome studies on normal and leukemic human leukocytesJ Natl Cancer Inst1960258510914427847
   PubMed Web of Science ®Google Scholar
• de KleinAvan KesselAGGrosveldGA cellular oncogene is translocated to the Philadelphia chromosome in chronic myelocytic leukaemiaNature198230058947657676960256
   PubMed Web of Science ®Google Scholar
• DrukerBJGuilhotFO’BrienSGFive-year follow-up of patients receiving imatinib for chronic myeloid leukemiaN Engl J Med2006355232408241717151364
   PubMed Web of Science ®Google Scholar
• BixbyDTalpazMMechanisms of resistance to tyrosine kinase inhibitors in chronic myeloid leukemia and recent therapeutic strategies to overcome resistanceHematology Am Soc Hematol Educ Program200946147620008232
   PubMedGoogle Scholar
• ZhangWWCortesJEYaoHPredictors of primary imatinib resistance in chronic myelogenous leukemia are distinct from those in secondary imatinib resistanceJ Clin Oncol200927223642364919506164
   PubMed Web of Science ®Google Scholar
• GorreMEMohammedMEllwoodKClinical resistance to STI-571 cancer therapy caused by BCR-ABL gene mutation or amplificationScience2001293553187688011423618
   PubMed Web of Science ®Google Scholar
• LiermanESmitsSCoolsJDewaeleBDebiec-RychterMVandenberghePPonatinib is active against imatinib-resistant mutants of FIP1L1-PDGFRA and KIT, and against FGFR1-derived fusion kinasesLeukemia20122671693169522301675
   PubMed Web of Science ®Google Scholar
• McLeodHLKrynetskiEYRellingMVEvansWEGenetic polymorphism of thiopurine methyltransferase and its clinical relevance for childhood acute lymphoblastic leukemiaLeukemia200014456757210764140
   PubMed Web of Science ®Google Scholar
• RellingMVHancockMLRiveraGKMercaptopurine therapy intolerance and heterozygosity at the thiopurine S-methyltransferase gene locusJ Natl Cancer Inst199991232001200810580024
   PubMedGoogle Scholar
• StanullaMSchaeffelerEFlohrTThiopurine methyltransferase (TPMT) genotype and early treatment response to mercaptopurine in childhood acute lymphoblastic leukemiaJAMA2005293121485148915784872
   PubMed Web of Science ®Google Scholar
• StoccoGCheokMHCrewsKRGenetic polymorphism of inosine triphosphate pyrophosphatase is a determinant of mercaptopurine metabolism and toxicity during treatment for acute lymphoblastic leukemiaClin Pharmacol Ther200985216417218685564
   PubMed Web of Science ®Google Scholar
• Food and Drug AdministrationPurinetholSilver Spring, MDFood and Drug Administration2003 Available from: http://www.accessdata.fda.gov/drugsatfda_docs/label/2004/09053s024lbl.pdfAccessed February 17, 2016
   Google Scholar
• YangJJLandierWYangWInherited NUDT15 variant is a genetic determinant of mercaptopurine intolerance in children with acute lymphoblastic leukemiaJ Clin Oncol201533111235124225624441
   PubMed Web of Science ®Google Scholar
• HeinrichMCCorlessCLDemetriGDKinase mutations and imatinib response in patients with metastatic gastrointestinal stromal tumorJ Clin Oncol200321234342434914645423
   PubMed Web of Science ®Google Scholar
• DjalalovSBecaJHochJSCost efectiveness of EML4-ALK fusion testing and first-line crizotinib treatment for patients with advanced ALK-positive non-small-cell lung cancerJ Clin Oncol201432101012101924567430
   PubMed Web of Science ®Google Scholar
• BuettnerRWolfJThomasRKLessons learned from lung cancer genomics: the emerging concept of individualized diagnostics and treatmentJ Clin Oncol201331151858186523589544
   PubMed Web of Science ®Google Scholar
• DeverkaPADreyfusJCClinical integration of next generation sequencing: coverage and reimbursement challengesJ Law Med Ethics201442Suppl 1224125298289
   PubMed Web of Science ®Google Scholar
• StrattonMRCampbellPJFutrealPAThe cancer genomeNature2009458723971972419360079
   PubMed Web of Science ®Google Scholar
• CampbellPJYachidaSMudieLJThe patterns and dynamics of genomic instability in metastatic pancreatic cancerNature201046773191109111320981101
   PubMed Web of Science ®Google Scholar
• GerlingerMRowanAJHorswellSIntratumor heterogeneity and branched evolution revealed by multiregion sequencingN Engl J Med20123661088389222397650
   PubMed Web of Science ®Google Scholar
• VandinFUpfalERaphaelBJDe novo discovery of mutated driver pathways in cancerGenome Res201222237538521653252
   PubMed Web of Science ®Google Scholar
• MillerDGOn the nature of susceptibility to cancer. The presidential addressCancer1980466130713187417931
   PubMed Web of Science ®Google Scholar
• MendelsohnJPersonalizing oncology: perspectives and prospectsJ Clin Oncol201331151904191123589547
   PubMed Web of Science ®Google Scholar
• SchinzelACHahnWCOncogenic transformation and experimental models of human cancerFront Biosci200813718417981529
   PubMed Web of Science ®Google Scholar
• MacconaillLEVan HummelenPMeyersonMHahnWCClinical implementation of comprehensive strategies to characterize cancer genomes: opportunities and challengesCancer Discov20111429721935500
   PubMed Web of Science ®Google Scholar
• Meric-BernstamFFarhangfarCMendelsohnJMillsGBBuilding a personalized medicine infrastructure at a major cancer centerJ Clin Oncol201331151849185723589548
   PubMed Web of Science ®Google Scholar
• Alix-PanabieresCPantelKCirculating tumor cells: liquid biopsy of cancerClin Chem201359111011823014601
   PubMed Web of Science ®Google Scholar
• FlahertyKTInfanteJRDaudACombined BRAF and MEK inhibition in melanoma with BRAF V600 mutationsN Engl J Med2012367181694170323020132
   PubMed Web of Science ®Google Scholar
• SchilskyRLMichelsDLKearbeyAHYuPPHudisCABuilding a rapid learning health care system for oncology: the regulatory framework of CancerLinQJ Clin Oncol201432222373237924912897
   PubMed Web of Science ®Google Scholar
• AbernethyAPEtheredgeLMGanzPARapid-learning system for cancer careJ Clin Oncol201028274268427420585094
   PubMed Web of Science ®Google Scholar
• ScheunerMTde VriesHKimBMeiliRCOlmsteadSHTelekiSAre electronic health records ready for genomic medicine?Genet Med200911751051719478682
   PubMed Web of Science ®Google Scholar
• KohaneISUsing electronic health records to drive discovery in disease genomicsNat Rev Genet201112641742821587298
   PubMed Web of Science ®Google Scholar
• RogauschAPrauseDSchallenbergABrockmollerJHimmelWPatients’ and physicians’ perspectives on pharmacogenetic testingPharmacogenomics200671495916354124
   PubMed Web of Science ®Google Scholar
• ZhangSCBruceCHaydenMRiederMJPublic perceptions of pharmacogeneticsPediatrics20141335e1258e126724777223
   PubMed Web of Science ®Google Scholar
• BlanchettePSSpreaficoAMillerFAGenomic testing in cancer: patient knowledge, attitudes, and expectationsCancer2014120193066307324962202
   PubMed Web of Science ®Google Scholar
• HagaSBLaPointeNMThe potential impact of pharmacogenetic testing on medication adherencePharmacogenomics J201313648148323999596
   PubMed Web of Science ®Google Scholar
• StanekEJSandersCLTaberKAAdoption of pharmacogenomic testing by US physicians: results of a nationwide surveyClin Pharmacol Ther201291345045822278335
   PubMed Web of Science ®Google Scholar
• FruehFWAmurSMummaneniPPharmacogenomic biomarker information in drug labels approved by the United States food and drug administration: prevalence of related drug usePharmacotherapy200828899299818657016
   PubMed Web of Science ®Google Scholar
• McLeodHLCancer pharmacogenomics: early promise, but concerted effort neededScience201333961271563156623539596
   PubMed Web of Science ®Google Scholar
• PatelJNVilladolidJCancer Drug Delivery: Pharmacogenetics, biomarkers and targeted therapiesHandbook of Research on Novel Approaches for Drug DeliveryKesharwaniRajesh KumarHershey, PAIGI Global2015in press
   Google Scholar
• Table of Pharmacogenomic Biomarkers in Drug Labeling [webpage on the Internet]Silver Spring, MDUS Food and Drug Administration2015 Available from: http://www.fda.gov/drugs/scienceresearch/researchareas/pharmacogenetics/ucm083378.htmAccessed May 5, 2016
   Google Scholar