ArticleScientific reports2019
PCA-PAM50 improves consistency between breast cancer intrinsic and clinical subtyping reclassifying a subset of luminal A tumors as luminal B.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it, 61 citations in OpenAlex.
- A systematic review of datasets that can help elucidate relationships among gene expression, race, and immunohistochemistry-defined subtypes in breast cancer.Cancer biology & therapy · 2021Pooled it
- Navigating luminal heterogeneity: etiology-based proteogenomic subtyping for targeted treatment strategies in breast cancer.Molecular cancer · 2026Article
- Novel nested conformal prediction analysis to unravel complexity in patient subtyping.Frontiers in artificial intelligence · 2026Article
- Enhanced PAM50 subtyping of breast cancer implemented in the PCAPAM50 R package.Scientific reports · 2025Article
- Proteogenomic characterization of invasive breast tumors in young women.NPJ breast cancer · 2025Article
- miRNAs as emerging predictors of tamoxifen resistance in breast cancer.Naunyn-Schmiedeberg's archives of pharmacology · 2025Review
- The Breast Cancer Classifier refines molecular breast cancer classification to delineate the HER2-low subtype.NPJ breast cancer · 2025Article
- Modeling intratumor heterogeneity in breast cancer.Biofabrication · 2024Review
- DeePathNet: A Transformer-Based Deep Learning Model Integrating Multiomic Data with Cancer Pathways.Cancer research communications · 2024Article
- Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection.Breast cancer research : BCR · 2024Article
- Clinically relevant gene signatures provide independent prognostic information in older breast cancer patients.Breast cancer research : BCR · 2024Article
- The Role of Transcription Factors in the Loss of Inter-Chromosomal Co-Expression for Breast Cancer Subtypes.International journal of molecular sciences · 2023Article
- Deconvolution of cancer cell states by the XDec-SM method.PLoS computational biology · 2023Article
- Advances in understanding the role and mechanisms of tumor stem cells in HER2-positive breast cancer treatment resistance (Review).International journal of oncology · 2023Review
- Immature natural killer cells promote progression of triple-negative breast cancer.Science translational medicine · 2023Article
- A Simple Method for Robust and Accurate Intrinsic Subtyping of Breast Cancer.Cancer informatics · 2023Article
- The Transcriptomic Landscape of Pediatric Astrocytoma.International journal of molecular sciences · 2022Article
- ROLE OF ANDROGEN RECEPTOR-TARGETED AGENTS IN LOCALIZED PROSTATE CANCER.Acta clinica Croatica · 2022Review
- Common tumor-suppressive signaling of thyroid hormone receptor beta in breast and thyroid cancer cells.Molecular carcinogenesis · 2021Article
- What is beyond LncRNAs in breast cancer: A special focus on colon cancer-associated Transcript-1 (CCAT-1).Non-coding RNA research · 2021Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The PAM50 classifier is widely used for breast tumor intrinsic subtyping based on gene expression. Clinical subtyping, however, is based on immunohistochemistry assays of 3-4 biomarkers. Subtype calls by these two methods do not completely match even on comparable subtypes. Nevertheless, the estrogen receptor (ER)-balanced subset for gene-centering in PAM50 subtyping, is selected based on clinical ER status. Here we present a new method called Principle Component Analysis-based iterative PAM50 subtyping (PCA-PAM50) to perform intrinsic subtyping in ER status unbalanced cohorts. This method leverages PCA and iterative PAM50 calls to derive the gene expression-based ER status and a subsequent ER-balanced subset for gene centering. Applying PCA-PAM50 to three different breast cancer study cohorts, we observed improved consistency (by 6-9.3%) between intrinsic and clinical subtyping for all three cohorts. Particularly, a more aggressive subset of luminal A (LA) tumors as evidenced by higher MKI67 gene expression and worse patient survival outcomes, were reclassified as luminal B (LB) increasing the LB subtype consistency with IHC by 25-49%. In conclusion, we show that PCA-PAM50 enhances the consistency of breast cancer intrinsic and clinical subtyping by reclassifying an aggressive subset of LA tumors into LB. PCA-PAM50 code is available at ftp://ftp.wriwindber.org/ .
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