The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
Open accessAbstract
The systematic translation of cancer genomic data into knowledge of tumour biology and therapeutic possibilities remains challenging. Such efforts should be greatly aided by robust preclinical model systems that reflect the genomic diversity of human cancers and for which detailed genetic and pharmacological annotation is available. Here we describe the Cancer Cell Line Encyclopedia (CCLE): a compilation of gene expression, chromosomal copy number and massively parallel sequencing data from 947 human cancer cell lines. When coupled with pharmacological profiles for 24 anticancer drugs across 479 of the cell lines, this collection allowed identification of genetic, lineage, and gene-expression-based predictors of drug sensitivity. In addition to known predictors, we found that plasma cell lineage correlated with sensitivity to IGF1 receptor inhibitors; AHR expression was associated with MEK inhibitor efficacy in NRAS-mutant lines; and SLFN11 expression predicted sensitivity to topoisomerase inhibitors. Together, our results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents. The generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of 'personalized' therapeutic regimens.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“The CCLE dataset has previously been used to identify biomarkers for drug resistance and susceptibility (Barretina et al., 2012).”
From Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model (2018) · cites this paper as Barretina et al., 2012
In the citing paper
“JDQ443 antiproliferative activity was assessed by a high-throughput cell viability assay in a large panel of KRASG12C-mutated (N = 17) and non–G12C-mutated (N = 225) cell lines from the Cancer Cell Line Encyclopedia (29). JDQ443 demonstrated potent antiproliferative activity selectively toward the KRASG12C-mutated lines (Fig. 2A and B).”
In the citing paper
“However, large-scale drug sensitivity studies using the MEK and ERK inhibitors did not reveal the same degree of selectivity in KRAS mutant cells (69, 70) (Figure 4).”
From KRAS mutation in pancreatic cancer (2021) · cites this paper as [69]
In the citing paper
“Large-scale efforts aimed at linking tumor genomic alterations with sensitivity to cytotoxic and targeted therapies have uncovered a wealth of pharmacogenomic interactions in NSCLC and other cancer types149–152.”
From Co-occurring genomic alterations in non-small-cell lung cancer biology and therapy (2019) · cites this paper as [151]
In the citing paper
“interrogation of the expression data from the cancer cell line encyclopedia20 (CCLE) database revealed that classical SCLC cell lines have significantly reduced levels of EGFR mRNA compared with adenocarcinoma cell lines”
From RB loss in resistant EGFR mutant lung adenocarcinomas that transform to small-cell lung cancer (2015) · cites this paper as [20]
In the citing paper
“Other expression datasets integrated into the latest version are the Cancer Cell Line Encyclopedia (16) and cell perturbation expression data from the Library of Integrated Network-Based Cellular Signatures (17).”
From TCRD and pharos 2021: mining the human proteome for disease biology (2021) · cites this paper as [16]
In the citing paper
“The Passport model name is accompanied by synonyms and most importantly unique identifiers utilized by established resources such as Research Resource Identifiers (RRID) (19), the Catalogue of Somatic Mutations in Cancer (COSMIC) (20) and CCLE (6) to aid data integration and alignment.”
From Cell Model Passports-a hub for clinical, genetic and functional datasets of preclinical cancer models (2019) · cites this paper as [6]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Regularization and Variable Selection Via the Elastic Net
Zou, H., & Hastie, T. (2005) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.1467-9868.2005.00503.x · Cited by 20,957
The landscape of somatic copy-number alteration across human cancers
Beroukhim, R., Mermel, C. H., Porter, D., Wei, G., Raychaudhuri, S., Donovan, J., Barretina, J., Boehm, J. S., Dobson, J., Urashima, M., et al. (2010) · Nature · doi:10.1038/nature08822 · Cited by 4,017
Self-citationA collection of breast cancer cell lines for the study of functionally distinct cancer subtypes
Neve, R. M., Chin, K., Fridlyand, J., Yeh, J., Baehner, F. L., Fevr, T., Clark, L., Bayani, N., Coppé, J., Tong, F. K., et al. (2006) · Cancer Cell · doi:10.1016/j.ccr.2006.10.008 · Cited by 3,224
Systematic identification of genomic markers of drug sensitivity in cancer cells
Garnett, M. J., Edelman, E. J., Heidorn, S. J., Greenman, C. D., Dastur, A., Lau, K. W., Greninger, P., Thompson, I. R., Luo, X., Soares, J., et al. (2012) · Nature · doi:10.1038/nature11005 · Cited by 2,456
Systematic variation in gene expression patterns in human cancer cell lines
Ross, D. T., Scherf, U., Eisen, M. B., Perou, C. M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S. S., Van de Rijn, M., Waltham, M., et al. (2000) · Nature Genetics · doi:10.1038/73432 · Cited by 2,088
Garraway, L. A., Widlund, H. R., Rubin, M. A., Getz, G., Berger, A. J., Ramaswamy, S., Beroukhim, R., Milner, D. A., Granter, S. R., Du, J., et al. (2005) · Nature · doi:10.1038/nature03664 · Cited by 1,548
Self-citationDiscovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity
Tsai, J., Lee, J. T., Wang, W., Zhang, J., Cho, H., Mamo, S., Bremer, R., Gillette, S., Kong, J., Haass, N. K., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0711741105 · Cited by 1,346
Self-citationBRAF mutation predicts sensitivity to MEK inhibition
Solit, D. B., Garraway, L. A., Pratilas, C. A., Sawai, A., Getz, G. A., Basso, A., Ye, Q., Lobo, J. M., She, Y., Osman, I., et al. (2005) · Nature · doi:10.1038/nature04304 · Cited by 1,326
Self-citationAn Information-Intensive Approach to the Molecular Pharmacology of Cancer
Weinstein, J. N., Myers, T. G., O'Connor, P. M., Friend, S. H., Fornace, A. J., Kohn, K. W., Fojo, T., Bates, S. E., Rubinstein, L., Anderson, N. L., et al. (1997) · Science · doi:10.1126/science.275.5298.343 · Cited by 1,183
High-throughput oncogene mutation profiling in human cancer
Thomas, R. K., Baker, A. C., Debiasi, R. M., Winckler, W., LaFramboise, T., Lin, W. M., Wang, M., Feng, W., Zander, T., MacConaill, L. E., et al. (2007) · Nature Genetics · doi:10.1038/ng1975 · Cited by 978
Self-citation
Cited by
Sorted by citations
Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal
Gao, J., Aksoy, B. A., Dogrusoz, U., Dresdner, G., Gross, B., Sumer, S. O., Sun, Y., Jacobsen, A., Sinha, R., Larsson, E., et al. (2013) · Science Signaling · doi:10.1126/scisignal.2004088 · Cited by 15,160
The Molecular Signatures Database Hallmark Gene Set Collection
Liberzon, A., Birger, C., Thorvaldsdóttir, H., Ghandi, M., Mesirov, J. P., & Tamayo, P. (2015) · Cell Systems · doi:10.1016/j.cels.2015.12.004 · Cited by 13,807
Self-citationInferring tumour purity and stromal and immune cell admixture from expression data
Yoshihara, K., Shahmoradgoli, M., Martínez, E., Vegesna, R., Kim, H., Torres-Garcia, W., Treviño, V., Shen, H., Laird, P. W., Levine, D. A., et al. (2013) · Nature Communications · doi:10.1038/ncomms3612 · Cited by 9,778
Self-citationThe cancer genome atlas pan-cancer analysis project
The Cancer Genome Atlas Research Network, Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., Shmulevich, I., Sander, C., & Stuart, J. M. (2013) · Nature Genetics · doi:10.1038/ng.2764 · Cited by 9,092
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
Chen, E. Y., Tan, C. M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G. V., Clark, N. R., & Ma’ayan, A. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-128 · Cited by 7,814
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
Doench, J. G., Fusi, N., Sullender, M., Hegde, M., Vaimberg, E. W., Donovan, K. F., Smith, I., Tothova, Z., Wilen, C., Orchard, R., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3437 · Cited by 4,637
Charoentong, P., Finotello, F., Angelova, M., Mayer, C., Efremova, M., Rieder, D., Hackl, H., & Trajanoski, Z. (2017) · Cell Reports · doi:10.1016/j.celrep.2016.12.019 · Cited by 5,041
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016) · Science · doi:10.1126/science.aad0501 · Cited by 4,944
Self-citationDrug repurposing: progress, challenges and recommendations
Pushpakom, S., Iorio, F., Eyers, P. A., Escott, K. J., Hopper, S., Wells, A., Doig, A., Guilliams, T., Latimer, J., McNamee, C., et al. (2019) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2018.168 · Cited by 4,718
xCell: digitally portraying the tissue cellular heterogeneity landscape
Aran, D., Hu, Z., & Butte, A. J. (2017) · Genome Biology · doi:10.1186/s13059-017-1349-1 · Cited by 4,397
Yang, W., Soares, J., Greninger, P., Edelman, E. J., Lightfoot, H., Forbes, S., Bindal, N., Beare, D., Smith, J. A., Thompson, I. R., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1111 · Cited by 4,051
Molecular and genetic properties of tumors associated with local immune cytolytic activity
Rooney, M. S., Shukla, S. A., Wu, C. J., Getz, G., & Hacohen, N. (2015) · Cell · doi:10.1016/j.cell.2014.12.033 · Cited by 3,825
Self-citationNext-generation characterization of the Cancer Cell Line Encyclopedia
Ghandi, M., Huang, F. W., Jané-Valbuena, J., Kryukov, G. V., Lo, C. C., McDonald, E. R., Barretina, J., Gelfand, E. T., Bielski, C. M., Li, H., et al. (2019) · Nature · doi:10.1038/s41586-019-1186-3 · Cited by 3,394
Self-citationmiRDB: an online database for prediction of functional microRNA targets
Chen, Y., & Wang, X. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkz757 · Cited by 3,277
Defining a Cancer Dependency Map
Tsherniak, A., Vazquez, F., Montgomery, P. G., Weir, B. A., Kryukov, G., Cowley, G. S., Gill, S., Harrington, W. F., Pantel, S., Krill-Burger, J. M., et al. (2017) · Cell · doi:10.1016/j.cell.2017.06.010 · Cited by 3,276
Self-citationCancer epigenetics: from mechanism to therapy
Dawson, M. A., & Kouzarides, T. (2012) · Cell · doi:10.1016/j.cell.2012.06.013 · Cited by 3,203
Triple-negative breast cancer: challenges and opportunities of a heterogeneous disease
Bianchini, G., Balko, J. M., Mayer, I. A., Sanders, M. E., & Gianni, L. (2016) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2016.66 · Cited by 3,079
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., Hsu, P. D., Habib, N., Gootenberg, J. S., Nishimasu, H., et al. (2015) · Nature · doi:10.1038/nature14136 · Cited by 2,825
Geeleher, P., Cox, N. J., & Huang, R. S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0107468 · Cited by 2,444
Systematic identification of genomic markers of drug sensitivity in cancer cells
Garnett, M. J., Edelman, E. J., Heidorn, S. J., Greenman, C. D., Dastur, A., Lau, K. W., Greninger, P., Thompson, I. R., Luo, X., Soares, J., et al. (2012) · Nature · doi:10.1038/nature11005 · Cited by 2,456
Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients
van de Wetering, M., Francies, H. E., Francis, J. M., Bounova, G., Iorio, F., Pronk, A., van Houdt, W., van Gorp, J., Taylor-Weiner, A., Kester, L., et al. (2015) · Cell · doi:10.1016/j.cell.2015.03.053 · Cited by 2,408
Self-citationA Landscape of Pharmacogenomic Interactions in Cancer
Iorio, F., Knijnenburg, T. A., Vis, D. J., Bignell, G. R., Menden, M. P., Schubert, M., Aben, N., Gonçalves, E., Barthorpe, S., Lightfoot, H., et al. (2016) · Cell · doi:10.1016/j.cell.2016.06.017 · Cited by 2,090
Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes
Cristescu, R., Lee, J., Nebozhyn, M., Kim, K.-M., Ting, J. C., Wong, S. S., Liu, J., Yue, Y. G., Wang, J., Yu, K., et al. (2015) · Nature Medicine · doi:10.1038/nm.3850 · Cited by 2,223
Self-citationFrampton, G. M., Fichtenholtz, A., Otto, G. A., Wang, K., Downing, S. R., He, J., Schnall-Levin, M., White, J., Sanford, E. M., An, P., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2696 · Cited by 2,157
Self-citationDrugging the undruggable RAS: Mission Possible?
Cox, A. D., Fesik, S. W., Kimmelman, A. C., Luo, J., & Der, C. J. (2014) · Nature Reviews Drug Discovery · doi:10.1038/nrd4389 · Cited by 1,997
Meyers, R. M., Bryan, J. G., McFarland, J. M., Weir, B. A., Sizemore, A. E., Xu, H., Dharia, N. V., Montgomery, P. G., Cowley, G. S., Pantel, S., et al. (2017) · Nature Genetics · doi:10.1038/ng.3984 · Cited by 1,952
Self-citationHigh-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.
Hart, T., Chandrashekhar, M., Aregger, M., Steinhart, Z., Brown, K. R., MacLeod, G., Mis, M., Zimmermann, M., Fradet-Turcotte, A., Sun, S., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.015 · Cited by 1,571
Mass-spectrometry-based draft of the human proteome
Wilhelm, M., Schlegl, J., Hahne, H., Gholami, A. M., Lieberenz, M., Savitski, M. M., Ziegler, E., Butzmann, L., Gessulat, S., Marx, H., et al. (2014) · Nature · doi:10.1038/nature13319 · Cited by 1,820
Highly Recurrent TERT Promoter Mutations in Human Melanoma
Huang, F. W., Hodis, E., Xu, M. J., Kryukov, G. V., Chin, L., & Garraway, L. A. (2013) · Science · doi:10.1126/science.1229259 · Cited by 1,816
Self-citationSchulze, K., Imbeaud, S., Letouzé, E., Alexandrov, L. B., Calderaro, J., Rebouissou, S., Couchy, G., Meiller, C., Shinde, J., Soysouvanh, F., et al. (2015) · Nature Genetics · doi:10.1038/ng.3252 · Cited by 1,803
Drost, J., & Clevers, H. (2018) · Nature Reviews Cancer · doi:10.1038/s41568-018-0007-6 · Cited by 1,790
Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing
Imielinski, M., Berger, A. H., Hammerman, P. S., Hernandez, B., Pugh, T. J., Hodis, E., Cho, J., Suh, J., Capelletti, M., Sivachenko, A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.08.029 · Cited by 1,789
Self-citationPatient-Derived Xenograft Models: An Emerging Platform for Translational Cancer Research
Hidalgo, M. M., Amant, F. C., Biankin, A. V., Budínská, E., Byrne, A. T., Caldas, C., Clarke, R. B., de Jong, S., Jonkers, J., Mælandsmo, G. M., et al. (2014) · Cancer Discovery · doi:10.1158/2159-8290.cd-14-0001 · Cited by 1,797
Identification and characterization of essential genes in the human genome
Wang, T., Birsoy, K., Hughes, N. W., Krupczak, K. M., Post, Y., Wei, J. J., Lander, E. S., & Sabatini, D. M. (2015) · Science · doi:10.1126/science.aac7041 · Cited by 1,617
Multi-omics Data Integration, Interpretation, and Its Application
Subramanian, I., Verma, S., Kumar, S., Jere, A., & Anamika, K. (2020) · Bioinformatics and Biology Insights · doi:10.1177/1177932219899051 · Cited by 1,609
The landscape of genomic alterations across childhood cancers
ICGC PedBrain-Seq Project, Gröbner, S. N., ICGC MMML-Seq Project, Worst, B. C., Weischenfeldt, J., Buchhalter, I., Kleinheinz, K., Rudneva, V. A., Johann, P. D., Balasubramanian, G. P., et al. (2018) · Nature · doi:10.1038/nature25480 · Cited by 1,572
Self-citationOrganoid Cultures Derived from Patients with Advanced Prostate Cancer
Gao, D., Vela, I., Sboner, A., Iaquinta, P. J., Karthaus, W. R., Gopalan, A., Dowling, C., Wanjala, J. N., Undvall, E. A., Arora, V. K., et al. (2014) · Cell · doi:10.1016/j.cell.2014.08.016 · Cited by 1,559
Organoid modeling of the tumor immune microenvironment
Neal, J. T., Li, X., Zhu, J., Giangarra, V., Grzeskowiak, C. L., Ju, J., Liu, I. H., Chiou, S.-H., Salahudeen, A. A., Smith, A. R., et al. (2018) · Cell · doi:10.1016/j.cell.2018.11.021 · Cited by 1,556
Finotello, F., Mayer, C., Plattner, C., Laschober, G. T., Rieder, D., Hackl, H., Krogsdam, A., Loncová, Z., Posch, W., Wilflingseder, D., et al. (2019) · Genome Medicine · doi:10.1186/s13073-019-0638-6 · Cited by 1,550
Three-dimensional in vitro cell culture models in drug discovery and drug repositioning
Langhans, S. A. (2018) · Frontiers in Pharmacology · doi:10.3389/fphar.2018.00006 · Cited by 1,522
The cellular thermal shift assay for evaluating drug target interactions in cells
Jafari, R., Almqvist, H., Axelsson, H., Ignatushchenko, M., Lundbäck, T., Nordlund, P., & Molina, D. M. (2014) · Nature Protocols · doi:10.1038/nprot.2014.138 · Cited by 1,548
Rouillard, A. D., Gundersen, G. W., Fernandez, N. F., Wang, Z., Monteiro, C. D., McDermott, M. G., & Ma’ayan, A. (2016) · Database · doi:10.1093/database/baw100 · Cited by 1,515
Induced protein degradation: an emerging drug discovery paradigm
Lai, A. C., & Crews, C. M. (2017) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.211 · Cited by 1,486
Proteogenomic characterization of human colon and rectal cancer
CPTAC, T. N., Zhang, B., Wang, J., Wang, X., Zhu, J., Liu, Q., Shi, Z., Chambers, M. C., Zimmerman, L. J., Shaddox, K. F., et al. (2014) · Nature · doi:10.1038/nature13438 · Cited by 1,462
Self-citationEvaluating cell lines as tumour models by comparison of genomic profiles
Domcke, S., Sinha, R., Levine, D. A., Sander, C., & Schultz, N. D. (2013) · Nature Communications · doi:10.1038/ncomms3126 · Cited by 1,457
LeBleu, V. S., O’Connell, J. T., Herrera, K. N. G., Wikman, H., Pantel, K., Haigis, M. C., de Carvalho, F. M., Damascena, A. S., Chinen, L. T. D., Rocha, R. M., et al. (2014) · Nature Cell Biology · doi:10.1038/ncb3039 · Cited by 1,438
Gao, H., Korn, J. M., Ferretti, S., Monahan, J. E., Wang, Y., Singh, M., Zhang, C., Schnell, C., Yang, G., Zhang, Y., et al. (2015) · Nature Medicine · doi:10.1038/nm.3954 · Cited by 1,393
Self-citationBirsoy, K., Wang, T., Chen, W. W., Freinkman, E., Abu-Remaileh, M., & Sabatini, D. M. (2015) · Cell · doi:10.1016/j.cell.2015.07.016 · Cited by 1,388
Rethinking ovarian cancer II: reducing mortality from high-grade serous ovarian cancer
Bowtell, D. D. L., Böhm, S., Ahmed, A. A., Aspuria, P.-J. P., Bast, R. C., Beral, V., Berek, J. S., Birrer, M. J., Blagden, S. P., Bookman, M. A., et al. (2015) · Nature reviews. Cancer · doi:10.1038/nrc4019 · Cited by 1,395
A Proteome-Scale Map of the Human Interactome Network
Rolland, T., Taşan, M., Charloteaux, B., Pevzner, S. J., Zhong, Q., Sahni, N., Yi, S. S., Lemmens, I. H., Fontanillo, C., Mosca, R., et al. (2014) · Cell · doi:10.1016/j.cell.2014.10.050 · Cited by 1,381
Primary Resistance to PD-1 Blockade Mediated by JAK1/2 Mutations
Shin, D. S., Zaretsky, J. M., Escuin-Ordinas, H., Garcia-Diaz, A., Hu-Lieskovan, S., Kalbasi, A., Grasso, C. S., Hugo, W., Sandoval, S., Torrejon, D. Y., et al. (2017) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-1223 · Cited by 1,337
Cytoplasmic chromatin triggers inflammation in senescence and cancer
Dou, Z., Ghosh, K., Vizioli, M. G., Zhu, J., Sen, P., Wangensteen, K. J., Simithy, J., Lan, Y., Lin, Y., Zhou, Z., et al. (2017) · Nature · doi:10.1038/nature24050 · Cited by 1,335
Lessons from the Cancer Genome
Garraway, L. A., & Lander, E. S. (2013) · Cell · doi:10.1016/j.cell.2013.03.002 · Cited by 1,377
Self-citationMDM2, MDMX and p53 in oncogenesis and cancer therapy
Wade, M., Li, Y.-C., & Wahl, G. M. (2013) · Nature Reviews Cancer · doi:10.1038/nrc3430 · Cited by 1,279
Molecular subtypes of small cell lung cancer: a synthesis of human and mouse model data
Rudin, C. M., Poirier, J. T., Byers, L. A., Dive, C., Dowlati, A., George, J., Heymach, J. V., Johnson, J. E. B., Lehman, J. M., MacPherson, D. P., et al. (2019) · Nature reviews. Cancer · doi:10.1038/s41568-019-0133-9 · Cited by 1,251
Activation of the PD-1 Pathway Contributes to Immune Escape in EGFR-Driven Lung Tumors
Akbay, E. A., Koyama, S., Carretero, J., Altabef, A. B., Tchaicha, J. H., Christensen, C. L., Mikse, O. R., Cherniack, A. D., Beauchamp, E. M., Pugh, T. J., et al. (2013) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0310 · Cited by 1,250
Self-citationTumour heterogeneity in the clinic
Bedard, P. L., Hansen, A. R., Ratain, M. J., & Siu, L. L. (2013) · Nature · doi:10.1038/nature12627 · Cited by 1,231
Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma
Krauthammer, M., Kong, Y., Ha, B. H., Evans, P., Bacchiocchi, A., McCusker, J. P., Cheng, E., Davis, M. J., Goh, G., Choi, M., et al. (2012) · Nature Genetics · doi:10.1038/ng.2359 · Cited by 1,191
Cancer Genetics and Epigenetics: Two Sides of the Same Coin?
You, J. S., & Jones, P. A. (2012) · Cancer Cell · doi:10.1016/j.ccr.2012.06.008 · Cited by 1,206
Benchmark and integration of resources for the estimation of human transcription factor activities
Garcia-Alonso, L., Holland, C. H., Ibrahim, M. M., Turei, D., & Saez-Rodriguez, J. (2019) · Genome Research · doi:10.1101/gr.240663.118 · Cited by 1,122
Combinatorial drug therapy for cancer in the post-genomic era
Al-Lazikani, B., Banerji, U., & Workman, P. (2012) · Nature Biotechnology · doi:10.1038/nbt.2284 · Cited by 1,070
Antitumor activity of the glutaminase inhibitor CB-839 in triple-negative breast cancer
Gross, M. I., Demo, S. D., Dennison, J. B., Chen, L., Chernov-Rogan, T., Goyal, B., Janes, J. R., Laidig, G. J., Lewis, E. R., Li, J., et al. (2014) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-13-0870 · Cited by 1,068
Co-occurring genomic alterations in non-small-cell lung cancer biology and therapy
Skoulidis, F., & Heymach, J. V. (2019) · Nature Reviews Cancer · doi:10.1038/s41568-019-0179-8 · Cited by 1,019
Sadanandam, A., Lyssiotis, C. A., Homicsko, K., Collisson, E. A., Gibb, W. J., Wullschleger, S., Ostos, L. C. G., Lannon, W. A., Grotzinger, C., Del Rio, M., et al. (2013) · Nature Medicine · doi:10.1038/nm.3175 · Cited by 960
Sensitive tumour detection and classification using plasma cell-free DNA methylomes
Shen, S. Y., Singhania, R., Fehringer, G., Chakravarthy, A., Roehrl, M. H. A., Chadwick, D., Zuzarte, P. C., Borgida, A., Wang, T. T., Li, T., et al. (2018) · Nature · doi:10.1038/s41586-018-0703-0 · Cited by 983
Next-Generation Machine Learning for Biological Networks
Camacho, D. M., Collins, K. M., Powers, R. K., Costello, J. C., & Collins, J. J. (2018) · Cell · doi:10.1016/j.cell.2018.05.015 · Cited by 1,012
Alvarez, M. J., Shen, Y., Giorgi, F. M., Lachmann, A., Ding, B. B., Ye, B. H., & Califano, A. (2016) · Nature Genetics · doi:10.1038/ng.3593 · Cited by 966
Quantitative Proteomics of the Cancer Cell Line Encyclopedia
Nusinow, D. P., Szpyt, J., Ghandi, M., Rose, C. M., McDonald, E. R., Kalocsay, M., Jané-Valbuena, J., Gelfand, E., Schweppe, D. K., Jedrychowski, M., et al. (2020) · Cell · doi:10.1016/j.cell.2019.12.023 · Cited by 957
Self-citation5-fluorouracil and other fluoropyrimidines in colorectal cancer: Past, present and future
Vodenkova, S., Buchler, T., Cervena, K., Veskrnova, V., Vodicka, P., & Vymetalkova, V. (2020) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2019.107447 · Cited by 956
Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine
Pauli, C., Hopkins, B. D., Prandi, D., Shaw, R. C., Fedrizzi, T., Sboner, A., Sailer, V., Augello, M. A., Puca, L., Rosati, R., et al. (2017) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-1154 · Cited by 964
Genetic and transcriptional evolution alters cancer cell line drug response
Ben-David, U., Siranosian, B., Ha, G., Tang, H., Oren, Y., Hinohara, K., Strathdee, C. A., Dempster, J., Lyons, N. J., Burns, R., et al. (2018) · Nature · doi:10.1038/s41586-018-0409-3 · Cited by 931
Self-citationAllosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases
Chen, Y.-N. P., LaMarche, M. J., Chan, H. M., Fekkes, P., Garcia-Fortanet, J., Acker, M. G., Antonakos, B., Chen, C. H.-T., Chen, Z., Cooke, V. G., et al. (2016) · Nature · doi:10.1038/nature18621 · Cited by 925
Self-citationEpigenetic and genetic features of 24 colon cancer cell lines
Ahmed, D., Eide, P. W., Eilertsen, I. A., Danielsen, S. A., Eknæs, M., Hektoen, M., Lind, G. E., & Lothe, R. A. (2013) · Oncogenesis · doi:10.1038/oncsis.2013.35 · Cited by 933
Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis
Chen, S., Sanjana, N. E., Zheng, K., Shalem, O., Lee, K., Shi, X., Scott, D. A., Song, J., Pan, J. Q., Weissleder, R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.02.038 · Cited by 862
Correlating chemical sensitivity and basal gene expression reveals mechanism of action
Rees, M. G., Seashore-Ludlow, B. A., Cheah, J. H., Adams, D., Price, E. V., Gill, S., Javaid, S., Coletti, M. E., Jones, V., Bodycombe, N. E., et al. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1986 · Cited by 883
Self-citationSubgroup-specific structural variation across 1,000 medulloblastoma genomes
Northcott, P. A., Shih, D. J. H., Peacock, J., Garzia, L., Morrissy, A. S., Zichner, T., Stütz, A. M., Korshunov, A., Reimand, J., Schumacher, S. E., et al. (2012) · Nature · doi:10.1038/nature11327 · Cited by 887
Self-citationGeeleher, P., Cox, N. J., & Huang, R. S. (2014) · Genome biology · doi:10.1186/gb-2014-15-3-r47 · Cited by 897
Zou, Y., Palte, M. J., Deik, A. A., Li, H., Eaton, J. K., Wang, W., Tseng, Y.-Y., Deasy, R., Kost-Alimova, M., Dančík, V., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09277-9 · Cited by 887
Discovering the anticancer potential of non-oncology drugs by systematic viability profiling
Corsello, S. M., Nagari, R. T., Spangler, R. D., Rossen, J., Kocak, M., Bryan, J. G., Humeidi, R., Peck, D., Wu, X., Tang, A. A., et al. (2020) · Nature Cancer · doi:10.1038/s43018-019-0018-6 · Cited by 878
Self-citationProteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma
Gillette, M. A., Satpathy, S., Cao, S., Dhanasekaran, S. M., Vasaikar, S. V., Krug, K., Petralia, F., Li, Y., Liang, W.-W., Reva, B., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.013 · Cited by 820
Self-citationScalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
Ellrott, K., Bailey, M. H., Saksena, G., Covington, K. R., Kandoth, C., Stewart, C., Hess, J. M., Ma, S., Chiotti, K., McLellan, M. D., et al. (2018) · Cell Systems · doi:10.1016/j.cels.2018.03.002 · Cited by 846
Self-citationDrugging Topoisomerases: Lessons and Challenges
Pommier, Y. G. (2012) · ACS Chemical Biology · doi:10.1021/cb300648v · Cited by 867
Basu, A. B., Bodycombe, N. E., Cheah, J. H., Price, E. V., Liu, K., Schaefer, G. I., Ebright, R. Y., Stewart, M. L., Ito, D., Wang, S. Y., et al. (2013) · Cell · doi:10.1016/j.cell.2013.08.003 · Cited by 828
Self-citationTargeting RAF kinases for cancer therapy: BRAF-mutated melanoma and beyond
Holderfield, M. T., Deuker, M. M., McCormick, F. P., & McMahon, M. (2014) · Nature reviews. Cancer · doi:10.1038/nrc3760 · Cited by 850
Schug, Z. T., Peck, B., Jones, D. T., Zhang, Q., Grosskurth, S., Alam, I. S., Goodwin, L. M., Smethurst, E., Mason, S., Blyth, K., et al. (2015) · Cancer Cell · doi:10.1016/j.ccell.2014.12.002 · Cited by 820
Ooft, S. N., Weeber, F., Dijkstra, K. K., McLean, C. M., Kaing, S., van Werkhoven, E., Schipper, L., Hoes, L., Vis, D. J., van de Haar, J., et al. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aay2574 · Cited by 813
Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset
Seashore-Ludlow, B., Rees, M. G., Cheah, J. H., Cokol, M., Price, E. V., Coletti, M. E., Jones, V., Bodycombe, N. E., Soule, C. K., Gould, J., et al. (2015) · Cancer Discovery · doi:10.1158/2159-8290.cd-15-0235 · Cited by 813
Self-citationThe Cellosaurus, a Cell-Line Knowledge Resource
Bairoch, A. (2018) · Journal of Biomolecular Techniques JBT · doi:10.7171/jbt.18-2902-002 · Cited by 807
Tan, T. Z., Miow, Q. H., Miki, Y., Noda, T., Mori, S., Huang, R. Y., & Thiery, J. P. (2014) · EMBO Molecular Medicine · doi:10.15252/emmm.201404208 · Cited by 792
NFS1 undergoes positive selection in lung tumours and protects cells from ferroptosis
Alvarez, S. W., Sviderskiy, V. O., Terzi, E. M., Papagiannakopoulos, T., Moreira, A. L., Adams, S., Sabatini, D. M., Birsoy, K., & Possemato, R. (2017) · Nature · doi:10.1038/nature24637 · Cited by 787
Biochemical and Structural Analysis of Common Cancer-Associated KRAS Mutations
Hunter, J. C., Manandhar, A., Carrasco, M. A., Gurbani, D., Gondi, S., & Westover, K. D. (2015) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-15-0203 · Cited by 786
Sustained proliferation in cancer: Mechanisms and novel therapeutic targets
Feitelson, M. A., Arzumanyan, A. L., Kulathinal, R. J., Blain, S. W., Holcombe, R. F., Mahajna, J. A., Marino, M., Martínez‐Chantar, M. L., Nawroth, R., Sánchez-García, I., et al. (2015) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2015.02.006 · Cited by 818
Beyond GWASs: Illuminating the Dark Road from Association to Function
Edwards, S. L., Beesley, J., French, J. D., & Dunning, A. M. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.012 · Cited by 784
Artificial Intelligence in Cancer Research and Precision Medicine
Bhinder, B., Gilvary, C., Madhukar, N. S., & Elemento, O. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-0090 · Cited by 781
A community effort to assess and improve drug sensitivity prediction algorithms
Community, N. D., Costello, J. C., Heiser, L. M., Georgii, E., Gönen, M., Menden, M. P., Wang, N. J., Bansal, M., Ammad-ud-din, M., Hintsanen, P., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2877 · Cited by 782
Long noncoding RNA MALAT1 suppresses breast cancer metastasis
Kim, J., Piao, H.-L., Kim, B., Yao, F., Han, Z., Wang, Y., Xiao, Z., Siverly, A. N., Lawhon, S. E., Ton, B. N., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0252-3 · Cited by 767
De Sousa E Melo, F., Wang, X., Jansen, M., Fessler, E., Trinh, A., de Rooij, L. P. M. H., de Jong, J. H., de Boer, O. J., van Leersum, R., Bijlsma, M. F., et al. (2013) · Nature Medicine · doi:10.1038/nm.3174 · Cited by 771
β-Catenin-Driven Cancers Require a YAP1 Transcriptional Complex for Survival and Tumorigenesis
Rosenbluh, J., Nijhawan, D., Cox, A. G., Li, X., Neal, J. T., Schafer, E. J., Zack, T. I., Wang, X., Tsherniak, A., Schinzel, A. C., et al. (2012) · Cell · doi:10.1016/j.cell.2012.11.026 · Cited by 757
Self-citationIn Vitro Tumor Models: Advantages, Disadvantages, Variables, and Selecting the Right Platform
Katt, M. E., Placone, A. L., Wong, A. D., Xu, Z. S., & Searson, P. C. (2016) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2016.00012 · Cited by 754
Metadata
- Authors
- Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A. A., Kim, S., Wilson, C. J., Lehár, J., Kryukov, G. V., Sonkin, D., Reddy, A., Liu, M., Murray, L., Berger, M. F., Monahan, J. E., Morais, P., Meltzer, J., Korejwa, A., Jané-Valbuena, J., Mapa, F. A., Thibault, J., Bric-Furlong, E., Raman, P., Shipway, A., Engels, I. H., Cheng, J., Yu, G. K., Yu, J., Aspesi, P., de Silva, M., Jagtap, K., Jones, M. D., Wang, L., Hatton, C., Palescandolo, E., Gupta, S., Mahan, S., Sougnez, C., Onofrio, R. C., Liefeld, T., MacConaill, L., Winckler, W., Reich, M., Li, N., Mesirov, J. P., Gabriel, S. B., Getz, G., Ardlie, K., Chan, V., Myer, V. E., Weber, B. L., Porter, J., Warmuth, M., Finan, P., Harris, J. L., Meyerson, M., Golub, T. R., Morrissey, M. P., Sellers, W. R., Schlegel, R., & Garraway, L. A.
- Affiliations
- Broad Institute (US)
- Genomics Institute of the Novartis Research Foundation (US)
- Harvard University (US)
- Corresponding author
- Schlegel, Robert
- Garraway, Levi A.
- ORCID
- Barretina, Jordi
- Stransky, Nicolas
- Venkatesan, Kavitha
- Wilson, Christopher J.
- Lehár, Joseph
- Kryukov, Gregory V.
- Sonkin, Dmitriy
- Reddy, Anupama
- Liu, Manway
- Murray, Lauren
- Berger, Michael F.
- Monahan, John E.
- Mapa, Felipa A.
- Raman, Pichai
- Yu, Guoying K.
- Yu, Jianjun
- Aspesi, Peter
- Jones, Michael D.
- Wang, Li
- Gupta, Supriya
- Liefeld, Ted
- MacConaill, Laura
- Winckler, Wendy
- Reich, Michael
- Li, Nanxin
- Mesirov, Jill P.
- Gabriel, Stacey B.
- Getz, Gad
- Ardlie, Kristin
- Chan, Vivien
- Myer, Vic E.
- Weber, Barbara L.
- Meyerson, Matthew
- Golub, Todd R.
- Sellers, William R.
- Garraway, Levi A.
- Venue
- Nature
- Published
- 2012-03-28
- Volume
- 483
- Issue
- 7391
- Pages
- 603-607
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3320027
- OpenAlex
- W2043398720
- Cited by
- 7,950
- References
- 28
- Citations by year
- 2026: 361 · 2025: 501 · 2024: 617 · 2023: 719 · 2022: 723 · 2021: 839 · 2020: 682 · 2019: 687 · 2018: 628 · 2017: 500 · 2016: 516 · 2015: 436 · 2014: 348 · 2013: 283 · 2012: 103
- FWCI
- 124.24
- Type
- journal article
- Language
- en
- Update notices
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health (DP2OD002750)
- National Human Genome Research Institute (U54HG003067)
- National Cancer Institute (R33CA155554, R33CA126674)
- National Institute of General Medical Sciences (R01GM074024)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- Cancer Cell Line Encyclopedia, anticancer drug sensitivity, drug resistance, cancer cell lines, Ewing sarcoma, PARP inhibitors, SLFN11, topoisomerase inhibitors, MEK inhibitors, NRAS mutation, aryl hydrocarbon receptor, gene expression profiles, chromosomal copy number, predictive modeling, precision oncology
- MeSH terms
- Antineoplastic Agents, Chromosomes, Human, Clinical Trials as Topic, Drug Screening Assays, Antitumor, Encyclopedias as Topic, Humans, Models, Biological, Neoplasms, Pharmacogenetics, Plasma Cells, Genes, ras, Genome, Human, Gene Expression Regulation, Neoplastic, Databases, Factual, Sequence Analysis, DNA, Receptor, IGF Type 1, Receptors, Aryl Hydrocarbon, Cell Lineage, Gene Expression Profiling, Mitogen-Activated Protein Kinase Kinases, Genomics, Cell Line, Tumor, Precision Medicine, Topoisomerase Inhibitors
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
