A comparison of the frequencies of somatic mutations affecting the 410 cancer genes between PALB2 and non-BRCA1/2/PALB2-associated breast cancers revealed that PALB2, NOTCH3, KMT2A, BRIP1, DNMT3A, FGFR4, GNAQ, and CD79A (all P < 0.05; Fisher’s exact test) were more frequently mutated in the 24 PALB2-associated breast cancers than in the 683 ER−/HER2− and ER+ non-BRCA1/2/PALB2-associated breast cancers (Fig. 4a), however only PALB2 and NOTCH3 remained significantly differently mutated between the two groups after bootstrap resampling (P < 0.01; Supplementary Table 5). Here, FGFR4 is linked to breast cancer.