ArticleScientific reports2018
Methylation-to-Expression Feature Models of Breast Cancer Accurately Predict Overall Survival, Distant-Recurrence Free Survival, and Pathologic Complete Response in Multiple Cohorts.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- A comprehensive review of cancer survival prediction using multi-omics integration and clinical variables.Briefings in bioinformatics · 2025Review
- MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer.Nature communications · 2020Article
- Improving survival prediction using a novel feature selection and feature reduction framework based on the integration of clinical and molecular data.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2020Article
- Severity Detection for the Coronavirus Disease 2019 (COVID-19) Patients Using a Machine Learning Model Based on the Blood and Urine Tests.Frontiers in cell and developmental biology · 2020Article
- Review
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3 authors.
Funding
Abstract
Prognostic biomarkers serve a variety of purposes in cancer treatment and research, such as prediction of cancer progression, and treatment eligibility. Despite growing interest in multi-omic data integration for defining prognostic biomarkers, validated methods have been slow to emerge. Given that breast cancer has been the focus of intense research, it is amenable to studying the benefits of multi-omic prognostic models due to the availability of datasets. Thus, we examined the efficacy of our methylation-to-expression feature model (M2EFM) approach to combining molecular and clinical predictors to create risk scores for overall survival, distant metastasis, and chemosensitivity in breast cancer. Gene expression, DNA methylation, and clinical variables were integrated via M2EFM to build models of overall survival using 1028 breast tumor samples and applied to validation cohorts of 61 and 327 samples. Models of distant recurrence-free survival and pathologic complete response were built using 306 samples and validated on 182 samples. Despite different populations and assays, M2EFM models validated with good accuracy (C-index or AUC ≥ 0.7) for all outcomes and had the most consistent performance compared to other methods. Finally, we demonstrated that M2EFM identifies functionally relevant genes, which could be useful in translating an M2EFM biomarker to the clinic.
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