CN analysis revealed that the 17 BRCA1-associated breast cancers with bi-allelic inactivation had higher frequencies of gains of 3q and 6p and losses of 17q, among other differences (P < 0.05, Fisher’s exact test; Supplementary Fig. 5a), as compared to the 16 PALB2-associated breast cancers with bi-allelic inactivation. Here, PALB2 is linked to breast cancer.