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Classification of breast cancer subtypes by combining gene expression and DNA methylation data

Markus List, Anne-Christin Hauschild, Qihua Tan, Torben A Kruse, Jan Mollenhauer, Jan Baumbach, Richa Batra
2014 Journal of Integrative Bioinformatics  
We obtained bootstrap errors of 10-20% and classification error of 1-50%, depending on breast cancer subtype and model.  ...  However, the methylation model was able to identify unique features not considered as relevant by the gene expression model, which might provide deeper insights into breast cancer subtype differentiation  ...  , in order to investigate the potential benefits of using DNA methylation data for breast cancer subtype classification.  ... 
doi:10.2390/biecoll-jib-2014-236 pmid:24953305 fatcat:mpuy5hmt4rg55n7hrl6oq7eoau

Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data

Markus List, Anne-Christin Hauschild, Qihua Tan, Torben A. Kruse, Jan Baumbach, Richa Batra
2014 Journal of Integrative Bioinformatics  
We obtained bootstrap errors of 10-20% and classification error of 1-50%, depending on breast cancer subtype and model.  ...  However, the methylation model was able to identify unique features not considered as relevant by the gene expression model, which might provide deeper insights into breast cancer subtype differentiation  ...  , in order to investigate the potential benefits of using DNA methylation data for breast cancer subtype classification.  ... 
doi:10.1515/jib-2014-236 fatcat:rmdgjvi4ufb4vaiuvmkuhtabry

Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer

J.-K. Rhee, K. Kim, H. Chae, J. Evans, P. Yan, B.-T. Zhang, J. Gray, P. Spellman, T. H.- M. Huang, K. P. Nephew, S. Kim
2013 Nucleic Acids Research  
Aberrant DNA methylation of CpG islands, CpG island shores and first exons is known to play a key role in the altered gene expression patterns in all human cancers.  ...  On the computational side, our goal is to develop methylome data analysis protocols for the integrated analysis of DNA methylation and gene expression data on the genome scale.  ...  To better understand the relationship between DNA methylation and gene expression in breast cancer molecular subtypes, we used next-generation DNA methylation sequencing data and gene expression profiles  ... 
doi:10.1093/nar/gkt643 pmid:23887935 pmcid:PMC3794600 fatcat:6viql6scdzhaxkdwxighgai6ge

DNA methylation signatures for breast cancer classification and prognosis

Moshe Szyf
2012 Genome Medicine  
I discuss the role of DNA methylation in normal gene regulation, the aberrations in DNA methylation in cancer, and candidate-gene and whole-genome approaches to classify breast cancer subtypes using DNA  ...  Classifications based on gene expression profiles have expanded the detailed classification of breast cancer by revealing cellular identity profiles, with particular emphasis on presence of stem cells  ...  Not all CGs are methylated in vertebrate genomes, and the Table 1 Intrinsic classification of breast cancer by gene expression profiles and cell surface hormonal expression ER-negative, PR-negative,  ... 
doi:10.1186/gm325 pmid:22494847 pmcid:PMC3446276 fatcat:hnjqkqkyx5fmbg4e6w2nk7azba

Specific breast cancer prognosis-subtype distinctions based on DNA methylation patterns

Shumei Zhang, Yihan Wang, Yue Gu, Jiang Zhu, Ce Ci, Zhongfu Guo, Chuangeng Chen, Yanjun Wei, Wenhua Lv, Hongbo Liu, Dongwei Zhang, Yan Zhang
2018 Molecular Oncology  
These specific classifications by DNA methylation can explain the heterogeneity of previous molecular subgroups in breast cancer and will help in the development of personalized treatments for the new  ...  DNA methylation is an important regulator of gene expression, thus characterizing tumour heterogeneity by epigenetic features can be clinically informative.  ...  Acknowledgements This work was supported by National Natural Science Foundation of China (grant number 81573021), the Natural Science Foundation of Heilongjiang Province (grant number ZD2015003) and the  ... 
doi:10.1002/1878-0261.12309 pmid:29675884 pmcid:PMC6026876 fatcat:cutfx7ow5nh2ddyn6uv2yb35li

Classifying Breast Cancer Subtypes Using Multiple Kernel Learning Based on Omics Data

Mingxin Tao, Tianci Song, Wei Du, Siyu Han, Chunman Zuo, Ying Li, Yan Wang, Zekun Yang
2019 Genes  
We collected mRNA data, methylation data and copy number variation (CNV) data from TCGA to classify breast cancer subtypes.  ...  In this article, we use estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) to define breast cancer subtypes and classify any two breast cancer subtypes  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/genes10030200 pmid:30866472 pmcid:PMC6471546 fatcat:md742vuanrhtnjbku6sngw4tay

A DNA methylation-based definition of biologically distinct breast cancer subtypes

Olafur A. Stefansson, Sebastian Moran, Antonio Gomez, Sergi Sayols, Carlos Arribas-Jorba, Juan Sandoval, Holmfridur Hilmarsdottir, Elinborg Olafsdottir, Laufey Tryggvadottir, Jon G. Jonasson, Jorunn Eyfjord, Manel Esteller
2014 Molecular Oncology  
Keywords: Breast cancer DNA methylation Microarrays Biological subtypes Prognosis A B S T R A C T In cancer, epigenetic states are deregulated and thought to be of significance in cancer development and  ...  The identified methylation signatures were validated against a cohort of 212 tumors annotated for breast cancer subtypes by the PAM50 method (The Cancer Genome Atlas).  ...  Financial support The Conflicts of interest The authors declare no conflicts of interests. Appendix A. Supplementary data  ... 
doi:10.1016/j.molonc.2014.10.012 pmid:25468711 pmcid:PMC5528700 fatcat:dnesnmkekbeb5otwnk3hlw2afi

The integrative epigenomic-transcriptomic landscape of ER positive breast cancer

Yang Gao, Allison Jones, Peter A. Fasching, Matthias Ruebner, Matthias W. Beckmann, Martin Widschwendter, Andrew E. Teschendorff
2015 Clinical Epigenetics  
While recent integrative analyses of copy number and gene expression data in breast cancer have revealed a complex molecular landscape with multiple subtypes and many oncogenic/tumour suppressor driver  ...  Integrative clustering of the matched messenger RNA (mRNA) and DNA methylation data over these genes resulted in only two clusters, which correlated very strongly with the luminal-A and luminal B subtypes  ...  In spite of this, the integrative analysis of DNA methylation and gene expression data in breast cancer remains largely unexplored [2, 9] .  ... 
doi:10.1186/s13148-015-0159-0 pmid:26664652 pmcid:PMC4673726 fatcat:hlazdj6ebnc7nog7voq7j6thj4

Multi-Omics Marker Analysis Enables Early Prediction of Breast Tumor Progression

Haifeng Xu, Tonje Lien, Helga Bergholtz, Thomas Fleischer, Lounes Djerroudi, Anne Vincent-Salomon, Therese Sørlie, Tero Aittokallio
2021 Frontiers in Genetics  
Even though the gene expression-based model features led to the highest classification accuracy alone, methylation data provided a complementary source of features and improved especially the sensitivity  ...  The marker panel was not specific to any of the established breast cancer subtypes, suggesting that the 10-gene signature may provide a subtype-agnostic and cost-effective approach for breast cancer detection  ...  ACKNOWLEDGMENTS We thank Zhi Zhao (OUH/OCBE) for his help with the predictive modeling, Jørgen Ankill (OUH) for his help with the methylation data processing, and Arnoldo Frigessi (OCBE) for fruitful discussions  ... 
doi:10.3389/fgene.2021.670749 pmid:34149812 pmcid:PMC8209521 fatcat:nma2tbc7zrat7dsjkgee44m62a

Basal-like breast cancer displays distinct patterns of promoter methylation

Ji Shin Lee, Mary Jo Fackler, Jae Hyuk Lee, Chan Choi, Min Ho Park, Jung Han Yoon, Zhe Zhang, Saraswati Sukumar
2010 Cancer Biology & Therapy  
These results suggest that gene methylation in breast cancer can potentially serve as epigenetic biomarkers and may contribute further to current breast cancer classification.  ...  The methylation status of a panel of four genes (APC1, CDH, BRCA1 and RAR-β) in luminal and HER2 subtypes were dissimilar, where HER2 tumors showed a significantly higher level of methylation compared  ...  Detection of methylation levels for some genes is potentially useful as epigenetic markers in breast cancer classification.  ... 
doi:10.4161/cbt.9.12.11804 pmid:20505321 pmcid:PMC3094906 fatcat:u4ehexb7y5dipic5imnwvttpdq

MethCORR infers gene expression from DNA methylation and allows molecular analysis of ten common cancer types using fresh-frozen and formalin-fixed paraffin-embedded tumor samples

Trine B. Mattesen, Claus L. Andersen, Jesper B. Bramsen
2021 Clinical Epigenetics  
Molecular pathway analysis and transcriptional subtyping were performed for breast, prostate, and lung cancer samples to illustrate the general usability of the inferred gene expression profiles: overall  ...  Results Regression models to infer gene expression information from DNA methylation were developed for ten common cancer types using matched RNA sequencing and DNA methylation profiles (HumanMethylation450  ...  Availability of data and materials The RNA sequencing data and HM-450K DNA methylation datasets from the TCGA cancer cohorts analyzed during the current study are available from the UCSC XENA Public Data  ... 
doi:10.1186/s13148-021-01000-0 pmid:33509261 pmcid:PMC7842045 fatcat:kodmwsrxbjdhppu4wylr32gx3u

Hypomethylation of the MMP7 promoter and increased expression of MMP7 distinguishes the basal-like breast cancer subtype from other triple-negative tumors

Steven T. Sizemore, Gina M. Sizemore, Christine N. Booth, Cheryl L. Thompson, Paula Silverman, Gurkan Bebek, Fadi W. Abdul-Karim, Stefanie Avril, Ruth A. Keri
2014 Breast Cancer Research and Treatment  
Methylation of the MMP7 promoter was assessed by methylation-specific PCR in a panel of breast cancer cell lines and patient tumor samples.  ...  This study investigates the association of MMP7 expression and MMP7 promoter methylation with subtype and outcome in breast cancer patient cohorts.  ...  Combined, our data demonstrate that elevated MMP7 expression and promoter hypomethylation may improve TN breast cancer classification and prognosis, and advocates for future studies to assess the efficacy  ... 
doi:10.1007/s10549-014-2989-4 pmid:24847890 pmcid:PMC4716673 fatcat:oqfu5jthyfhdfm7ngoz36ukhke

DNA methylation epigenotypes in breast cancer molecular subtypes

Naiara G Bediaga, Amelia Acha-Sagredo, Isabel Guerra, Amparo Viguri, Carmen Albaina, Irune Ruiz Diaz, Ricardo Rezola, María Jesus Alberdi, Joaquín Dopazo, David Montaner, Mertxe de Renobales, Agustín F Fernández (+4 others)
2010 Breast Cancer Research  
Identification of gene expression-based breast cancer subtypes is considered a critical means of prognostication.  ...  Methods: By using a microarray approach, we analyzed DNA methylation in regulatory regions of 806 cancerrelated genes in 28 breast cancer paired samples.  ...  ), BIO2008-04212, and RD06/0020/1019 (Red Tematica de Investigacion Cooperativa en Cancer, RTICC) from the MICINN.  ... 
doi:10.1186/bcr2721 pmid:20920229 pmcid:PMC3096970 fatcat:2iilexuzmnhz5edoh64sfj7ufu

Unraveling the Genomic-Epigenomic Interaction Landscape in Triple Negative and Non-Triple Negative Breast Cancer

Jiande Wu, Tarun Karthik Kumar Mamidi, Lu Zhang, Chindo Hicks
2020 Cancers  
We hypothesized that within breast cancers, there are differences in somatic mutation, DNA methylation and gene expression signatures between TNBC and non-TNBC.  ...  The recent surge of next generation sequencing of breast cancer genomes has enabled development of comprehensive catalogues of somatic mutations and expanded the molecular classification of subtypes of  ...  Acknowledgments: The authors wish to thank the participants who donated the samples to the TCGA project used to generate the data used in this project, technical support from TCGA and GDC staff as well  ... 
doi:10.3390/cancers12061559 pmid:32545594 fatcat:czsd35fikzb63dm3frw3z5vcjy

Low methylation levels of the SFRP1 gene are associated with the basal-like subtype of breast cancer

2013 Oncology Reports  
By using pyrosequencing, we analyzed the DNA methylation status of 5 candidate genes in 60 breast cancer samples.  ...  In this study, we analyzed the methylation status of breast cancer-related genes in relation to the molecular subtypes and investigated whether the basal-like subtype displays distinct methylation profiles  ...  Acknowledgements The present research has been supported by Korea Breast Cancer Foundation.  ... 
doi:10.3892/or.2013.2335 pmid:23467623 fatcat:ko7nwcom3fg2dmqrujm77reg5a
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