For the top 10% most frequent genes on each chromosome separately for loss and gain groups, gene set enrichment analysis (Supplementary Table S1) showed that somatic aberrations on chromosome 1 interact closely with the genes involved in “regulation of humoral immune response (GO:002920).” Overexpression of immune responses against tumor associated antigens has been frequently reported in breast cancer patients (e.g., 82% antibodies against Her2/neu in cases with strong expression versus no antibodies in cases with weak expression) (Reuschenbach et al., 2009). Here, ERBB2 is linked to breast cancer.