Breast Cancer Consensus Subtypes: A system for subtyping breast cancer tumors based on gene expression

Christina Horr; Steven A Buechler

doi:10.1038/s41523-021-00345-2

Breast Cancer Consensus Subtypes: A system for subtyping breast cancer tumors based on gene expression

NPJ Breast Cancer. 2021 Oct 12;7(1):136. doi: 10.1038/s41523-021-00345-2.

Authors

Christina Horr¹, Steven A Buechler^{2

3}

Affiliations

¹ Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN, USA.
² Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN, USA. steve@nd.edu.
³ Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA. steve@nd.edu.

Abstract

Breast cancer is heterogeneous in prognoses and drug responses. To organize breast cancers by gene expression independent of statistical methodology, we identified the Breast Cancer Consensus Subtypes (BCCS) as the consensus groupings of six different subtyping methods. Our classification software identified seven BCCS subtypes in a study cohort of publicly available data (n = 5950) including METABRIC, TCGA-BRCA, and data assayed by Affymetrix arrays. All samples were fresh-frozen from primary tumors. The estrogen receptor-positive (ER+) BCCS subtypes were: PCS1 (18%) good prognosis, stromal infiltration; PCS2 (15%) poor prognosis, highly proliferative; PCS3 (13%) poor prognosis, highly proliferative, activated IFN-gamma signaling, cytotoxic lymphocyte infiltration, high tumor mutation burden; PCS4 (18%) good prognosis, hormone response genes highly expressed. The ER- BCCS subtypes were: NCS1 (11%) basal; NCS2 (10%) elevated androgen response; NCS3 (5%) cytotoxic lymphocyte infiltration; unclassified tumors (9%). HER2+ tumors were heterogeneous with respect to BCCS.