Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms

Breast cancers with BRCA1 germline mutation have a characteristic DNA copy number (CN) pattern. We developed a test that assigns CN profiles to be ‘BRCA1-like’ or ‘non-BRCA1-like’, which refers to resembling a BRCA1-mutated tumor or resembling a tumor without a BRCA1 mutation, respectively. Approximately one third of the BRCA1-like breast...

A Critical Perspective On Microarray Breast Cancer Gene Expression Profiling

Microarrays offer biologists an exciting tool that allows the simultaneous assessment of gene expression levels for thousands of genes at once. At the time of their inception, microarrays were hailed as the new dawn in cancer biology and oncology practice with the hope that within a decade diseases like breast cancer would be solved. Various...

Genome-wide epigenetic profiling of breast cancer tumors treated with aromatase inhibitors

Aromatase inhibitors (AI) are extensively used in the treatment of estrogen receptor-positive breast cancers, however resistance to AI treatment is commonly observed. Apart from Estrogen receptor (ER?) expression, no predictive biomarkers for response to AI treatment are clinically applied. Yet, since other therapeutic options exist in the...

Current composite-feature classification methods do not outperform simple single-genes classifiers in breast cancer prognosis

Integrating gene expression data with secondary data such as pathway or protein-protein interaction data has been proposed as a promising approach for improved outcome prediction of cancer patients. Methods employing this approach usually aggregate the expression of genes into new composite features, while the secondary data guide this...