ArticleCell2016
A Landscape of Pharmacogenomic Interactions in Cancer.
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Article in Cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,251 papers.
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1,251citing papers in PubMed
70.3field-weighted citation impact, top 1% of its field
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Who cites it
1,251 citing papers in PubMed, 2,211 citations in OpenAlex.
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- DECANT: decoupling mechanism from context in single-cell drug perturbation representation.Bioinformatics (Oxford, England) · 2026Article
- OX40 (TNFRSF4) Tracks Immune Infiltration in Small Cell Lung Cancer and Shows a Cohort-Specific, Non-Replicated Association with the POU2F3/SCLC-P Subtype: A Multi-Source In Silico Analysis.International journal of molecular sciences · 2026Article
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- Exceptional treatment responses and molecular markers among 103 colorectal cancer cell lines.Molecular biomedicine · 2026Article
1,191 more citing papers are in PubMed but not listed here.
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Authors and funding
39 authors at 16 institutions in 5 countries.
Francesco IorioEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
Theo A KnijnenburgInstitute for Systems Biology, Seattle, WA 98109, USA; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands.
Daniel J VisDivision of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands.
Graham R BignellWellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
Michael P MendenEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK; Faculty of Medicine, Joint Research Centre for Computational Biomedicine, RWTH Aachen University, Aachen 52057, Germany.
Michael SchubertEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
Nanne AbenDivision of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands; Department of EEMCS, Delft University of Technology, Delft 2628 CD, the Netherlands.
Emanuel GonçalvesEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
Syd BarthorpeWellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
Howard LightfootWellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
Thomas CokelaerEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
Patricia GreningerCenter for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
Ewald van DykDivision of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands.
Han ChangGenetically Defined Diseases and Genomics, Bristol-Myers Squibb Research and Development, Hopewell, NJ 08534, USA.
Heshani de SilvaGenetically Defined Diseases and Genomics, Bristol-Myers Squibb Research and Development, Hopewell, NJ 08534, USA.
Holger HeynCancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet 08908, Barcelona, Catalonia, Spain.
Xianming DengDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA.
Regina K EganCenter for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
Qingsong LiuDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA.
Tatiana MironenkoWellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
Xeni MitropoulosCenter for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
Laura RichardsonWellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
Jinhua WangDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA.
Tinghu ZhangDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA.
Sebastian MoranCancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet 08908, Barcelona, Catalonia, Spain.
Sergi SayolsCancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet 08908, Barcelona, Catalonia, Spain.
Maryam SoleimaniWellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
David TamboreroResearch Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Barcelona 08003, Spain.
Nuria Lopez-BigasResearch Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Barcelona 08003, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain.
Petra Ross-MacdonaldGenetically Defined Diseases and Genomics, Bristol-Myers Squibb Research and Development, Hopewell, NJ 08534, USA.
Manel EstellerCancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet 08908, Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain; Department of Physiological Sciences II of the School of Medicine, University of Barcelona, L'Hospitalet 08908, Barcelona, Catalonia, Spain.
Nathanael S GrayDepartment of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA.
Daniel A HaberCenter for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
Michael R StrattonWellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
Cyril H BenesCenter for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
Lodewyk F A WesselsDivision of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands; Department of EEMCS, Delft University of Technology, Delft 2628 CD, the Netherlands; Cancer Genomics Netherlands, Uppsalalaan 8, Utrecht 3584CT, the Netherlands.
Julio Saez-RodriguezEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK; Faculty of Medicine, Joint Research Centre for Computational Biomedicine, RWTH Aachen University, Aachen 52057, Germany.
Ultan McDermottWellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK. Electronic address: um1@sanger.ac.uk.
Mathew J GarnettWellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK. Electronic address: mg12@sanger.ac.uk.
Wellcome Sanger Institute · GBEuropean Bioinformatics Institute · GBBristol-Myers Squibb (United States) · USDana-Farber Cancer Institute · USHarvard University · USInstitut d'Investigació Biomédica de Bellvitge · ESCenter for Cancer Research · USJoint Research Centre · DEOncode Institute · NLThe Netherlands Cancer Institute · NLDelft University of Technology · NLHoward Hughes Medical Institute · USInstitució Catalana de Recerca i Estudis Avançats · ESMassachusetts General Hospital · USMunicipal Institute for Medical Research · ESPompeu Fabra University · ES
Funding
Center for Systems Analysis of the Cancer RegulomeU24CA143835 · NCI · INSTITUTE FOR SYSTEMS BIOLOGY · PI SHMULEVICH, ILYA · 2009 to 2016
$10.6MCancer Research UKEuropean Research Council 268626Marie CurieNCI NIH HHS U24 CA143835Wellcome TrustWellcome Trust 086375Wellcome Trust 102696
Abstract
Systematic studies of cancer genomes have provided unprecedented insights into the molecular nature of cancer. Using this information to guide the development and application of therapies in the clinic is challenging. Here, we report how cancer-driven alterations identified in 11,289 tumors from 29 tissues (integrating somatic mutations, copy number alterations, DNA methylation, and gene expression) can be mapped onto 1,001 molecularly annotated human cancer cell lines and correlated with sensitivity to 265 drugs. We find that cell lines faithfully recapitulate oncogenic alterations identified in tumors, find that many of these associate with drug sensitivity/resistance, and highlight the importance of tissue lineage in mediating drug response. Logic-based modeling uncovers combinations of alterations that sensitize to drugs, while machine learning demonstrates the relative importance of different data types in predicting drug response. Our analysis and datasets are rich resources to link genotypes with cellular phenotypes and to identify therapeutic options for selected cancer sub-populations.
Indexed as
Analysis of VarianceAntineoplastic AgentsCell Line, TumorDNA MethylationDrug Resistance, NeoplasmGene DosageHumansModels, GeneticMutationNeoplasmsOncogenesPrecision MedicineAntineoplastic Agents
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.