Table 3.

False negative BRCA1-aberrant samples

False negatives	Phenotype	BRCA1-like parameter
BRCA1 mutation
K1727X	Invasive ductal, borderline ER-negativity, BRCA1 copy number 71 % of normal control	0,18
L639X	Ductulo-lobular, borderline ER-negativity, BRCA1 copy number 82 % of normal control	0,21
fs1829X	Invasive ductal, BRCA1 copy number 85 % of normal control	0,48
BRCA1 methylation
20 %	Medullary	0,30
30 %	Invasive ductal, high CD3 counts (2+)	0,499

Cut-off for BRCA1-like parameter: ≥ 0.5; cut-off for positive methylation: ≥20 %

BRCA1 variants are pathogenic mutations with familial background. ER immunoreactivity was classified by Remmele’ score [29]; Loss of heterozygocity (LOH) was analysed by mean copy number loss of BRCA1 probes. T-lymphocyte infiltration was determined by anti-CD3 immunohistochemistry