Deletions at 1q42.2-q42.3, 2q21.3-q22.1, 4q22.3, 5q21.1 (CHD1), 6q14.3-q15 and 13q14.13 and amplifications at 3q22.1-q21.3, 7p11.2 (EGFR), 8q11.1-q11.21, 8q21.11-q22.1, 8q24.21, 9q33.1, 12q23.1 and 14q13.3-q21.1 (FOXA1) were more commonly present in ETS-negative cancers (Fisher’s exact test, p < 0.05). Here, FOXA1 is linked to cancer.