ArticleBMC genomics2013
A simple and reproducible breast cancer prognostic test.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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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
28 citing papers in PubMed.
- Article
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- Hepatic G Protein-Coupled Receptor 180 Deficiency Ameliorates High Fat Diet-Induced Lipid Accumulation via the Gi-PKA-SREBP Pathway.Nutrients · 2023Article
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- Cancer Cells Enter an Adaptive Persistence to Survive Radiotherapy and Repopulate Tumor.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Distinct immune signature predicts progression of vestibular schwannoma and unveils a possible viral etiology.Journal of experimental & clinical cancer research : CR · 2022Article
- ZNF92, an unexplored transcription factor with remarkably distinct breast cancer over-expression associated with prognosis and cell-of-origin.NPJ breast cancer · 2022Article
- A top scoring pairs classifier for recent HIV infections.Statistics in medicine · 2021Article
- Characterization and Proteome of Circulating Extracellular Vesicles as Potential Biomarkers for NASH.Hepatology communications · 2020Article
- Overview of Breast Cancer and Implications of Overtreatment of Early-Stage Breast Cancer: An Indian Perspective.JCO global oncology · 2020Review
- A qualitative transcriptional signature for predicting the biochemical recurrence risk of prostate cancer patients after radical prostatectomy.The Prostate · 2020Article
- Oncotype DX Breast Cancer recurrence score resists inter-assay reproducibility with RTScientific reports · 2019Article
- A biological function based biomarker panel optimization process.Scientific reports · 2019Article
- Article
- Digitizing omics profiles by divergence from a baseline.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Cloud computing for genomic data analysis and collaboration.Nature reviews. Genetics · 2018Review
- Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer.Nature communications · 2017Article
- Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO.BMC bioinformatics · 2017Article
- Meta-analytic support vector machine for integrating multiple omics data.BioData mining · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundA small number of prognostic and predictive tests based on gene expression are currently offered as reference laboratory tests. In contrast to such success stories, a number of flaws and errors have recently been identified in other genomic-based predictors and the success rate for developing clinically useful genomic signatures is low. These errors have led to widespread concerns about the protocols for conducting and reporting of computational research. As a result, a need has emerged for a template for reproducible development of genomic signatures that incorporates full transparency, data sharing and statistical robustness.
resultsHere we present the first fully reproducible analysis of the data used to train and test MammaPrint, an FDA-cleared prognostic test for breast cancer based on a 70-gene expression signature. We provide all the software and documentation necessary for researchers to build and evaluate genomic classifiers based on these data. As an example of the utility of this reproducible research resource, we develop a simple prognostic classifier that uses only 16 genes from the MammaPrint signature and is equally accurate in predicting 5-year disease free survival.
conclusionsOur study provides a prototypic example for reproducible development of computational algorithms for learning prognostic biomarkers in the era of personalized medicine.
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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.