A paired t-test showed that VAFs of the two driver genes were significantly higher than that of HMCN1 (TP53; P < 0.01, PIK3CA; P < 0.01) (Supplementary Figure 5), indicating that mutations in HMCN1 occurred later in the tumor evolutionary process than the mutations in TP53 and PIK3CA. This finding suggests that the mutations in HMCN1 might be involved in breast cancer progression. Here, HMCN1 is linked to breast cancer.