ArticleNature communications2019
Genetic determinants of the molecular portraits of epithelial cancers.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed.
- Molecular evaluation of residual disease following neoadjuvant chemotherapy in triple-negative breast cancer CALGB 40603 (Alliance).The Journal of clinical investigation · 2026Trial
- Identifying Locally Recurrent Versus Second Primary Breast Cancer: Genomic Versus Clinical Criteria from Carolina Breast Cancer Study Phase III.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2026Trial
- Identification and Characterization of Cancer-Related Risk Metabolic Subpathways Reveal Their Functional Significance in Cancer.International journal of molecular sciences · 2026Article
- Quantitative HER2 tissue and plasma profiling predicts the activity of trastuzumab deruxtecan for breast cancer.NPJ precision oncology · 2026Article
- Luminal and Basal Subtypes Across Carcinomas: Molecular Programs Beyond Tissue of Origin.Cancers · 2025Review
- Prognostic and molecular multi-platform analysis of CALGB 40603 (Alliance) and public triple-negative breast cancer datasets.NPJ breast cancer · 2025Article
- Defining the regulatory logic of breast cancer using single-cell epigenetic and transcriptome profiling.Cell genomics · 2025Article
- Understanding metastasis mixed-treatment responses through genomic analyses.NPJ breast cancer · 2025Article
- Patritumab deruxtecan in HER2-negative breast cancer: part B results of the window-of-opportunity SOLTI-1805 TOT-HER3 trial and biological determinants of early response.Nature communications · 2024Article
- Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling.bioRxiv : the preprint server for biology · 2024Article
- Applying a GAN-based classifier to improve transcriptome-based prognostication in breast cancer.PLoS computational biology · 2023Article
- Whole-exome sequencing identifies a set of genes as markers of hepatocellular carcinoma early recurrence.Hepatology international · 2023Article
- Circulating tumor DNA reveals complex biological features with clinical relevance in metastatic breast cancer.Nature communications · 2023Article
- Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis.Nature cancer · 2023Article
- Invention of 3Mint for feature grouping and scoring in multi-omics.Frontiers in genetics · 2023Article
- Integrated DNA and RNA Sequencing Reveals Drivers of Endocrine Resistance in Estrogen Receptor-Positive Breast Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Article
- Gene-Level Germline Contributions to Clinical Risk of Recurrence Scores in Black and White Patients with Breast Cancer.Cancer research · 2022Article
- Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy.Frontiers in genetics · 2021Article
- Elastic Net Models Based on DNA Copy Number Variations Predicts Clinical Features, Expression Signatures, and Mutations in Lung Adenocarcinoma.Frontiers in genetics · 2021Article
- Bimodal age distribution at diagnosis in breast cancer persists across molecular and genomic classifications.Breast cancer research and treatment · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The ability to characterize and predict tumor phenotypes is crucial to precision medicine. In this study, we present an integrative computational approach using a genome-wide association analysis and an Elastic Net prediction method to analyze the relationship between DNA copy number alterations and an archive of gene expression signatures. Across breast cancers, we are able to quantitatively predict many gene signatures levels within individual tumors with high accuracy based upon DNA copy number features alone, including proliferation status and Estrogen-signaling pathway activity. We can also predict many other key phenotypes, including intrinsic molecular subtypes, estrogen receptor status, and TP53 mutation. This approach is also applied to TCGA Pan-Cancer, which identify repeatedly predictable signatures across tumor types including immune features in lung squamous and basal-like breast cancers. These Elastic Net DNA predictors could also be called from DNA-based gene panels, thus facilitating their use as biomarkers to guide therapeutic decision making.
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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.