Table 1. Results of similarity comparisons among BRCA aberration groups.

We compared somatic-mutation signatures or gene-expression profiles between groups of patients who harbored aberrations in BRCA1 or BRCA2. We evaluated whether patients in one group (e.g., those who harbored a BRCA1 germline mutation) were more similar to patients in a second group (e.g., those with BRCA2 germline mutation) than random patient subsets of the same sizes. The numbers in this table represent empirical p-values from our resampling approach. In cases where an individual harbored an aberration in both comparison groups, we excluded that patient from the comparison. We used Holm’s method to correct for testing multiple hypotheses.

Aberration Type 1	Aberration Type 2	Gene Expression	Mutational Signatures
BRCA1 germline mutation (n = 22)	BRCA2 germline mutation (n = 22)	1.0	1.4e-04
BRCA1 germline mutation (n = 22)	BRCA1 somatic mutation (n = 14)	1.0	1.4e-04
BRCA1 germline mutation (n = 22)	BRCA1 homozygous deletion (n = 8)	1.0	0.30
BRCA1 germline mutation (n = 22)	BRCA1 hypermethylation (n = 36)	0.013	1.4e-04
BRCA2 germline mutation (n = 22)	BRCA2 somatic mutation (n = 12)	1.0	1.4e-04
BRCA2 germline mutation (n = 22)	BRCA2 homozygous deletion (n = 19)	1.0	1.4e-04
BRCA2 germline mutation (n = 22)	BRCA2 hypermethylation (n = 2)	1.0	5.4e-04