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
Data files supporting the related publication: Estrogen Receptor Variants in ER-positive Basal-type Breast Cancers Responding to Therapy like ER-negative Breast Cancers
Study design and methods
The related study reports the link between molecular reclassification from Luminal to Basal type tumors and the expression of dominant-negative ER variants.
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.
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.
Sample size and wider cohort size:
694 ER positive tumours (based on IHC) of 1072 from the wider cohort NBRST cohort.
Raw data files (listed by figure/table in related article)
IHC = immunohistochemistry
FF = fresh frozen samples
FFPE = formalin-fixed paraffin embedded samples.
pCR = pathological complete response
RD = residual disease
Data supporting Figure 1.xlsx - normalised total ERα mRNA expression levels by sample number for the subgroups: Normal breast, ER+/Basal and ER+/Luminal-B
Data supporting Figure 2.xlsx - 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.
Data supporting Figure 3.xlsx - 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.
Data supporting Figure 4.xlsx - Statistical data supporting Kaplan Meier curves for distant metastasis free interval (DMFI) in HER2-negative patients in NBRST study with follow-up (N=538). A, DMFI for all patients stratified by ER status and molecular subtyping. 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.
Data supporting Table 1.xlsx - 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.
Data supporting Table 2.xlsx - 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.
Data supporting supplementary figures 1-3 - 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.
