As we expected, the neoepitope burden across all breast cancers is highly correlated with the number of expressed neoepitopes (R2 = 0.94, p < 0.001) (Fig. 3b), as well as each of the three subtypes individually (Additional file 8: Figure S6): TNBC (R2 = 0.93, p < 0.001), HER-2(+) (R2 = 0.99, p < 0.001), ER/PR(+)HER-2(−) (R2 = 0.95, p < 0.001). Here, PGR is linked to breast carcinoma.