Further, our search for co-occurring or mutually exclusive germline truncation/somatic mutations across 12 cancer types revealed a number of important insights in terms of genes and pathways involved including: (1) the association between germline BRCA1/2 germline truncations and frequent TP53 and infrequent PIK3CA somatic mutations confirm breast cancer clinical subtype classification; and (2) ATM as a bona fide (third frequently truncated) susceptibility gene demonstrated by both burden and LOH analyses is the only common gene highly mutated at both germline and somatic levels. Here, BRCA1 is linked to breast cancer.