ArticleBMC genomics2019
Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT01560663 (Predictors of Response to Neoadjuvant Docetaxel-Carboplatin Chemotherapy for Patients With Stage II and III Triple Negative Breast Cancer), which is not on this map. Cited by 39 papers.
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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.
Predictors of Response to Neoadjuvant Docetaxel-Carboplatin Chemotherapy for Patients With Stage II and III Triple Negative Breast Cancer
Who cites it
39 citing papers in PubMed, 59 citations in OpenAlex.
- The spatially informed mFISHseq assay resolves biomarker discordance and predicts treatment response in breast cancer.Nature communications · 2025Trial
- Genomic and transcriptomic profiles associated with response to eribulin and nivolumab combination in HER-2-negative metastatic breast cancer.Cancer immunology, immunotherapy : CII · 2024Trial
- Triple-Negative PAM50 Non-Basal Breast Cancer Subtype Predicts Benefit from Extended Adjuvant Capecitabine.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Trial
- Evaluating the efficacy of a priming dose of cyclophosphamide prior to pembrolizumab to treat metastatic triple negative breast cancer.Journal for immunotherapy of cancer · 2022Trial
- Multi-state modeling associates proliferation genes with early estrogen receptor-positive breast cancer recurrence and survival.Research square · 2026Article
- Transcriptome predictors of second breast events in ductal carcinoma in situ: a case‒control study including Black and White women.Breast cancer research : BCR · 2026Article
- Characterization, immune cell phenotyping and differential gene expression analysis of brain metastases and primary breast cancer samples.Scientific reports · 2026Article
- Prediction of molecular subtypes from histology: AI-driven analysis of prostate cancer morphological patterns and therapeutic implications.NPJ precision oncology · 2026Article
- CD24, NFIL3, FN1, and KLRK1 signature predicts melanoma immunotherapy response and survival.Journal of molecular medicine (Berlin, Germany) · 2025Article
- Defining the regulatory logic of breast cancer using single-cell epigenetic and transcriptome profiling.Cell genomics · 2025Article
- SyntheVAEiser: augmenting traditional machine learning methods with VAE-based gene expression sample generation for improved cancer subtype predictions.Genome biology · 2024Article
- Fish in focus: Navigating organ damage assessment through analytical avenues - A comprehensive review.Toxicology reports · 2024Review
- Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages.Nature cancer · 2024Article
- Evaluating cell type deconvolution in FFPE breast tissue: application to benign breast disease.NAR genomics and bioinformatics · 2024Review
- Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling.bioRxiv : the preprint server for biology · 2024Article
- Deep learning-based risk stratification of preoperative breast biopsies using digital whole slide images.Breast cancer research : BCR · 2024Article
- The VEGF-Hypoxia Signature Is Upregulated in Basal-like Breast Tumors from Women of African Ancestry and Associated with Poor Outcomes in Breast Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2024Article
- Survivin Expression in Luminal Breast Cancer and Adjacent Normal Tissue for Immuno-Oncology Applications.International journal of molecular sciences · 2023Article
- Omics-Based Investigations of Breast Cancer.Molecules (Basel, Switzerland) · 2023Review
- A Case Series Exploration of Multi-Regional Expression Heterogeneity in Triple-Negative Breast Cancer Patients.International journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
20 authors at 7 institutions in 3 countries.
Funding
Abstract
backgroundFull RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification agreement between RNA-Seq and a digital multiplexed gene expression platform, and the subtype call after running the PAM50 assay in a series of breast cancer patients classified as triple negative by IHC/FISH. The goal of this study is to analyze the concordance between both expression platforms overall, and for calling PAM50 triple negative breast cancer intrinsic subtypes in particular.
resultsThe analyses were performed in paraffin-embedded tissues from 96 patients recruited in a multicenter, prospective, non-randomized neoadjuvant triple negative breast cancer trial (NCT01560663). Pre-treatment core biopsies were obtained following clinical practice guidelines and conserved as FFPE for further RNA extraction. PAM50 was performed on both digital multiplexed gene expression and RNA-Seq platforms. Subtype assignment was based on the nearest centroid classification following this procedure for both platforms and it was concordant on 96% of the cases (N = 96). In four cases, digital multiplexed gene expression analysis and RNA-Seq were discordant. The Spearman correlation to each of the centroids and the risk of recurrence were above 0.89 in both platforms while the agreement on Proliferation Score reached up to 0.97. In addition, 82% of the individual PAM50 genes showed a correlation coefficient > 0.80.
conclusionsIn our analysis, the subtype calling in most of the samples was concordant in both platforms and the potential discordances had reduced clinical implications in terms of prognosis. If speed and cost are the main driving forces then the preferred technique is the digital multiplexed platform, while if whole genome patterns and subtype are the driving forces, then RNA-Seq is the preferred method.
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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.