Aberrations of the number of copies (CNA) in the genome of luminal B breast tumor

Abstract

Aim. To describe the CNA (Copy Number Aberration) landscape of luminal B breast tumor before treatment. Materials and methods. The study included 100 patients with breast cancer (BC) of luminal B subtype for which a biopsy of the tumor material was performed prior to neoadjuvant chemotherapy (NAC). The tumor DNA was examined using a CytoScan HD Array microarray (Affymetrix, USA). The obtained microarray data were correlated with NAC efficacy. Results. The study showed that loci 1q32.1-32.3, 1q41-42.2, and 8q24.21 had the highest frequency of amplifications (in more than 65% of patients). The highest deletion frequency (in more than 60% of patients) was found in loci 16q21, 16q22.1, 16q23.1-24.1, 17p13.1, and 17p12. Trisomy was most often observed in chromosomes 7, 8, 12, and 17, and monosomy in chromosomes 3, 4, 9, 11, 18, and X-chromosomes. The CNA landscape of luminal B subtype breast tumors is different from triple-negative breast cancer. The largest difference in the frequency of amplifications between patients with an objective response to NAC and patients with no response to NAC was shown in 1q24.2-42.2 loci (46%), and the largest difference in the frequency of deletions (more than 30%) between groups was in regions 6q16. 3, 11p15.4, 11q23.1, and 16q22.2-22.3. These loci can be considered potential predictive markers. Conclusion. The research determined loci with the highest amplification and deletion frequencies for luminal B breast cancer. Potential predictive markers for the given molecular subtype were identified.