ArticleGenome biology2016
Cancer biomarker discovery is improved by accounting for variability in general levels of drug sensitivity in pre-clinical models.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it, 43 citations in OpenAlex.
- Tissue specificity of in vitro drug sensitivity.Journal of the American Medical Informatics Association : JAMIA · 2018Pooled it
- DeepCCDS: Interpretable Deep Learning Framework for Predicting Cancer Cell Drug Sensitivity through Characterizing Cancer Driver Signals.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Drug molecular representations for drug response predictions: a comprehensive investigation via machine learning methods.Scientific reports · 2025Article
- A precision oncology-focused deep learning framework for personalized selection of cancer therapy.bioRxiv : the preprint server for biology · 2024Article
- Overcoming limitations in current measures of drug response may enable AI-driven precision oncology.NPJ precision oncology · 2024Article
- Modeling combination therapies in patient cohorts and cell cultures using correlated drug action.iScience · 2024Article
- Development of prognostic signatures and risk index related to lipid metabolism in ccRCC.Frontiers in oncology · 2024Article
- Clinical forecasting of acute myeloid leukemia using ex vivo drug-sensitivity profiling.Cell reports methods · 2023Article
- Patient-Derived In Vitro and In Vivo Models of Cancer.Advances in experimental medicine and biology · 2022Article
- oncoPredict: an R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data.Briefings in bioinformatics · 2021Article
- Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia.NPJ precision oncology · 2021Article
- PaccManniScience · 2021Article
- Deep generative neural network for accurate drug response imputation.Nature communications · 2021Article
- An Improved Anticancer Drug-Response Prediction Based on an Ensemble Method Integrating Matrix Completion and Ridge Regression.Molecular therapy. Nucleic acids · 2020Article
- PaccMann: a web service for interpretable anticancer compound sensitivity prediction.Nucleic acids research · 2020Article
- Network-based Biased Tree Ensembles (NetBiTE) for Drug Sensitivity Prediction and Drug Sensitivity Biomarker Identification in Cancer.Scientific reports · 2019Article
- Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction.Nucleic acids research · 2019Article
- Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features.PLoS computational biology · 2019Article
- The 4717C > G polymorphism in periplakin modulates sensitivity to EGFR inhibitors.Scientific reports · 2019Article
- Computational Analyses Connect Small-Molecule Sensitivity to Cellular Features Using Large Panels of Cancer Cell Lines.Methods in molecular biology (Clifton, N.J.) · 2019Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
We show that variability in general levels of drug sensitivity in pre-clinical cancer models confounds biomarker discovery. However, using a very large panel of cell lines, each treated with many drugs, we could estimate a general level of sensitivity to all drugs in each cell line. By conditioning on this variable, biomarkers were identified that were more likely to be effective in clinical trials than those identified using a conventional uncorrected approach. We find that differences in general levels of drug sensitivity are driven by biologically relevant processes. We developed a gene expression based method that can be used to correct for this confounder in future studies.
Identifiers
What OpenQuestion holds
Registered trials
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.