Those tumours were from individuals who developed invasive primary breast tumours and did not carry a deleterious variant in ATM, BRCA1 or BRCA2. In addition to LOH at the ATM locus, which was observed more frequently in ATM-associated tumours (67%) than in the TCGA ‘sporadic’ tumours (40.1%) (P = 0.02), several genes at other loci appeared more frequently lost in ATM-associated tumours, including TPTE (21p11.2-p11.1), GSTT1, GSTTP1 and GSTTP2 (22q11.23), as well as LCP1, RB1 (13q14), YWHAE, USP6, RABEP1 and MAP2K4 (17p13.3-p12) (Additional file 3: Table S2). Here, BRCA1 is linked to breast neoplasm.