Importantly, we have identified a currently uncatalogued signature, which we have designated O/TN, that is associated with triple negative breast cancer (p = 0.007), which was validated in 109 TCGA TNBC samples (p = 0.001); we found that PIK3CA pH1047R hotspot mutation is more frequent in proliferative disease without atypia (PDWA) compared to non-proliferative disease (p < 0.001); we observed multiple recurrent CNVs as well, including a MLH3 deletion, which is significantly associated with a mismatch repair signature (p < 0.001). The gene discussed is MLH3; the disease is triple-negative breast carcinoma.