Kamalakaran S, Varadan V, Janevski A, Banerjee N, Tuck D, McCombie WR, et al. Translating next generation sequencing to practice: opportunities and necessary steps. Mol Oncol. 2013;7(4):743–55.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lyon GJ, Wang K. Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. Genome Med. 2012;4:7–58.
Article
Google Scholar
Andre F, Mardis E, Salm M, Soria JC, Siu LL, Swanton C. Prioritizing targets for precision cancer medicine. Ann Oncol. 2014;25:2295–303.
Article
PubMed
CAS
Google Scholar
Hyman DM, Taylor BS, Baselga J. Implementing genome-driven oncology. Cell. 2017;168(4):584–99.
Article
PubMed
PubMed Central
CAS
Google Scholar
Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA Jr, Kinzler KW. Cancer genome landscapes. Science. 2013;339(6127):1546–58.
Article
PubMed
PubMed Central
CAS
Google Scholar
Van Allen EM, Wagle N, Stojanov P, Perrin DL, Cibulskis K, Marlow S, et al. Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. Nat Med. 2014;20(6):682–8.
Article
PubMed
CAS
Google Scholar
Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K, Van Loo P, et al. Universal patterns of selection in cancer and somatic tissues. Cell. 2017;171(5):1029–41.
Article
PubMed
PubMed Central
CAS
Google Scholar
Cheng J, Demeulemeester J, Wedge DC, Vollan HKM, Pitt JJ, Russnes HG, et al. Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors. Nat Commun. 2017;1:1221.
Article
CAS
Google Scholar
Peterson TA, Gauran IIM, Park J, Park D, Kann MG. Oncodomains: a protein domain-centric framework for analyzing rare variants in tumor samples. PLoS Comput Biol. 2017;4:e1005428. https://doi.org/10.1371/journal.pcbi.1005428
Article
CAS
Google Scholar
Wei CH, Phan L, Feltz J, Maiti R, Hefferon T, Lu Z. tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine. Bioinformatics. 2018;34:80–7. https://doi.org/10.1093/bioinformatics/btx541
Article
PubMed
Google Scholar
Yang H, Robinson PN, Wang K. Phenolyzer: phenotype-based prioritization of candidate genes for human diseases. Nat Methods. 2015;12(9):841–3.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ghosh R, Oak N, Plon SE. Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines. Genome Biol. 2017;18:225.
Article
PubMed
PubMed Central
Google Scholar
Eilbeck K, Quinlan A, Yandell M. Settling the score: variant prioritization and Mendelian disease. Nat Rev Genet. 2017;18(10):599–612. https://doi.org/10.1038/nrg.2017.52
Article
PubMed
PubMed Central
CAS
Google Scholar
Griffith M, Griffith OL, Coffman AC, Weible JV, McMichael JF, Spies NC, et al. DGIdb 2.0: mining clinically relevant drug–gene interactions. Nat Methods. 2013;10:1209–10.
Article
PubMed
PubMed Central
CAS
Google Scholar
Chakravarty D, Gao J, Phillips SM, Kundra R, Zhang H, Wang J, et al. OncoKB: A Precision Oncology Knowledge Base. JCO Precis Oncol. 2017; https://doi.org/10.1200/PO.17.00011
Tamborero D, Rubio-Perez C, Deu-Pons J, Schroeder MP, Vivancos A, Rovira A, et al. Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations. Genome Med. 2018;10:25. https://doi.org/10.1101/140475
Article
PubMed
PubMed Central
Google Scholar
Amadoz A, Sebastian-Leon P, Vidal E, Salavert F, Dopazo J. Using activation status of signaling pathways as mechanism-based biomarkers to predict drug sensitivity. Sci Rep. 2015;5:18494. https://doi.org/10.1038/srep18494
Article
PubMed
PubMed Central
CAS
Google Scholar
Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature. 2012;483(7391):570–5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Basu A, Bodycombe NE, Cheah JH, Price EV, Liu K, Schaefer GI, et al. An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell. 2013;154:1151–61.
Article
PubMed
PubMed Central
CAS
Google Scholar
Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, et al. A landscape of pharmacogenomic interactions in cancer. Cell. 2016;166(3):740–54.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bollag G, Tsai J, Zhang J, Zhang C, Ibrahim P, Nolop K, et al. Vemurafenib: the first drug approved for BRAF-mutant cancer. Nat Rev Drug Discov. 2012;11(11):873–86.
Article
PubMed
CAS
Google Scholar
Bryant HE, Schultz N, Thomas HD, Parker KM, Flower D, Lopez E, et al. Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase. Nature. 2005;434(7035):913–7.
Article
PubMed
CAS
Google Scholar
De Roock W, De Vriendt V, Normanno N, Ciardiello F, Tejpar S. KRAS, BRAF, PIK3CA, and PTEN mutations: implications for targeted therapies in metastatic colorectal cancer. Lancet Oncol. 2011;12(6):594–603.
Article
PubMed
CAS
Google Scholar
Iyer G, Hanrahan AJ, Milowsky MI, Al-Ahmadie H, Scott SN, Janakiraman M. Genome sequencing identifies a basis for everolimus sensitivity. Science. 2012;338(6104):221.
Article
PubMed
PubMed Central
CAS
Google Scholar
Perini GF, Campregher PV, Ross JS, Ali S, Hamerschlak N, Santos FPS. Clinical response to everolimus in a patient with Hodgkin's lymphoma harboring a TSC2 mutation. Blood Cancer J. 2016;6(e420) https://doi.org/10.1038/bcj.2016.25.
Faber AC, Li D, Song Y, Liang MC, Yeap BY, Bronson RT, et al. Differential induction of apoptosis in HER2 and EGFR addicted cancers following PI3K inhibition. Proc Natl Acad Sci U S A. 2009;106(46):19503–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhu Z, Aref AR, Cohoon TJ, Barbie TU, Imamura Y, Yang S, et al. Inhibition of KRAS-driven tumorigenicity by interruption of an autocrine cytokine circuit. Cancer Discov. 2014;4(4):452–65.
Article
PubMed
PubMed Central
CAS
Google Scholar
Butler DE, Marlein C, Walker HF, Frame FM, Mann VM, Simms MS, et al. Inhibition of the PI3K/AKT/mTOR pathway activates autophagy and compensatory Ras/Raf/MEK/ERK signalling in prostate cancer. Oncotarget. 2017;8(34):56698–713.
Article
PubMed
PubMed Central
Google Scholar
Lee HJ, Zhuang G, Cao Y, Du P, Kim HJ, Settleman J. Drug resistance via feedback activation of Stat3 in oncogene-addicted cancer cells. Cancer Cell. 2014;26(2):207–21.
Article
PubMed
CAS
Google Scholar
Forbes SA, Beare D, Boutselakis H, Bamford S, Bindal N, Tate J, et al. COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res. 2017;45(D1):D777–83.
Article
PubMed
CAS
Google Scholar
Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature. 2014;505(7484):495–501. https://doi.org/10.1038/nature12912
Article
PubMed
PubMed Central
CAS
Google Scholar
Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep. 2013;3:2650.
Article
PubMed
PubMed Central
Google Scholar
Schlicker A, Michaut M, Rahman R, Wessels LF. OncoScape: Exploring the cancer aberration landscape by genomic data fusion. Sci Rep. 2016;6:28103.
Article
PubMed
PubMed Central
CAS
Google Scholar
Cowley GS, Weir BA, Vazquez F, Tamayo P, Scott JA, Rusin S, et al. Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies. Sci Data. 2014;1:140035.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shao DD, Tsherniak A, Gopal S, Weir BA, Tamayo P, Stransky N, et al. ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens. Genome Res. 2013;23(4):665–78.
Article
PubMed
PubMed Central
CAS
Google Scholar
Salavert F, Hidalgo MR, Amadoz A, Çubuk C, Medina I, Crespo D, et al. Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models. Nucleic Acids Res. 2016;44(W1):W212–6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Workman P, Al-Lazikani B. Drugging cancer genomes. Nat Rev Drug Discov. 2013;12(12):889–90.
Article
PubMed
CAS
Google Scholar
Editorial. It's all druggable. Nat Genet. 2017;49(2):169. https://doi.org/10.1038/ng.3788.
Article
CAS
Google Scholar
Engelman JA, Zejnullahu K, Mitsudomi T, Song Y, Hyland C, Park J, et al. MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. Science. 2007;316(5827):1039–43.
Article
PubMed
CAS
Google Scholar
Turke AB, Zejnullahu K, Wu YL, Song Y, Dias-Santagata D, Lifshits E, et al. Preexistence and clonal selection of MET amplification in EGFR mutant NSCLC. Cancer Cell. 2010;17(1):77–88.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gainor JF, Niederst MJ, Lennerz JK, Dagogo-Jack I, Stevens S, Shaw AT, et al. Dramatic response to combination erlotinib and crizotinib in a patient with advanced, EGFR-mutant lung cancer harboring De Novo MET amplification. J Thorac Oncol. 2016;11(7):83–5.
Article
Google Scholar
Tricker EM, Xu C, Uddin S, Capelletti M, Ercan D, Ogino A, et al. Combined EGFR/MEK inhibition prevents the emergence of resistance in EGFR-Mutant lung cancer. Cancer Discov. 2015;5(9):960–71.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ortiz-Cuaran S, Scheffler M, Plenker D, Dahmen L, Scheel AH, Fernandez-Cuesta L, et al. Heterogeneous mechanisms of primary and acquired resistance to third-generation EGFR inhibitors. Clin Cancer Res. 2016;22(19):4837–47.
Article
PubMed
CAS
Google Scholar
Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502(7471):333–9. https://doi.org/10.1038/nature12634
Article
PubMed
PubMed Central
CAS
Google Scholar
Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, et al. A census of human cancer genes. Nat Rev Cancer. 2004;4(3):177–83.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dienstmann R, Jang IS, Bot B, Friend S, Guinney J. Database of genomic biomarkers for cancer drugs and clinical targetability in solid tumors. Cancer Discov. 2015;5(2):118–23.
Article
PubMed
PubMed Central
CAS
Google Scholar
Rubio-Perez C, Tamborero D, Schroeder MP, Antolín AA, Deu-Pons J, Perez-Llamas C, et al. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities. Cancer Cell. 2015;27(3):382–96.
Article
PubMed
CAS
Google Scholar
Gohlke BO, Nickel J, Otto R, Dunkel M, Preissner R. CancerResource--updated database of cancer-relevant proteins, mutations and interacting drugs. Nucleic Acids Res. 2016;44(D1):D932–7.
Article
PubMed
CAS
Google Scholar
Patterson SE, Liu R, Statz CM, Durkin D, Lakshminarayana A, Mockus SM. The clinical trial landscape in oncology and connectivity of somatic mutational profiles to targeted therapies. Hum Genomics. 2016;10:4.
Article
PubMed
PubMed Central
CAS
Google Scholar
Goldman M, Zhang J, Fonseca NA, Xiang Q, Craft B, Piñeiro-Yáñez E, et al. Online resources for PCAWG data exploration, visualization, and discovery. https://www.biorxiv.org/content/early/2017/10/20/163907
Garralda E, Paz K, López-Casas PP, Jones S, Katz A, Kann LM, et al. Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment. Clin Cancer Res. 2014;20(9):2476–84.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dhillon AS, Hagan S, Rath O, Kolch W. MAP kinase signalling pathways in cancer. Oncogene. 2007;26(22):3279–90.
Article
PubMed
CAS
Google Scholar
Mendoza MC, Er EE, Blenis J. The Ras-ERK and PI3K-mTOR pathways: cross-talk and compensation. Trends Biochem Sci. 2011;36(6):320–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gómez-López G, Dopazo J, Cigudosa JC, Valencia A, Al-Shahrour F. Precision medicine needs pioneering clinical bioinformaticians. Brief Bioinform. 2017; https://doi.org/10.1093/bib/bbx144.
Dagogo-Jack I, Shaw AT. Tumour heterogeneity and resistance to cancer therapies. Nat Rev Clin Oncol. 2018:15, 81–94. https://doi.org/10.1038/nrclinonc.2017.166
Garraway LA, Verweij J, Ballman KV. Precision oncology: an overview. J Clin Oncol. 2013;31(15):1803–5.
Article
PubMed
Google Scholar
Califano A, Alvarez MJ. The recurrent architecture of tumour initiation, progression and drug sensitivity. Nat Rev Cancer. 2017;17(2):116–30.
Article
PubMed
CAS
Google Scholar
Naulaerts S, Dang CC, Ballester PJ. Precision and recall oncology: combining multiple gene mutations for improved identification of drug-sensitive tumours. Oncotarget. 2017;8:97025–40.
Article
PubMed
PubMed Central
Google Scholar
Schneider G, Schmidt-Supprian M, Rad R, Saur D. Tissue-specific tumorigenesis: context matters. Nat Rev Cancer. 2017;17(4):239–53. https://doi.org/10.1038/nrc.2017.5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mina M, Raynaud F, Tavernari D, Battistello E, Sungalee S, Saghafinia S, et al. Conditional selection of genomic alterations dictates cancer evolution and oncogenic dependencies. Cancer Cell. 2017;32(2):155–68.
Article
PubMed
CAS
Google Scholar
Letai A. Functional precision cancer medicine-moving beyond pure genomics. Nat Med. 2017;23(9):1028–35.
Article
PubMed
CAS
Google Scholar
Tsherniak A, Vazquez F, Montgomery PG, Weir BA, Kryukov G, Cowley GS, et al. Defining a cancer dependency map. Cell. 2017;170(3):564–76.
Article
PubMed
CAS
PubMed Central
Google Scholar
McDonald ER, de Weck A, Schlabach MR, Billy E, Mavrakis KJ, Hoffman GR, et al. Project DRIVE: a compendium of cancer dependencies and synthetic lethal relationships uncovered by large-scale, deep RNAi screening. Cell. 2017;170(3):577–92.
Article
PubMed
CAS
Google Scholar
Ivanov AA, Revennaugh B, Rusnak L, Gonzalez-Pecchi V, Mo X, Johns MA, et al. The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery. Bioinformatics. 2018;34:1183–91. https://doi.org/10.1093/bioinformatics/btx743
Article
PubMed
Google Scholar
Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Peat G, et al. Transcription factor activities enhance markers of drug sensitivity in cancer. Cancer Res. 2018;78:3,769–80.
Article
PubMed
Google Scholar
Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, et al. Perturbation-response genes reveal signaling footprints in cancer gene expression. Nat Commun. 2018;9(1):20.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sharp ME. Toward a comprehensive drug ontology: extraction of drug-indication relations from diverse information sources. J Biomed Semantics. 2017;8(1):2.
Article
PubMed
PubMed Central
Google Scholar