Metadata supporting data files in the published article: DNA Methylation Markers Predict Recurrence-free Interval in Triple- Negative Breast Cancer
Creators: name: Fackler, MaryJo
name: Soonweng Cho
name: Cope, Leslie
name: Gabrielson, Edward
name: Visvanathan, Kala
name: Wilsbach, Kathleen
name: Meir-Levi, Danielle
name: Lynch, Charles F
name: Marks, Jeffrey
name: Geradts, Joseph
name: Regan, Meredith M.
name: Viale, Giuseppe
name: Wolff, Antonio C.
name: Sukumar, Saraswati
name: Umbricht, Christopher B.
Publisher: name: figshare
Year: 2020
Subjects: subject: Cancer
subject: 60404 Epigenetics (incl. Genome Methylation and Epigenomics)
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: 60405 Gene Expression (incl. Microarray and other genome-wide approaches)
subject: Medicine
subject: 111201 Cancer Cell Biology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: 111203 Cancer Genetics

description: In this study, the authors identified DNA methylation markers that predict recurrence-free interval in Triple-Negative Breast Cancer (TNBC). <b>Data access: </b>The data that support the findings of this study, derived from Institutional patient samples, are available through the GEO repository at https://identifiers.org/geo:GSE141441. All data derived from the IBCSG study samples have been deposited to the IBCSG Statistical Center. Access to IBCSG-derived datasets are contingent upon IBSCG review and approval, for which a Data Use Agreement may be required. To request access to data, contact the IBCSG Statistical Center (stat_center@ibcsg.org). The IBCSG requires notification and opportunity to review before any public dissemination of results. <b> </b> <b>Study approval: </b>All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. Women enrolling in the study signed an informed consent approved by the Institutional Review Boards of participating institutions (Johns Hopkins University, Duke University, University of Iowa). For IBCSG study samples, Institutional review boards reviewed and approved the protocols, and informed consent was required according to the criteria established within the individual countries. <b> </b> <b>Study aims and methodology:</b> The objectives of this study were to develop prognostic tools for TNBC that can distinguish breast cancers with a favorable natural history versus those with a high risk of recurrence. The authors hypothesized that methylated gene markers present in primary TNBC will help identify: 1) The majority of early stage patients (60%) whose cancer will not recur after locoregional therapy alone, and therefore may not benefit from chemotherapy, and 2) those who will draw benefit from chemotherapy (20%), and 3) those who will not benefit (20%) and therefore need alternate treatment approaches. To achieve this objective, the authors performed a genome-wide search for DNA methylation markers using the available archival tumor samples of node-negative TNBC from three institutions (Johns Hopkins University, University of Iowa, Duke University) as well as available samples from TNBC patients enrolled in International Breast Cancer Study Group (IBCSG) Trials VIII and IX. Methylation array analysis was performed on 110 samples treated by locoregional therapy obtained from Institutional cohorts. Discovered marker sets were then tested by Kaplan Meier analyses in a prospectively collected TNBC cohort of 49 samples from the no chemotherapy arms of IBCSG trials VIII and IX, and by logistic regression in a chemotherapy-treated cohort of 121 TNBCs from combined IBCSG trials and Institutional repositories. <b>Datasets supporting the figures, tables and supplementary tables in the published article:</b> <b>Data supporting figure 2, table 1 and supplementary table 3: </b>Array based DNA methylation data<b> </b>from Institutional patient samples (Institutional Discovery set (in GEO), Institutional Chemo Test set (in GEO)) and from IBCSG-derived patient samples (IBCSG NoChemo Test set, IBCSG Chemo Test set). <b>Data supporting supplementary table 1: </b>Array based DNA methylation data<b> </b>from Institutional patient samples (Institutional Discovery set (in GEO)). <b> </b> <b>Data supporting supplementary table 2: </b>Array based DNA methylation data<b> </b>from Institutional patient samples (Institutional Chemo Test set (GEO)) and from IBCSG-derived patient samples (IBCSG Chemo Test set).<b></b><br>Clinical patient data are in .<b>xlsx</b> file format. Processed methylation array data and Iluminadata are in .<b>txt </b>file format and raw methylation array data are in <b>.idat</b> file format.<br>