DOI: 10.6084/m9.figshare.7855742
title: Clinical and expression analysis data files supporting study into molecular reclassification from Luminal to Basal-type breast cancer and links with expression of dominant-negative ER variants

description: Data files supporting the related publication: Estrogen Receptor Variants in ER-positive Basal-type Breast Cancers Responding to Therapy like ER-negative Breast Cancers<br><b>Study design and methods</b><br>The related study reports the link between molecular reclassification from Luminal to Basal type tumors and the expression of dominant-negative ER variants. <br><br>The study examines the expression of total ER and ER variants mRNA in ER+/Basal breast cancer patients enrolled in the prospective neoadjuvant NBRST registry trial (NCT01479101) and compare these expression values to patients with ER+/Luminal B breast cancer. The study also investigates pathological complete response rates to neoadjuvant therapy and 3-year follow-up data for both patient groups within the NBRST trial and compares those to ER-/Basal breast cancer patients.<br><br>The MammaPrint 70-gene expression profile (risk of recurrence signature) and BluePrint 80 gene expression profile (molecular subtyping signature) were employed to reclassify the luminal and basal types in the study.<br><b>Sample size and wider cohort size:</b><br>694 ER positive tumours (based on IHC) of 1072 from the wider cohort NBRST cohort.<br><b><br></b><b>Clinical trial registration number: </b>NCT01479101<b><br></b><b>S</b><b>oftware needed to access data:</b><br>All files in this repository are in <b>.xlsx </b>spreadsheet format, accessible via MS Excel or open office software.<br><b>Data access:</b><br><br>All files available in this repository are openly accessible under the licence stated. <br>MammaPrint and BluePrint analyses were run in a central laboratory involving collaboration with diagnostic company Agendia, which included the sharing of RNA samples and relevant clinical information and outcome data of this special subgroup of breast cancers, but does not cover making raw array data generally available. <br><br>Files from the NBRST clinical database are held in institutional file storage and are available on request from Dr Groenendijk. Only requests under CC BY-NC-ND terms will be accepted. <br>The NBRST clinical database is not publicly available because data were used under license for the current study. Data are however available upon reasonable request and with permission of Agendia. Access requirements includes application submission and signing of a confidentiality agreement.<br><br>Please apply to Dr Groenendijk with data access requests: Department of Pathology, Erasmus MC Cancer Institute P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands email: f.groenendijk@erasmusmc.nl <b><br></b><b>Raw data files</b> (listed by figure/table in related article)<br>IHC = immunohistochemistryFF = fresh frozen samplesFFPE = formalin-fixed paraffin embedded samples.pCR = pathological complete responseRD = residual disease<br><b>Data supporting Figure 1.xlsx - </b>normalised total ERα mRNA expression levels by sample number for the subgroups: Normal breast, ER+/Basal and ER+/Luminal-B<br><b>Data supporting Figure 2.xlsx</b> - total ERα mRNA expression and the percentage of ER positivity by IHC. Sample versus subgroups: ER IHC %, ER+/Basal FFPE, ER+/Basal FF, ER+/Luminal-B FF, ER+/Luminal-B FFPE. <br><b>Data supporting Figure 3.xlsx </b>- ratio of ERd7 mRNA expression and total ERalpha mRNA expression for ER+/Basal tumors, ER+/Luminal B tumors and normal breast tissues. Sample versus ER+/Basal FF, ER+/Luminal-B FF, ER+/Basal FFPE, ER+/Luminal-B FFPE, Normal breast FF.<br><b>Data supporting Figure 4.xlsx </b>- Statistical data supporting Kaplan Meier curves for distant metastasis free interval (DMFI) in HER2-negative patients in NBRST study with follow-up (N=538). <b>A,</b> DMFI for all patients stratified by ER status and molecular subtyping. <b>B,</b> DMFI of Basal patients (N=252) stratified by ER status and response to neoadjuvant therapy. 3 tabs consisting of raw statistics: time (months), n.risk, n.event, survival, standard error, and lower and upper 95 confidence intervals. <br><b>Data supporting Table 1.xlsx</b> - classification of ER-positive tumors (IHC ≥1%) in NBRST (N=694). Tumor sample (by ID) by MammaPrint and BluePrint in terms of risk, HER2 and ER statuses, ER%, PR statuses and PR%, all via IHC, as well as ER+ borderline classification.<br><b>Data supporting Table 2.xlsx </b>- clinical characteristics of subset of HER-2 negative patients in NBRST study with follow-up (N=538). Tumor sample (by ID), ER status via IHC and BluePrint, Age, Ethnicity, Menopausal.status, cT.stage, cN.stage, Histopathologic tumor type, Histological grade, classification via MammaPrint and BluePrint, Neoadjuvant.therapy, Adjuvant endocrine therapy, Event DMFI (1 or 0), Days to DMFI.<br><b>Data supporting supplementary figures 1-3 </b>- holding for basal, luminal and normal subgroups (FF and FFPE): mRNA expression values for Total ER, ERa-36, ERΔ3, ERΔ5, ERΔ7 and the relative expression of ERΔ3, as well as statistical data supporting Kaplan Meier curves by PR status.<br>