ArticleBioinformatics (Oxford, England)2017
Accounting for tumor purity improves cancer subtype classification from DNA methylation data.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- MOSAIC: Methylation-Oriented Site Analysis and Information Classifier for Robust Epigenomic Classification of Acute Leukemia in Clinical Cohorts with Variable Tumor Purity.medRxiv : the preprint server for health sciences · 2026Article
- A MAGIBU-based model for pediatric and juvenile CNS tumors: an in-house epigenetic decision-support framework compared with online DNA methylation classifiers.Free neuropathology · 2026Article
- MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model.Nature communications · 2025Article
- A revision of the InfiniumPurify R package for genome-wide correction of tumor purity in Infinium DNA methylation array data.Genes & diseases · 2023Article
- A Bayesian model for identifying cancer subtypes from paired methylation profiles.Briefings in bioinformatics · 2023Article
- Recursive integration of synergised graph representations of multi-omics data for cancer subtypes identification.Scientific reports · 2022Article
- Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types.BMC bioinformatics · 2022Article
- Obtaining spatially resolved tumor purity maps using deep multiple instance learning in a pan-cancer study.Patterns (New York, N.Y.) · 2022Article
- Tumor purity adjusted beta values improve biological interpretability of high-dimensional DNA methylation data.PloS one · 2022Article
- The Analysis of Gene Expression Data Incorporating Tumor Purity Information.Frontiers in genetics · 2021Article
- A novel single-cell based method for breast cancer prognosis.PLoS computational biology · 2020Article
- Kernel Fusion Method for Detecting Cancer Subtypes via Selecting Relevant Expression Data.Frontiers in genetics · 2020Article
- Interrogating Mutant Allele Expression via Customized Reference Genomes to Define Influential Cancer Mutations.Scientific reports · 2019Article
- RF_Purify: a novel tool for comprehensive analysis of tumor-purity in methylation array data based on random forest regression.BMC bioinformatics · 2019Article
- Discovering Cancer Subtypes via an Accurate Fusion Strategy on Multiple Profile Data.Frontiers in genetics · 2019Article
- Assisted gene expression-based clustering with AWNCut.Statistics in medicine · 2018Article
- InfiniumPurify: An R package for estimating and accounting for tumor purity in cancer methylation research.Genes & diseases · 2018Article
- DECtp: Calling Differential Gene Expression Between Cancer and Normal Samples by Integrating Tumor Purity Information.Frontiers in genetics · 2018Article
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Authors and funding
4 authors.
Funding
Abstract
motivationTumor sample classification has long been an important task in cancer research. Classifying tumors into different subtypes greatly benefits therapeutic development and facilitates application of precision medicine on patients. In practice, solid tumor tissue samples obtained from clinical settings are always mixtures of cancer and normal cells. Thus, the data obtained from these samples are mixed signals. The 'tumor purity', or the percentage of cancer cells in cancer tissue sample, will bias the clustering results if not properly accounted for.
resultsIn this article, we developed a model-based clustering method and an R function which uses DNA methylation microarray data to infer tumor subtypes with the consideration of tumor purity. Simulation studies and the analyses of The Cancer Genome Atlas data demonstrate improved results compared with existing methods. AVAILABILITY AND IMPLEMENTATION: InfiniumClust is part of R package InfiniumPurify , which is freely available from CRAN ( https://cran.r-project.org/web/packages/InfiniumPurify/index.html ). CONTACT: hao.wu@emory.edu or xqzheng@shnu.edu.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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