Prognostic Value of Copy Number Alteration Burden in Early-Stage Breast Cancer and the Construction of an 11-Gene Copy Number Alteration Model

SIMPLE SUMMARY: Breast cancer is a malignancy that poses a significant threat to women’s health. The enormous disease burden has forced a wide range of researchers to develop more accurate prognostic models. Copy number alterations, which are amplifications or deletions of DNA fragments, often predict a poor prognosis. Instead, copy number alteration burden, i.e., the level of CNA, may have a good predictive value for disease prognosis. In this study, we developed a prognostic model for early breast cancer based on CNAB and simplified it. It performed excellently in two external validation sets. ABSTRACT: The increasing burden of breast cancer has prompted a wide range of researchers to search for new prognostic markers. Considering that tumor mutation burden (TMB) is low and copy number alteration burden (CNAB) is high in breast cancer, we built a CNAB-based model using a public database and validated it with a Chinese population. We collected formalin-fixed, paraffin-embedded (FFPE) tissue samples from 31 breast cancer patients who were treated between 2010 and 2014 at the National Cancer Center (CICAMS). METABRIC and TCGA data were downloaded via cBioPortal. In total, 2295 patients with early-stage breast cancer were enrolled in the study, including 1427 in the METABRIC cohort, 837 in the TCGA cohort, and 31 in the CICAMS cohort. Based on the ROC curve, we consider 2.2 CNA/MBp as the threshold for the CNAB-high and CNAB-low groupings. In both the TCGA cohort and the CICAMS cohort, CNAB-high had a worse prognosis than CNAB-low. We further simplified this model by establishing a prognostic nomogram for early breast cancer patients by 11 core genes, and this nomogram was highly effective in both the TCGA cohort and the CICAMS cohort. We hope that this model will subsequently help clinicians with prognostic assessments.