Figure 4.

Loss of chromosome 5q and 15q regions is associated with reduced cytotoxic immune activity (CYT) levels. A) Copy number aberration (CNA) status distribution according to the three different triple-negative breast cancer (TNBC) classifications of the 33 genes associated with high CNA loss and low CYT scores in chromosomal instability (CIN) high (CIN ≥ 0.38, third tertile) and CIN low (CIN ≤ 0.08, first tertile) tumors in cohort A. B) CNA status distribution of 27 of these 33 genes validated in cohort B associated with high CNA loss and low CYT scores in CIN high (CIN ≥ 0.39, third tertile) and CIN low (CIN ≤ 0.11, first tertile) tumors. Differences in CNA status between both CIN subgroups were assessed using a two-sided Fisher exact test. P values were adjusted for multiple testing using the Benjamini-Hochberg procedure. A logistic regression model was used to evaluate the association between each gene CNA loss with CYT activity. P values were obtained from parametric Mann-Whitney U tests and corrected for multi testing.