Machine learning approaches to decipher hormone and HER2 receptor status phenotypes in breast cancer

• Published in: Briefings in bioinformatics 2019-03, Vol.20 (2), p.504-514
• Main Authors: Adabor, Emmanuel S, Acquaah-Mensah, George K
• Format: Article
• Language: English
• Subjects: Algorithms; Artificial intelligence; Biomarkers, Tumor - metabolism; Breast cancer; Breast Neoplasms - classification; Breast Neoplasms - genetics; Breast Neoplasms - metabolism; Computational Biology - methods; Data collection; ErbB-2 protein; Estrogen receptors; Estrogens; Female; Gene expression; Gene Expression Profiling - methods; Genomes; Humans; Identification methods; Learning algorithms; Machine Learning; Medical prognosis; Menopause; Phenotype; Phenotypes; Progesterone; Progesterone receptors; Prognosis; Receptor, ErbB-2 - metabolism; Receptors; Receptors, Estrogen - metabolism; Receptors, Progesterone - metabolism
• ISSN: 1477-4054; 1467-5463; 1477-4054
• DOI: 10.1093/bib/bbx138

Abstract Breast cancer prognosis and administration of therapies are aided by knowledge of hormonal and HER2 receptor status. Breast cancer lacking estrogen receptors, progesterone receptors and HER2 receptors are difficult to treat. Regarding large data repositories such as The Cancer Genome Atlas, available wet-lab methods for establishing the presence of these receptors do not always conclusively cover all available samples. To this end, we introduce median-supplement methods to identify hormonal and HER2 receptor status phenotypes of breast cancer patients using gene expression profiles. In these approaches, supplementary instances based on median patient gene expression are introduced to balance a training set from which we build simple models to identify the receptor expression status of patients. In addition, for the purpose of benchmarking, we examine major machine learning approaches that are also applicable to the problem of finding receptor status in breast cancer. We show that our methods are robust and have high sensitivity with extremely low false-positive rates compared with the well-established methods. A successful application of these methods will permit the simultaneous study of large collections of samples of breast cancer patients as well as save time and cost while standardizing interpretation of outcomes of such studies.