ArticleBMC medical genomics2012
PAM50 breast cancer subtyping by RT-qPCR and concordance with standard clinical molecular markers.
Article in BMC medical genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT00129922 (Phase III Study to Compare 6 Courses of FEC), which is not on this map. Cited by 181 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Phase III Study to Compare 6 Courses of FEC (Fluorouracil, Epirubicin and Cyclophosphamide) vs. 4 Courses of FEC Followed by 8 Weekly Paclitaxel Administrations, as Adjuvant Treatment for Node Positive Operable BC Patients
Who cites it
181 citing papers in PubMed, 340 citations in OpenAlex.
- The spatially informed mFISHseq assay resolves biomarker discordance and predicts treatment response in breast cancer.Nature communications · 2025Trial
- Prognostic ability of EndoPredict compared to research-based versions of the PAM50 risk of recurrence (ROR) scores in node-positive, estrogen receptor-positive, and HER2-negative breast cancer. A GEICAM/9906 sub-study.Breast cancer research and treatment · 2016Trial
- Immunohistochemistry vs Molecular Breast Cancer Subtyping Among African Populations.JAMA network open · 2026Article
- Integrating Heterogeneous Real-World Cancer Data for Semantic Interoperability in Oncology and Medical Imaging: Development and Validation of the Cancer Image Europe Hyperontology.Journal of medical Internet research · 2026Article
- Age-Associated Four-Gene Prognostic Signature in Breast Cancer.Cancer reports (Hoboken, N.J.) · 2026Article
- Article
- Visceral adiposity and breast cancer outcomes: transcriptomic analysis of the tumor microenvironment by intrinsic subtype.Breast cancer research : BCR · 2026Article
- Etiology of gene expression-based subtypes of breast cancer in the Ghana Breast Health Study.International journal of cancer · 2026Article
- Age-stratified analysis of invasive lobular carcinoma reveals comparable clinicopathological and molecular features across age groups.Discover oncology · 2026Article
- Enhanced PAM50 subtyping of breast cancer implemented in the PCAPAM50 R package.Scientific reports · 2025Article
- Bioinformatic Approach to Identify Positive PrognosticInternational journal of molecular sciences · 2025Article
- Evaluation of Expression and Clinicopathological Relevance of Small Nucleolar RNAs (snoRNAs) in Invasive Breast Cancer.Non-coding RNA · 2025Article
- Metabolic Features of Saliva Before and After Breast Cancer Surgery.Metabolites · 2025Article
- RNA sequencing and immunohistochemistry jointly improve tumor biomarker interpretation.Scientific reports · 2025Article
- Assessment ofHealth science reports · 2025Article
- The Breast Cancer Classifier refines molecular breast cancer classification to delineate the HER2-low subtype.NPJ breast cancer · 2025Article
- Evaluation of agreement between common clustering strategies for DNA methylation-based subtyping of breast tumours.Epigenomics · 2025Article
- Classifications of triple-negative breast cancer: insights and current therapeutic approaches.Cell & bioscience · 2025Review
- Deep Learning Predicts Subtype Heterogeneity and Outcomes in Luminal A Breast Cancer Using Routinely Stained Whole-Slide Images.Cancer research communications · 2025Article
- BC-predict: mining of signal biomarkers and production of models for early-stage breast cancer subtyping and prognosis.Frontiers in bioinformatics · 2025Article
121 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
32 authors at 17 institutions in 3 countries.
Funding
Abstract
backgroundMany methodologies have been used in research to identify the "intrinsic" subtypes of breast cancer commonly known as Luminal A, Luminal B, HER2-Enriched (HER2-E) and Basal-like. The PAM50 gene set is often used for gene expression-based subtyping; however, surrogate subtyping using panels of immunohistochemical (IHC) markers are still widely used clinically. Discrepancies between these methods may lead to different treatment decisions.
methodsWe used the PAM50 RT-qPCR assay to expression profile 814 tumors from the GEICAM/9906 phase III clinical trial that enrolled women with locally advanced primary invasive breast cancer. All samples were scored at a single site by IHC for estrogen receptor (ER), progesterone receptor (PR), and Her2/neu (HER2) protein expression. Equivocal HER2 cases were confirmed by chromogenic in situ hybridization (CISH). Single gene scores by IHC/CISH were compared with RT-qPCR continuous gene expression values and "intrinsic" subtype assignment by the PAM50. High, medium, and low expression for ESR1, PGR, ERBB2, and proliferation were selected using quartile cut-points from the continuous RT-qPCR data across the PAM50 subtype assignments.
resultsESR1, PGR, and ERBB2 gene expression had high agreement with established binary IHC cut-points (area under the curve (AUC) ≥ 0.9). Estrogen receptor positivity by IHC was strongly associated with Luminal (A and B) subtypes (92%), but only 75% of ER negative tumors were classified into the HER2-E and Basal-like subtypes. Luminal A tumors more frequently expressed PR than Luminal B (94% vs 74%) and Luminal A tumors were less likely to have high proliferation (11% vs 77%). Seventy-seven percent (30/39) of ER-/HER2+ tumors by IHC were classified as the HER2-E subtype. Triple negative tumors were mainly comprised of Basal-like (57%) and HER2-E (30%) subtypes. Single gene scoring for ESR1, PGR, and ERBB2 was more prognostic than the corresponding IHC markers as shown in a multivariate analysis.
conclusionsThe standard immunohistochemical panel for breast cancer (ER, PR, and HER2) does not adequately identify the PAM50 gene expression subtypes. Although there is high agreement between biomarker scoring by protein immunohistochemistry and gene expression, the gene expression determinations for ESR1 and ERBB2 status was more prognostic.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.