We identified widespread genomic structural rearrangements that affect gene dosage and somatic subclonal sequence variants of known breast cancer-associated genes that control proliferation, cell death, metastasis, and genome integrity: PIK3CA, TP53, AKT1, MAP3K1, CDH1, RB1, NCOR1, MED12, CBFB, TBX3, and TSHR (Supplementary Fig. 8). Here, PIK3CA is linked to breast cancer.