Cited by 3,394Cancer Genomics and DiagnosticsChromatin Remodeling and CancerGene expression and cancer classification

The DOI matches its Crossref record; 67 of the 67 references it cites were found in a registry or an index.

Next-generation characterization of the Cancer Cell Line Encyclopedia

Open access

Ghandi, Mahmoud, Huang, Franklin W., Jané-Valbuena, Judit, Kryukov, Gregory V., Lo, Christopher C., McDonald, E. Robert, Barretina, Jordi, Gelfand, Ellen T., Bielski, Craig M., Li, Haoxin, Hu, Kevin, Andreev-Drakhlin, Alexander Y., Kim, Jaegil, Hess, Julian M., Haas, Brian J., Aguet, François, Weir, Barbara A., Rothberg, Michael V., Paolella, Brenton R., Lawrence, Michael S., Akbani, Rehan, Lu, Yiling, Tiv, Hong L., Gokhale, Prafulla C., de Weck, Antoine, Mansour, Ali Amin, Oh, Coyin, Shih, Juliann, Hadi, Kevin, Rosen, Yanay, Bistline, Jonathan, Venkatesan, Kavitha, Reddy, Anupama, Sonkin, Dmitriy, Liu, Manway, Lehar, Joseph, Korn, Joshua M., Porter, Dale A., Jones, Michael D., Golji, Javad, Caponigro, Giordano, Taylor, Jordan E., Dunning, Caitlin M., Creech, Amanda L., Warren, Allison C., McFarland, James M., Zamanighomi, Mahdi, Kauffmann, Audrey, Stransky, Nicolas, Imielinski, Marcin, Maruvka, Yosef E., Cherniack, Andrew D., Tsherniak, Aviad, Vazquez, Francisca, Jaffe, Jacob D., Lane, Andrew A., Weinstock, David M., Johannessen, Cory M., Morrissey, Michael P., Stegmeier, Frank, Schlegel, Robert, Hahn, William C., Getz, Gad, Mills, Gordon B., Boehm, Jesse S., Golub, Todd R., Garraway, Levi A., Sellers, William R.·2019·Nature

DOI 10.1038/s41586-019-1186-3PMC PMC6697103

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Abstract

Large panels of comprehensively characterized human cancer models, including the Cancer Cell Line Encyclopedia (CCLE), have provided a rigorous framework with which to study genetic variants, candidate targets, and small-molecule and biological therapeutics and to identify new marker-driven cancer dependencies. To improve our understanding of the molecular features that contribute to cancer phenotypes, including drug responses, here we have expanded the characterizations of cancer cell lines to include genetic, RNA splicing, DNA methylation, histone H3 modification, microRNA expression and reverse-phase protein array data for 1,072 cell lines from individuals of various lineages and ethnicities. Integration of these data with functional characterizations such as drug-sensitivity, short hairpin RNA knockdown and CRISPR–Cas9 knockout data reveals potential targets for cancer drugs and associated biomarkers. Together, this dataset and an accompanying public data portal provide a resource for the acceleration of cancer research using model cancer cell lines. The original Cancer Cell Line Encyclopedia (CCLE) is expanded with deeper characterization of over 1,000 cell lines, including genomic, transcriptomic, and proteomic data, and integration with drug-sensitivity and gene-dependency data.

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Authors: 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., Hu, K., Andreev-Drakhlin, A. Y., Kim, J., Hess, J. M., Haas, B. J., Aguet, F., Weir, B. A., Rothberg, M. V., Paolella, B. R., Lawrence, M. S., Akbani, R., Lu, Y., Tiv, H. L., Gokhale, P. C., de Weck, A., Mansour, A. A., Oh, C., Shih, J., Hadi, K., Rosen, Y., Bistline, J., Venkatesan, K., Reddy, A., Sonkin, D., Liu, M., Lehar, J., Korn, J. M., Porter, D. A., Jones, M. D., Golji, J., Caponigro, G., Taylor, J. E., Dunning, C. M., Creech, A. L., Warren, A. C., McFarland, J. M., Zamanighomi, M., Kauffmann, A., Stransky, N., Imielinski, M., Maruvka, Y. E., Cherniack, A. D., Tsherniak, A., Vazquez, F., Jaffe, J. D., Lane, A. A., Weinstock, D. M., Johannessen, C. M., Morrissey, M. P., Stegmeier, F., Schlegel, R., Hahn, W. C., Getz, G., Mills, G. B., Boehm, J. S., Golub, T. R., Garraway, L. A., & Sellers, W. R.
Affiliations: Broad Institute (US)
The University of Texas MD Anderson Cancer Center (US)
Cornell University (US)
National Cancer Institute (US)
Novartis Institutes for BioMedical Research (CH)
Dana-Farber Cancer Institute (US)
Corresponding author: Sellers, William R.
ORCID: Ghandi, Mahmoud
Huang, Franklin W.
Kryukov, Gregory V.
McDonald, E. Robert
Barretina, Jordi
Li, Haoxin
Hu, Kevin
Andreev-Drakhlin, Alexander Y.
Kim, Jaegil
Hess, Julian M.
Haas, Brian J.
Aguet, François
Rothberg, Michael V.
Paolella, Brenton R.
Lawrence, Michael S.
Akbani, Rehan
Lu, Yiling
Tiv, Hong L.
Gokhale, Prafulla C.
Oh, Coyin
Shih, Juliann
Hadi, Kevin
Rosen, Yanay
Venkatesan, Kavitha
Reddy, Anupama
Sonkin, Dmitriy
Liu, Manway
Korn, Joshua M.
Jones, Michael D.
Taylor, Jordan E.
Creech, Amanda L.
McFarland, James M.
Zamanighomi, Mahdi
Kauffmann, Audrey
Stransky, Nicolas
Imielinski, Marcin
Maruvka, Yosef E.
Cherniack, Andrew D.
Tsherniak, Aviad
Jaffe, Jacob D.
Lane, Andrew A.
Weinstock, David M.
Johannessen, Cory M.
Stegmeier, Frank
Hahn, William C.
Getz, Gad
Mills, Gordon B.
Boehm, Jesse S.
Golub, Todd R.
Garraway, Levi A.
Sellers, William R.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2019-05
Volume: 569
Issue: 7757
Pages: 503-508
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/s41586-019-1186-3
PMC: PMC6697103
OpenAlex: W2944727022
Semantic Scholar: b3631d8d2656c0c72ad92f3b0a77af2afde649a5
Cited by: 3,394
References: 67
Citations by year: 2026: 297 · 2025: 472 · 2024: 560 · 2023: 551 · 2022: 550 · 2021: 594 · 2020: 306 · 2019: 59
FWCI: 121.99
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
RePEc: Research Papers in Economics (submittedVersion)
eScholarship (California Digital Library) (submittedVersion)
Funders: European Hematology Association (TRTH56)
National Institutes of Health (5r21da025720-02)
National Institute on Drug Abuse (R21-DA025720)
National Cancer Institute (R50CA221675, P50CA217685, R01CA219943, P50CA098258, U24CA180922, U54CA224068, U24CA210949, U24CA210950, R50CA211461, R37CA225191, U01CA217842, U01CA176058, P30CA016672)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
Keywords: Cancer Cell Line Encyclopedia, cancer cell lines, drug sensitivity, gene dependency, RNA splicing, DNA methylation, histone H3 modifications, microRNA expression, reverse phase protein array, CRISPR/Cas9 knockout, shRNA knockdown, therapeutic target, biomarkers, multi-omics integration, public data portals
MeSH terms: Gene Editing, Antineoplastic Agents, Ethnicity, Histones, Humans, Neoplasms, RNA Splicing, Biomarkers, Tumor, Drug Resistance, Neoplasm, DNA Methylation, MicroRNAs, Protein Array Analysis, Cell Line, Tumor, Molecular Targeted Therapy

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