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Table 3 Individuals with discordant HER2 (IHC) status and HER2 (FISH) classification (individuals not expressing ER and PR are highlighted in bold)

From: Ensemble outlier detection and gene selection in triple-negative breast cancer data

Individual ER PR HER2 HER2 level HER2 status HER2 HER2 status Type
     (IHC) (IHC) (FISH) (IHC + FISH)  
TCGA-LL-A5YP 0.16(+) 0.05(-) 15.10 1+ - + + non-TNBC
TCGA-A2-A0EQ 2.13(-) 0.04(-) 30.5 3+ + - - TNBC
TCGA-BH-A18T 0.61(-) 0.04(-) 29.35 2+ + - - TNBC
TCGA-AO-A0JL 0.63(-) 0.08(-) 63.60 1+ - + + non-TNBC
TCGA-AN-A0XV 110.33(+) 3.50(+) 22.17 2+ + - - non-TNBC
TCGA-AO-A12C 18.88(+) 3.60(+) 95.67 3+ + - - non-TNBC
TCGA-BH-A18Q 2.83(-) 1.10(-) 20.93   + - - TNBC
TCGA-LL-A5YL 9.84(+) 0.52(-) 55.32 3+ + - - non-TNBC
TCGA-E2-A10A 59.40(+) 9.89(+) 32.99 2+ + - - non-TNBC
TCGA-AO-A03L 14.71(+) 1.35(+) 58.72 2+ + - - non-TNBC
TCGA-AO-A12G 40.39(+) 1.80(+) 45.03 2+ + - - non-TNBC
TCGA-BH-A1EX 5.50(+) 0.28(+) 41.46   + - - non-TNBC
TCGA-BH-A0AU 37.14(+) 16.19(+) 51.79   + - - non-TNBC
TCGA-A2-A04U 0.02(-) 0.02(-) 9.64 1+ - + + non-TNBC
TCGA-AN-A0XW 13.96(+) 5.32(+) 22.04 2+ + - - non-TNBC
  1. Individuals marked with asterisks show no concordance regarding HER2 labeling by different testing and are misclassified by logistic regression based on the 3 variables clinically used to classify breast cancer patients into TNBC