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Multi-layered knowledge graph neural network reveals pathway-level agreement of three breast cancer multi-gene assays.
Comput Struct Biotechnol J
December 2024
Department of Computer Science and Engineering, South Korea.
Multi-gene assays have been widely used to predict the recurrence risk for hormone receptor (HR)-positive breast cancer patients. However, these assays lack explanatory power regarding the underlying mechanisms of the recurrence risk. To address this limitation, we proposed a novel multi-layered knowledge graph neural network for the multi-gene assays.
View Article and Find Full Text PDFAddressing Social Determinants in the Era of Precision Medicine in Breast Cancer: Is It Sufficient to Reduce Disparities?
Cancer Epidemiol Biomarkers Prev
May 2024
Department of Public Health Sciences, University of Chicago, Chicago, Illinois.
The Oncotype DX (ODX) assay predicts recurrence risk and demonstrates the benefits of adjuvant therapy in patients with early-stage, hormone receptor (HR)-positive/HER2-negative breast cancer. ODX uptake varies by patients' racial/ethnic backgrounds and socioeconomic status (SES). However, community-level variability remains unknown, and research regarding the association between testing status and receipt of adjuvant chemotherapy is limited.
View Article and Find Full Text PDFStable feature selection utilizing Graph Convolutional Neural Network and Layer-wise Relevance Propagation for biomarker discovery in breast cancer.
Artif Intell Med
May 2024
Medical Bioinformatics, University Medical Center Göttingen, Goldschmidtstraße 1, Göttingen, 37077, Germany; Campus-Institute Data Science (CIDAS), University of Göttingen, Goldschmidtstraße 1, Göttingen, 37077, Germany. Electronic address:
High-throughput technologies are becoming increasingly important in discovering prognostic biomarkers and in identifying novel drug targets. With Mammaprint, Oncotype DX, and many other prognostic molecular signatures breast cancer is one of the paradigmatic examples of the utility of high-throughput data to deliver prognostic biomarkers, that can be represented in a form of a rather short gene list. Such gene lists can be obtained as a set of features (genes) that are important for the decisions of a Machine Learning (ML) method applied to high-dimensional gene expression data.
View Article and Find Full Text PDFRacial/ethnic differences in 21-gene recurrence score and survival among patients with estrogen receptor-positive breast cancer.
BMC Cancer
April 2024
Department of Radiation Oncology, The Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University Comprehensive Cancer Center, 460 West 10th Avenue, Columbus, OH, 43210, USA.
Background: Despite numerous studies on racial/ethnic disparities among patients with breast cancer, there is a paucity of literature evaluating racial/ethnic differences in 21-gene recurrence score (RS) and survival differences stratified by RS risk categories. We thus performed an observational cohort study to examine racial/ethnic disparities in the context of RS.
Methods: The National Cancer Database (NCDB) was queried for female patients diagnosed between 2006 and 2018 with estrogen receptor (ER)-positive, pT1-3N0-1aM0 breast cancer who received surgery followed by adjuvant endocrine therapy and had RS data available.
Incidence, Clinicopathologic Features, HER2 Fluorescence In Situ Hybridization Profile, and Oncotype DX Results of Human Epidermal Growth Factor Receptor 2-Low Breast Cancers: Experience From a Single Academic Center.
Mod Pathol
July 2023
Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, Ohio. Electronic address:
Human epidermal growth factor receptor 2 (HER2)-low breast cancer, defined by an immunohistochemical (IHC) score of 1+ or 2+ with negative in situ hybridization, is emerging as a predictive marker for the use of the antibody-drug conjugate. To understand how this category differs from HER2-zero cases, we investigated clinicopathological characteristics and HER2 fluorescence in situ hybridization results in a large cohort of 1309 continuous HER2-negative invasive breast carcinomas from 2018 to 2021 evaluated by the Food and Drug Administration-approved HER2 IHC test. Additionally, we compared Oncotype DX recurrence scores and HER2 mRNA expression between HER-low and HER2-zero cases in a separate cohort of 438 estrogen receptor-positive (ER+) early-stage breast carcinoma cases from 2014 to 2016.
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