Process Map Proposal for the Validation of Genomic Biomarkers

• Woodcock J : Importance of genomic biomarker validation in the context of pharmacogenomic initiatives at the FDA. Proceedings of the FDA, DIA, PhRMA, BIO, NIH and PWG Workshop on Application and Validation of Genomic Biomarkers for Use in Drug Development and Regulatory Submissions. Bethesda, MD, USA (2005).
   Google Scholar
• Orr MS , ScherfU: Large-scale gene expression analysis in molecular target discovery.Leukaemia16(4), 473–477 (2002).
   PubMed Web of Science ®Google Scholar
• Clarke P , MannJ, SimpsonJF, Rickard-DicksonK, PrimusFJ: Mice transgenic for human carcinoembryonic antigen as a model for immunotherapy.Cancer Res.58(7), 1469–1477 (1998).
   PubMed Web of Science ®Google Scholar
• Fielden MR , PearsonC, BrennanR, Kolaja KL: Preclinical drug safety analysis by chemogenomic profiling in the liver. Am. J. Pharmacogenomics5(3), 161–171 (2005).
   PubMedGoogle Scholar
• Floyd E , McShaneTM: Development and use of biomarkers in oncology drug development.Toxicol. Pathol.32(Suppl. 1), 106–115 (2004).
   PubMedGoogle Scholar
• Leighton JK , BrownP, EllisA et al.: Workgroup report: review of genomic data based on experience with mock submissions: view of the CDER pharmacology toxicology nonclinical pharmacogenomics subcommittee. Environ. Health Perspect.114(4), 573–578 (2005).
   Web of Science ®Google Scholar
• Salerno RA , LeskoLJ: Pharmacogenomic data: FDA voluntary and required submission guidance.Pharmacogenomics5(5), 503–505 (2004).
   PubMed Web of Science ®Google Scholar
• Innocenti F , UndeviaSD, IyerL et al.: Genetic variants in the UDP-glucoronosyltransferase 1A1 gene predict the risk of severe neutropenia of irinotecan. J. Clin. Oncol.22(8), 1382–1388 (2004).
   PubMed Web of Science ®Google Scholar
• Wadelius M , SorlinK, WallermanO et al.: Warfarin sensitivity related to CYP2C9, CYP3A5, ABCB1 (MDR1) and other factors. Pharmacogenomics J.4(1), 40–48 (2004).
   PubMed Web of Science ®Google Scholar
• Roskoski R Jr: Structure and regulation of Kit protein-tyrosine kinase – the stem cell factor receptor. Biochem. Biophys. Res. Commun.338(3), 1307–1315 (2005).
   PubMed Web of Science ®Google Scholar
• Burger H , den Bakker MA, Kros JM, van Tol H et al.: Activating mutations in c-KIT and PDGFRa are exclusively found in gastrointestinal stromal tumors and not in other tumors overexpressing these imatinib mesylate target genes. Cancer Biol. Ther.4(11), 1270–1274 (2005).
   PubMed Web of Science ®Google Scholar
• Sapone A , VairaD, TrespidiS et al.: The clinical role of cytochrome p450 genotypes in Helicobacter pylori management. Am. J. Gastroenterol.98(5), 1010–1015 (2003).
   PubMed Web of Science ®Google Scholar
• Shimatani T , InoueM, KuroiwaT et al.: Acid-suppressive effects of rabeprazole, omeprazole, and lansoprazole at reduced and standard doses: a crossover comparative study in homozygous extensive metabolizers of cytochrome P450 2C19. Clin. Pharmacol. Ther.79(1), 144–152 (2006).
   PubMed Web of Science ®Google Scholar
• Sim SC , RisingerC, DahlML et al.: A common novel CYP2C19 gene variant causes ultrarapid drug metabolism relevant for the drug response to proton pump inhibitors and antidepressants. Clin. Pharmacol. Ther.79(1), 103–113 (2006).
   PubMed Web of Science ®Google Scholar
• Chong E , EnsomMH: Pharmacogenetics of the proton pump inhibitors: a systematic review.Pharmacotherapy23(4), 460–471 (2003).
   PubMed Web of Science ®Google Scholar
• Rodrigues AD : Impact of CYP2C9 genotype on pharmacokinetics: are all cyclooxygenase inhibitors the same?Drug Metab. Dispos.33(11), 1567–1575 (2005).
   PubMed Web of Science ®Google Scholar
• Kirchheiner J , BrockmollerJ: Clinical consequences of cytochrome P450 2C9 polymorphisms.Clin. Pharmacol. Ther.77(1), 1–16 (2005).
   PubMed Web of Science ®Google Scholar
• Sanderson S , EmeryJ, HigginsJ: CYP2C9 gene variants, drug dose, and bleeding risk in warfarin-treated patients: a HuGEnet systematic review and meta-analysis.Genet Med.7(2), 97–104 (2005).
   PubMed Web of Science ®Google Scholar
• Klotz U : Pharmacological comparison of the statins.Arzneimittelforschung53(9), 605–611 (2003).
   PubMed Web of Science ®Google Scholar
• Guay DR : Update on fenofibrate.Cardiovasc. Drug Rev.20(4), 281–302 (2002).
   PubMedGoogle Scholar
• Mandrioli R , FortiGC, RaggiMA: Fluoxetine metabolism and pharmacological interactions: the role of cytochrome p450.Curr. Drug Metab.7(2), 127–133 (2006).
   PubMed Web of Science ®Google Scholar
• Scordo MG , SpinaE, DahlML et al.: Influence of CYP2C9, 2C19 and 2D6 genetic polymorphisms on the steady-state plasma concentrations of the enantiomers of fluoxetine and norfluoxetine. Basic Clin. Pharmacol. Toxicol.97(5), 296–301 (2005).
   PubMed Web of Science ®Google Scholar
• Rochat B : Role of cytochrome P450 activity in the fate of anticancer agents and in drug resistance: focus on tamoxifen, paclitaxel and imatinib metabolism.Clin. Pharmacokinet.44(4), 349–366 (2005).
   PubMed Web of Science ®Google Scholar
• Ingelman-Sundberg M : Genetic polymorphisms of cytochrome P450 2D6 (CYP2D6): clinical consequences, evolutionary aspects and functional diversity.Pharmacogenomics J.5(1), 6–13 (2005).
   PubMed Web of Science ®Google Scholar
• Kirchheiner J , NickchenK, BauerM et al.: Pharmacogenetics of antidepressants and antipsychotics: the contribution of allelic variations to the phenotype of drug response. Mol. Psychiatry.9(5), 442–473 (2004).
   PubMed Web of Science ®Google Scholar
• Charlier C , BrolyF, LhermitteM et al.: Polymorphisms in the CYP2D6 gene: association with plasma concentrations of fluoxetine and paroxetine. Ther. Drug Monit.25(6), 738–742 (2003).
   PubMed Web of Science ®Google Scholar
• Mattison LK , FourieJ, HiraoY et al.: The uracil breath test in the assessment of dihydropyrimidine dehydrogenase activity: pharmacokinetic relationship between expired 13CO2 and plasma [2–13C]dihydrouracil. Clin. Cancer Res.12(2), 549–555 (2006).
   PubMed Web of Science ®Google Scholar
• Lee A , EzzeldinH, FourieJ, DiasioR: Dihydropyrimidine dehydrogenase deficiency: impact of pharmacogenetics on 5-fluorouracil therapy.Clin. Adv. Hematol. Oncol.2(8), 527–532 (2004).
   PubMedGoogle Scholar
• Ezzeldin H , DiasioR: Dihydropyrimidine dehydrogenase deficiency, a pharmacogenetic syndrome associated with potentially life-threatening toxicity following 5-fluorouracil administration.Clin. Colorectal Cancer4(3), 181–189 (2004).
   PubMedGoogle Scholar
• van Kuilenburg AB : Dihydropyrimidine dehydrogenase and the efficacy and toxicity of 5-fluorouracil.Eur. J. Cancer.40(7), 939–950 (2004).
   PubMed Web of Science ®Google Scholar
• Snyder LC , AstsaturovI, WeinerLM: Overview of monoclonal antibodies and small molecules targeting the epidermal growth factor receptor pathway in colorectal cancer.Clin. Colorectal Cancer.5(Suppl. 2), S71–S80 (2005).
   PubMedGoogle Scholar
• Moroni M , VeroneseS, BenvenutiS et al.: Gene copy number for epidermal growth factor receptor (EGFR) and clinical response to antiEGFR treatment in colorectal cancer: a cohort study. Lancet Oncol.6(5), 279–286 (2005).
   PubMed Web of Science ®Google Scholar
• Tsao M -S, Sakurada S, Cutz J-C et al.: Erlotinib in lung cancer: molecular and clinical predictors of outcome. N. Engl J. Med.353, 133–144 (2005).
   PubMed Web of Science ®Google Scholar
• Hirsch F , Varella-GarciaM, McCoyJ et al.: Increased epidermal growth factor receptor gene copy number detected by fluorescence in situ hybridization associates with increased sensitivity to gefitinib in patients with bronchioloalveolar carcinoma subtypes: A Southwest Oncology Group Study. J. Clin. Oncol.23, 6838–6845 (2005).
   PubMed Web of Science ®Google Scholar
• Brant JM : Rasburicase: an innovative new treatment for hyperuricemia associated with tumor lysis syndrome.Clin. J. Oncol. Nurs.6(1), 12–16 (2002).
   PubMedGoogle Scholar
• Jalloh A , TantularIS, PusarawatiS et al.: Rapid epidemiologic assessment of glucose-6-phosphate dehydrogenase deficiency in malaria-endemic areas in Southeast Asia using a novel diagnostic kit. Trop. Med. Int. Health9(5), 615–623 (2004).
   PubMed Web of Science ®Google Scholar
• Raspollini MR , SusiniT, AmunniG et al.: Expression and amplification of HER-2/neu oncogene in uterine carcinosarcomas: a marker for potential molecularly targeted treatment? Int. J. Gynecol. Cancer16(1), 416–422 (2006).
   PubMed Web of Science ®Google Scholar
• Mass RD , PressMF, AndersonS et al.: Evaluation of clinical outcomes according to HER2 detection by fluorescence in situ hybridization in women with metastatic breast cancer treated with trastuzumab. Clin. Breast Cancer6(3), 240–246 (2005).
   PubMedGoogle Scholar
• Elkin EB , WeinsteinMC, WinerEP et al.: HER-2 testing and trastuzumab therapy for metastatic breast cancer: a cost-effectiveness analysis. J. Clin. Oncol.22(5), 854–863 (2004).
   PubMed Web of Science ®Google Scholar
• Augustynowicz-Kopec E , ZwolskaZ: Bioavailability factors of isoniazid in fast and slow acetylators, healthy volunteers.Acta. Pol. Pharm.59(6), 452–457 (2002).
   PubMedGoogle Scholar
• Innocenti F , IyerL, RatainMJ: Pharmacogenetics of anticancer agents: lessons from amonafide and irinotecan.Drug Metab. Dispos.29(4 Pt 2), 596–600 (2001).
   PubMed Web of Science ®Google Scholar
• Eichelbaum M , Ingelman-SundbergM, EvansWE: Pharmacogenomics and individualized drug therapy.Annu. Rev. Med.57, 119–137 (2006).
   PubMed Web of Science ®Google Scholar
• Coulthard S , HogarthL: The thiopurines: an update.Invest. New Drugs.23(6), 523–532 (2005).
   PubMed Web of Science ®Google Scholar
• Heckmann JM , LambsonEM, LittleF et al.: Thiopurine methyltransferase (TPMT) heterozygosity and enzyme activity as predictive tests for the development of azathioprine-related adverse events. J. Neurol. Sci.231(1–2), 71–80 (2005).
   PubMed Web of Science ®Google Scholar
• Coulthard SA , MathesonEC, HallAG, HogarthLA: The clinical impact of thiopurine methyltransferase polymorphisms on thiopurine treatment.Nucleosides Nucleotides Nucleic Acids.23(8–9), 1385–1391 (2004).
   PubMed Web of Science ®Google Scholar
• Hindorf U , PetersonC, AlmerS: Assessment of thiopurine methyltransferase and metabolite formation during thiopurine therapy: results from a large Swedish patient population.Ther. Drug Monit.26(6), 673–678 (2004).
   PubMed Web of Science ®Google Scholar
• Schaeffeler E , FischerC, BrockmeierD et al.: Comprehensive analysis of thiopurine S-methyltransferase phenotype–genotype correlation in a large population of German-Caucasians and identification of novel TPMT variants. Pharmacogenetics14(7), 407–417 (2004).
   PubMedGoogle Scholar
• Scaglia F , Brunetti-PierriN, KleppeS et al.: Clinical consequences of urea cycle enzyme deficiencies and potential links to arginine and nitric oxide metabolism. J. Nutr.134(10 Suppl), 2775S–2782S; discussion 2796S–2797S (2004).
   PubMed Web of Science ®Google Scholar
• Rouits E , Boisdron-CelleM, DumontA et al.: Relevance of different UGT1A1 polymorphisms in irinotecan-induced toxicity: a molecular and clinical study of 75 patients. Clin. Cancer Res.10(15), 5151–5159 (2004).
   PubMed Web of Science ®Google Scholar
• Meyerhardt JA , KwokA, RatainMJ et al.: Relationship of baseline serum bilirubin to efficacy and toxicity of single-agent irinotecan in patients with metastatic colorectal cancer. J. Clin. Oncol.22(8), 1439–1446 (2004).
   PubMed Web of Science ®Google Scholar
• Vecsler M , LoebsteinR, AlmogS et al.: Combined genetic profiles of components and regulators of the vitamin K-dependent γ-carboxylation system affect individual sensitivity to warfarin. Thromb. Haemost.95(2), 205–211 (2006).
   PubMed Web of Science ®Google Scholar
• Sconce EA , KhanTI, WynneHA et al.: The impact of CYP2C9 and VKORC1 genetic polymorphism and patient characteristics upon warfarin dose requirements: proposal for a new dosing regimen. Blood106(7), 2329–2333 (2005).
   PubMed Web of Science ®Google Scholar
• Rieder MJ , ReinerAP, GageBF et al.: Effect of VKORC1 haplotypes on transcriptional regulation and warfarin dose. N. Engl. J. Med.352(22), 2285–2293 (2005).
   PubMed Web of Science ®Google Scholar
• Yuan HY , ChenJJ, LeeMT et al.: A novel functional VKORC1 promoter polymorphism is associated with interindividual and interethnic differences in warfarin sensitivity. Hum. Mol. Genet.14(13), 1745–1751 (2005).
   PubMed Web of Science ®Google Scholar
• D'Andrea G , D'AmbrosioRL, Di Perna P et al.: A polymorphism in the VKORC1 gene is associated with an interindividual variability in the dose-anticoagulant effect of warfarin. Blood105(2), 645–649 (2005).
   PubMed Web of Science ®Google Scholar
• Rost S , FreginA, IvaskeviciusV et al.: Mutations in VKORC1 cause warfarin resistance and multiple coagulation factor deficiency type 2. Nature427(6974), 537–541 (2004).
   PubMed Web of Science ®Google Scholar

Websites

• FDA Guidance Document, 2005. Guidance for Industry. Pharmacogenomic Data Submissions. www.fda.gov/cder/guidance/6400fnl.pdf
   Google Scholar
• Critical Path Institute web page. http://www.c-path.org/
   Google Scholar
• FDA Whitepaper, 2005. Drug–Diagnostic Co-Development Concept Paper. www.fda.gov/cder/genomics/pharmacoconceptfn.pdf
   Google Scholar
• FDA Whitepaper, 2004. Innovation or stagnation, challenge and opportunity on the critical path to new medical products. www.fda.gov/oc/initiatives/criticalpath/whitepaper.html
   Google Scholar