ArticleProceedings of the National Academy of Sciences of the United States of America2006
Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 269 papers, 5 of them syntheses that pooled it.
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Who cites it
269 citing papers in PubMed, 5 syntheses or guidelines pooled it.
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- Concordance analysis of microarray studies identifies representative gene expression changes in Parkinson's disease: a comparison of 33 human and animal studies.BMC neurology · 2017Pooled it
- Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data.Scientific reports · 2016Pooled it
- A common gene signature across multiple studies relate biomarkers and functional regulation in tolerance to renal allograft.Kidney international · 2015Pooled it
- Development and validation of a quantitative real-time polymerase chain reaction classifier for lung cancer prognosis.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2011Trial
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- Activated Hippo Pathway is Associated with a Worse Response to Trastuzumab and Worse Survival in HER2-Positive Breast Cancer.Annals of surgical oncology · 2025Article
- Assessing Random Forest self-reproducibility for optimal short biomarker signature discovery.Briefings in bioinformatics · 2025Article
- All (remains) in the family? Using healthy relatives to define Crohn's gut microbiome alterations.Cell reports. Medicine · 2024Article
- Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification.BMC bioinformatics · 2024Article
- Robustness evaluations of pathway activity inference methods on gene expression data.BMC bioinformatics · 2024Article
- Gastric cancer with enhanced myogenesis is associated with less cell proliferation, enriched epithelial-to-mesenchymal transition and angiogenesis, and poor clinical outcomes.American journal of cancer research · 2024Article
209 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Predicting at the time of discovery the prognosis and metastatic potential of cancer is a major challenge in current clinical research. Numerous recent studies searched for gene expression signatures that outperform traditionally used clinical parameters in outcome prediction. Finding such a signature will free many patients of the suffering and toxicity associated with adjuvant chemotherapy given to them under current protocols, even though they do not need such treatment. A reliable set of predictive genes also will contribute to a better understanding of the biological mechanism of metastasis. Several groups have published lists of predictive genes and reported good predictive performance based on them. However, the gene lists obtained for the same clinical types of patients by different groups differed widely and had only very few genes in common. This lack of agreement raised doubts about the reliability and robustness of the reported predictive gene lists, and the main source of the problem was shown to be the small number of samples that were used to generate the gene lists. Here, we introduce a previously undescribed mathematical method, probably approximately correct (PAC) sorting, for evaluating the robustness of such lists. We calculate for several published data sets the number of samples that are needed to achieve any desired level of reproducibility. For example, to achieve a typical overlap of 50% between two predictive lists of genes, breast cancer studies would need the expression profiles of several thousand early discovery patients.
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