Bielinski SJ, Olson JE, Pathak J, Weinshilboum RM, Wang L, Lyke KJ, Ryu E, Targonski PV, Van Norstrand MD, Hathcock MA, et al. Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol. Mayo Clin Proc. 2014;89(1):25–33.
Article
PubMed
Google Scholar
Pinto N, Black M, Patel K, Yoo J, Mymryk JS, Barrett JW, Nichols AC. Genomically driven precision medicine to improve outcomes in anaplastic thyroid Cancer. J Oncol. 2014;2014:7. https://doi.org/10.1155/2014/936285.
Borad MJ, Egan JB, Condjella RM, Liang WS, Fonseca R, Ritacca NR, McCullough AE, Barrett MT, Hunt KS, Champion MD, et al. Clinical implementation of integrated genomic profiling in patients with advanced cancers. Sci Rep. 2016;6(1):25.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lazaridis KN, McAllister TM, Babovic-Vuksanovic D, Beck SA, Borad MJ, Bryce AH, Chanan-Khan AA, Ferber MJ, Fonseca R, Johnson KJ, et al. Implementing individualized medicine into the medical practice. Am J Med Genet C Semin Med Genet. 2014;166C(1):15–23.
Article
PubMed
Google Scholar
Johnson DB, Dahlman KH, Knol J, Gilbert J, Puzanov I, Means-Powell J, Balko JM, Lovly CM, Murphy BA, Goff LW, et al. Enabling a genetically informed approach to cancer medicine: a retrospective evaluation of the impact of comprehensive tumor profiling using a targeted next-generation sequencing panel. Oncologist. 2014;19(6):616–22.
Article
PubMed
PubMed Central
Google Scholar
Shih AH, Abdel-Wahab O, Patel JP, Levine RL. The role of mutations in epigenetic regulators in myeloid malignancies. Nat Rev Cancer. 2012;12(9):599–612.
Article
PubMed
CAS
Google Scholar
Piccart-Gebhart MJ, Procter M, Leyland-Jones B, Goldhirsch A, Untch M, Smith I, Gianni L, Baselga J, Bell R, Jackisch C, et al. Trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer. N Engl J Med. 2005;353(16):1659–72.
Article
PubMed
CAS
Google Scholar
Romond EH, Perez EA, Bryant J, Suman VJ, Geyer CE Jr, Davidson NE, Tan-Chiu E, Martino S, Paik S, Kaufman PA, et al. Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer. N Engl J Med. 2005;353(16):1673–84.
Article
PubMed
CAS
Google Scholar
Katsanis SH, Javitt G, Hudson K. Public health. A case study of personalized medicine. Science. 2008;320(5872):53–4.
Article
PubMed
CAS
Google Scholar
Hopkins AL, Groom CR. The druggable genome. Nat Rev Drug Discov. 2002;1(9):727–30.
Article
PubMed
CAS
Google Scholar
Griffith M, Griffith OL, Coffman AC, Weible JV, McMichael JF, Spies NC, Koval J, Das I, Callaway MB, Eldred JM, et al. DGIdb: mining the druggable genome. Nat Methods. 2013;10(12):1209–10.
Article
PubMed
PubMed Central
CAS
Google Scholar
Fang H, Gough J. The 'dnet' approach promotes emerging research on cancer patient survival. Genome Med. 2014;6(8):64.
PubMed
PubMed Central
Google Scholar
Relling MV, Klein TE. CPIC: clinical pharmacogenetics implementation consortium of the pharmacogenomics research network. Clin Pharmacol Ther. 2011;89(3):464–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, McGuire AL, Nussbaum RL, O'Daniel JM, Ormond KE, et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med. 2013;15(7):565–74.
Article
PubMed
PubMed Central
CAS
Google Scholar
Tuna MA, Christopher I. Chapter 14: activating mutations and targeted therapy in Cancer. In: Cooper PD, editor. Mutations in human genetic disease. London: InTech; 2012.
Patch AM, Christie EL, Etemadmoghadam D, Garsed DW, George J, Fereday S, Nones K, Cowin P, Alsop K, Bailey PJ, et al. Whole-genome characterization of chemoresistant ovarian cancer. Nature. 2015;521(7553):489–94.
Article
PubMed
CAS
Google Scholar
Vaidyanathan A, Sawers L, Gannon AL, Chakravarty P, Scott AL, Bray SE, Ferguson MJ, Smith G. ABCB1 (MDR1) induction defines a common resistance mechanism in paclitaxel- and olaparib-resistant ovarian cancer cells. Br J Cancer. 2016;115(4):431–41. Published online 2016 Jul 14. https://doi.org/10.1038/bjc.2016.203.
Bussey KJ, Chin K, Lababidi S, Reimers M, Reinhold WC, Kuo WL, Gwadry F, Ajay K-MH, Fridlyand J, et al. Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol Cancer Ther. 2006;5(4):853–67.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yamaguchi K, Arai Y, Kanda Y, Akagi K. Germline mutation of dihydropyrimidine dehydrogenese gene among a Japanese population in relation to toxicity to 5-fluorouracil. Jpn J Cancer Res. 2001;92(3):337–42.
Article
PubMed
PubMed Central
CAS
Google Scholar
Davies J, Davies D. Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev. 2010;74(3):417–33.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dever LA, Dermody TS. Mechanisms of bacterial resistance to antibiotics. Arch Intern Med. 1991;151(5):886–95.
Article
PubMed
CAS
Google Scholar
Atkinson AJ Jr, Kushner W. Clinical pharmacokinetics. Annu Rev Pharmacol Toxicol. 1979;19:105–27.
Article
PubMed
CAS
Google Scholar
Housman G, Byler S, Heerboth S, Lapinska K, Longacre M, Snyder N, Sarkar S. Drug resistance in cancer: an overview. Cancers (Basel). 2014;6(3):1769–92.
Article
CAS
Google Scholar
Shen DW, Pouliot LM, Hall MD, Gottesman MM. Cisplatin resistance: a cellular self-defense mechanism resulting from multiple epigenetic and genetic changes. Pharmacol Rev. 2012;64(3):706–21.
Article
PubMed
PubMed Central
CAS
Google Scholar
AbuHammad S, Zihlif M. Gene expression alterations in doxorubicin resistant MCF7 breast cancer cell line. Genomics. 2013;101(4):213–20.
Article
PubMed
CAS
Google Scholar
Harmsen S, Meijerman I, Beijnen JH, Schellens JH. Nuclear receptor mediated induction of cytochrome P450 3A4 by anticancer drugs: a key role for the pregnane X receptor. Cancer Chemother Pharmacol. 2009;64(1):35–43.
Article
PubMed
CAS
Google Scholar
Mochinaga K, Tsuchiya T, Nagasaki T, Arai J, Tominaga T, Yamasaki N, Matsumoto K, Miyazaki T, Nanashima A, Hayashi T, et al. High expression of dihydropyrimidine dehydrogenase in lung adenocarcinoma is associated with mutations in epidermal growth factor receptor: implications for the treatment of non--small-cell lung cancer using 5-fluorouracil. Clin Lung Cancer. 2014;15(2):136–44. e134
Article
PubMed
CAS
Google Scholar
Hagmann W, Jesnowski R, Faissner R, Guo C, Lohr JM. ATP-binding cassette C transporters in human pancreatic carcinoma cell lines. Upregulation in 5-fluorouracil-resistant cells. Pancreatology. 2009;9(1–2):136–44.
Article
PubMed
CAS
Google Scholar
Ishihama H, Chida M, Araki O, Karube Y, Seki N, Tamura M, Umezu H, Honma K, Masawa N, Miyoshi S. Comparison of 5-fluorouracil-related gene expression levels between adenocarcinomas and squamous cell carcinomas of the lung. Jpn J Clin Oncol. 2009;39(1):33–6.
Article
PubMed
Google Scholar
Gross E, Meul C, Raab S, Propping C, Avril S, Aubele M, Gkazepis A, Schuster T, Grebenchtchikov N, Schmitt M, et al. Somatic copy number changes in DPYD are associated with lower risk of recurrence in triple-negative breast cancers. Br J Cancer. 2013;109(9):2347–55.
Article
PubMed
PubMed Central
CAS
Google Scholar
Riddick DS, Lee C, Ramji S, Chinje EC, Cowen RL, Williams KJ, Patterson AV, Stratford IJ, Morrow CS, Townsend AJ, et al. Cancer chemotherapy and drug metabolism. Drug Metab Dispos. 2005;33(8):1083–96.
Article
PubMed
CAS
Google Scholar
Sahoo S, Haraldsdottir HS, Fleming RM, Thiele I. Modeling the effects of commonly used drugs on human metabolism. FEBS J. 2015;282(2):297–317.
Article
PubMed
CAS
Google Scholar
Szakacs G, Paterson JK, Ludwig JA, Booth-Genthe C, Gottesman MM. Targeting multidrug resistance in cancer. Nat Rev Drug Discov. 2006;5(3):219–34.
Article
PubMed
CAS
Google Scholar
Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502(7471):333–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer genome atlas pan-Cancer analysis project. Nat Genet. 2013;45(10):1113–20.
Article
PubMed
PubMed Central
CAS
Google Scholar
Larsen RJ, Marx ML. An introduction to mathematical statistics and its applications. 4th ed. Upper Saddle River, N.J: Pearson Prentice Hall; 2006.
Google Scholar
Parmigiani G, Garett ES, Irizarry RA, Zeger SL. The analysis of gene expression data: methods and software. New York: Springer; 2006.
Google Scholar
Whirl-Carrillo M, McDonagh EM, Hebert JM, Gong L, Sangkuhl K, Thorn CF, Altman RB, Klein TE. Pharmacogenomics knowledge for personalized medicine. Clin Pharmacol Ther. 2012;92(4):414–7.
Article
PubMed
CAS
Google Scholar
Law V, Knox C, Djoumbou Y, Jewison T, Guo AC, Liu Y, Maciejewski A, Arndt D, Wilson M, Neveu V, et al. DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res. 2014;42(Database issue):D1091–7.
Article
PubMed
CAS
Google Scholar
Drug Interactions: Cytochrome P450 Drug Interaction Table. Indiana University School of Medicine. http://medicine.iupui.edu/clinpharm/ddis.
NCCN Guidelines in Oncology: Breast Cancer (Version 1.2014). http://www.nccn.org/professionals/physician_gls/pdf/breast.pdf.
NCCN Guidelines in Oncology: Central Nervous System (Version 1.2014). http://www.nccn.org/professionals/physician_gls/pdf/cns.pdf.
NCCN Guidelines in Oncology: Colon Cancer (Version 3.2014). http://www.nccn.org/professionals/physician_gls/pdf/colon.pdf.
NCCN Guidelines in Oncology: Ovarian Cancer (Version 2.2014). http://www.nccn.org/professionals/physician_gls/pdf/ovarian.pdf.
Nelson SJ, Zeng K, Kilbourne J, Powell T, Moore R. Normalized names for clinical drugs: RxNorm at 6 years. J Am Med Inform Assoc. 2011;18(4):441–8.
Article
PubMed
PubMed Central
Google Scholar
RxNorm [dataset on the Internet]. Release 2014_02_03. http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html.
de Coronado S, Wright LW, Fragoso G, Haber MW, Hahn-Dantona EA, Hartel FW, Quan SL, Safran T, Thomas N, Whiteman L. The NCI thesaurus quality assurance life cycle. J Biomed Inform. 2009;42(3):530–9.
Article
PubMed
Google Scholar
Cremolini C, Loupakis F, Antoniotti C, Lonardi S, Masi G, Salvatore L, Cortesi E, Tomasello G, Spadi R, Zaniboni A, et al. Early tumor shrinkage and depth of response predict long-term outcome in metastatic colorectal cancer patients treated with first-line chemotherapy plus bevacizumab: results from phase III TRIBE trial by the Gruppo Oncologico del Nord Ovest. Ann Oncol. 2015;26(6):1188–94.
Article
PubMed
CAS
Google Scholar
Huang K, Sun H, Chen Z, Li X, Wang S, Zhao X, Tang F, Jia Y, Hu T, Du X, et al. Optimal pathological response indicated better long-term outcome among patients with stage IB2 to IIB cervical cancer submitted to neoadjuvant chemotherapy. Sci Rep. 2016;6:28278.
Article
PubMed
PubMed Central
CAS
Google Scholar
Jain P, Kantarjian H, Nazha A, O'Brien S, Jabbour E, Romo CG, Pierce S, Cardenas-Turanzas M, Verstovsek S, Borthakur G, et al. Early responses predict better outcomes in patients with newly diagnosed chronic myeloid leukemia: results with four tyrosine kinase inhibitor modalities. Blood. 2013;121(24):4867–74.
Article
PubMed
PubMed Central
CAS
Google Scholar
Maas M, Nelemans PJ, Valentini V, Das P, Rodel C, Kuo LJ, Calvo FA, Garcia-Aguilar J, Glynne-Jones R, Haustermans K, et al. Long-term outcome in patients with a pathological complete response after chemoradiation for rectal cancer: a pooled analysis of individual patient data. Lancet Oncol. 2010;11(9):835–44.
Article
PubMed
Google Scholar
Piessevaux H, Buyse M, Schlichting M, Van Cutsem E, Bokemeyer C, Heeger S, Tejpar S. Use of early tumor shrinkage to predict long-term outcome in metastatic colorectal cancer treated with cetuximab. J Clin Oncol. 2013;31(30):3764–75.
Article
PubMed
CAS
Google Scholar
Almendro V, Cheng YK, Randles A, Itzkovitz S, Marusyk A, Ametller E, Gonzalez-Farre X, Munoz M, Russnes HG, Helland A, et al. Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. Cell Rep. 2014;6(3):514–27.
Article
PubMed
PubMed Central
CAS
Google Scholar
Andor N, Graham TA, Jansen M, Xia LC, Aktipis CA, Petritsch C, Ji HP, Maley CC. Pan-cancer analysis of the extent and consequences of intratumor heterogeneity. Nat Med. 2016;22(1):105–13.
Article
PubMed
CAS
Google Scholar
Keenan T, Moy B, Mroz EA, Ross K, Niemierko A, Rocco JW, Isakoff S, Ellisen LW, Bardia A. Comparison of the genomic landscape between primary breast Cancer in African American versus white women and the Association of Racial Differences with Tumor Recurrence. J Clin Oncol. 2015;33(31):3621–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mroz EA, Rocco JW. MATH, a novel measure of intratumor genetic heterogeneity, is high in poor-outcome classes of head and neck squamous cell carcinoma. Oral Oncol. 2013;49(3):211–5.
Article
PubMed
CAS
Google Scholar
Walker E, Hernandez AV, Kattan MW. Meta-analysis: its strengths and limitations. Cleve Clin J Med. 2008;75(6):431–9.
Article
PubMed
Google Scholar
Haidich AB. Meta-analysis in medical research. Hippokratia. 2010;14(Suppl 1):29–37.
PubMed
PubMed Central
CAS
Google Scholar
Oncology endpoints in a changing landscape. Manag Care. 2016;11(suppl):–12. https://www.managedcaremag.com/sites/default/files/graphics/OncoEndpoints_MC.pdf.
Gourgou-Bourgade S, Cameron D, Poortmans P, Asselain B, Azria D, Cardoso F, A'Hern R, Bliss J, Bogaerts J, Bonnefoi H, et al. Guidelines for time-to-event end point definitions in breast cancer trials: results of the DATECAN initiative (definition for the assessment of time-to-event endpoints in CANcer trials)dagger. Ann Oncol. 2015;26(5):873–9.
Article
PubMed
CAS
Google Scholar
Kogan AJ, Haren M. Translating cancer trial endpoints into the language of managed care. Biotechnol Healthc. 2008;5(1):22–35.
PubMed
PubMed Central
Google Scholar
Pazdur R. Endpoints for assessing drug activity in clinical trials. Oncologist. 2008;13(Suppl 2):19–21.
Article
PubMed
Google Scholar
R Core Team. R. A language and environment for statistical computing: R Foundation for Statistical Computing; 2014. http://www.R-project.org
Klein DJ, Thorn CF, Desta Z, Flockhart DA, Altman RB, Klein TE. PharmGKB summary: tamoxifen pathway, pharmacokinetics. Pharmacogenet Genomics. 2013;23(11):643–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Oshiro C, Marsh S, McLeod H, Carrillo MW, Klein T, Altman R. Taxane pathway. Pharmacogenet Genomics. 2009;19(12):979–83.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yu Y, Gaillard S, Phillip JM, Huang TC, Pinto SM, Tessarollo NG, Zhang Z, Pandey A, Wirtz D, Ayhan A, et al. Inhibition of spleen tyrosine kinase potentiates paclitaxel-induced cytotoxicity in ovarian Cancer cells by stabilizing microtubules. Cancer Cell. 2015;28(1):82–96.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang CC, Yang JM, White E, Murphy M, Levine A, Hait WN. The role of MAP4 expression in the sensitivity to paclitaxel and resistance to vinca alkaloids in p53 mutant cells. Oncogene. 1998;16(12):1617–24.
Article
PubMed
CAS
Google Scholar
Wang D, Lippard SJ. Cellular processing of platinum anticancer drugs. Nat Rev Drug Discov. 2005;4(4):307–20.
Article
PubMed
CAS
Google Scholar
He Y, Ding Y, Wang D, Zhang W, Chen W, Liu X, Qin W, Qian X, Chen H, Guo Z. HMGB1 bound to cisplatin-DNA adducts undergoes extensive acetylation and phosphorylation in vivo. Chem Sci. 2015;6(3):2074–8.
Article
PubMed
CAS
Google Scholar
Park S, Lippard SJ. Redox state-dependent interaction of HMGB1 and cisplatin-modified DNA. Biochemistry. 2011;50(13):2567–74.
Article
PubMed
CAS
Google Scholar
Marsh S, McLeod H, Dolan E, Shukla SJ, Rabik CA, Gong L, Hernandez-Boussard T, Lou XJ, Klein TE, Altman RB. Platinum pathway. Pharmacogenet Genomics. 2009;19(7):563–4.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ugrinova I, Zlateva S, Pashev IG, Pasheva EA. Native HMGB1 protein inhibits repair of cisplatin-damaged nucleosomes in vitro. Int J Biochem Cell Biol. 2009;41(7):1556–62.
Article
PubMed
CAS
Google Scholar
Philips S, Zhou J, Li Z, Skaar TC, Li L. A translational bioinformatic approach in identifying and validating an interaction between vitamin a and CYP19A1. BMC Genomics. 2015;16(Suppl 7):S17.
Article
PubMed
PubMed Central
CAS
Google Scholar
Westbrook K, Stearns V. Pharmacogenomics of breast cancer therapy: an update. Pharmacol Ther. 2013;139(1):1–11.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lu C, Xie M, Wendl MC, Wang J, McLellan MD, Leiserson MD, Huang KL, Wyczalkowski MA, Jayasinghe R, Banerjee T, et al. Patterns and functional implications of rare germline variants across 12 cancer types. Nat Commun. 2015;6:10086.
Article
PubMed
CAS
Google Scholar
Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646–74.
Article
PubMed
CAS
Google Scholar
Wang L, Liu H, Chute CG, Zhu Q. Cancer based pharmacogenomics network supported with scientific evidences: from the view of drug repurposing. BioData Min. 2015;8:9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Schilsky RL. Personalized medicine in oncology: the future is now. Nat Rev Drug Discov. 2010;9(5):363–6.
Article
PubMed
CAS
Google Scholar