Asad, Sarah

Collier, Katharine

et al,

Metzger-Filho, Otto

Watson, Mark

English

Digital Commons@Becker

 Supplementary Data  Matched Cohort Study of Germline BRCA Mutation Carriers with Triple-Negative Breast Cancer in BrighTNess Trial  Supplementary Figures: 1 Supplementary Tables: 4        Supplementary Figure 1. Correlation plot for proliferation, CIN70, and GeparSixto scores. Size of circle and darkness of color indicate magnitude of Pearson’s r. Blue indicates a positive correlation and red indicates a negative correlation. Non-significant correlations are indicated with an “x”.    Supplementary Table 1. BRCA status stratified analyses of pathologic complete response by treatment.   Germline BRCA mutated (gBRCA) Non-gBRCA  N %  N % Arm A 24/39 61.5 47/78 60.3 Arm B 9/18 50.0 23/36 63.9 Arm C 8/18 44.4 9/36 25.0  Supplementary Table 2. BRCA status stratified analyses of pathologic complete response by treatment.   Germline BRCA mutated (gBRCA) Non-gBRCA  Odds Ratio 95% Confidence Interval p-value Odds Ratio 95% Confidence Interval p-value Arm A vs. C 2.0 (0.65,6.2) 0.23 4.5 (1.9,11.0) 0.0007 Arm B vs. C 1.3 (0.34,4.6) 0.74 5.3 (1.9,14.7) 0.001    Supplementary Table 3. Single Sample Hallmark Gene Set Enrichment Analysis of Germline BRCA Mutated Cases versus Matched Controls   Signature T.test_Pvalue FDR_PvalueHALLMARK_WNT_BETA_CATENIN_SIGNALING 0.032812987 0.885565934HALLMARK_PROTEIN_SECRETION 0.129824967 0.885565934HALLMARK_ALLOGRAFT_REJECTION 0.137540348 0.885565934HALLMARK_ESTROGEN_RESPONSE_EARLY 0.150629922 0.885565934HALLMARK_GLYCOLYSIS 0.179441125 0.885565934HALLMARK_KRAS_SIGNALING_UP 0.183980092 0.885565934HALLMARK_APICAL_JUNCTION 0.19917611 0.885565934HALLMARK_NOTCH_SIGNALING 0.20454539 0.885565934HALLMARK_COMPLEMENT 0.261703241 0.885565934HALLMARK_DNA_REPAIR 0.265367764 0.885565934HALLMARK_TNFA_SIGNALING_VIA_NFKB 0.268393765 0.885565934HALLMARK_UNFOLDED_PROTEIN_RESPONSE 0.312149705 0.885565934HALLMARK_INFLAMMATORY_RESPONSE 0.314928077 0.885565934HALLMARK_SPERMATOGENESIS 0.324627538 0.885565934HALLMARK_TGF_BETA_SIGNALING 0.33856888 0.885565934HALLMARK_APOPTOSIS 0.340159966 0.885565934HALLMARK_ANGIOGENESIS 0.379319253 0.885565934HALLMARK_CHOLESTEROL_HOMEOSTASIS 0.389575707 0.885565934HALLMARK_PANCREAS_BETA_CELLS 0.415323297 0.885565934HALLMARK_COAGULATION 0.430364402 0.885565934HALLMARK_UV_RESPONSE_DN 0.438149373 0.885565934HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 0.453465358 0.885565934HALLMARK_HEME_METABOLISM 0.474087948 0.885565934HALLMARK_XENOBIOTIC_METABOLISM 0.498728702 0.885565934HALLMARK_BILE_ACID_METABOLISM 0.50695935 0.885565934HALLMARK_ESTROGEN_RESPONSE_LATE 0.521187964 0.885565934HALLMARK_MYOGENESIS 0.543984314 0.885565934HALLMARK_KRAS_SIGNALING 0.545898788 0.885565934HALLMARK_MTORC1_SIGNALING 0.551413552 0.885565934HALLMARK_ANDROGEN_RESPONSE 0.565042417 0.885565934HALLMARK_PEROXISOME 0.583716397 0.885565934HALLMARK_MYC_TARGETS_V2 0.604203365 0.885565934HALLMARK_E2F_TARGETS 0.616297805 0.885565934HALLMARK_UV_RESPONSE 0.618384249 0.885565934HALLMARK_HEDGEHOG_SIGNALING 0.640043188 0.885565934HALLMARK_PI3K_AKT_MTOR_SIGNALING 0.64682362 0.885565934HALLMARK_OXIDATIVE_PHOSPHORYLATION 0.653270694 0.885565934HALLMARK_INTERFERON_GAMMA_RESPONSE 0.675133373 0.885565934HALLMARK_APICAL_SURFACE 0.679193238 0.885565934HALLMARK_KRAS_SIGNALING_DN 0.681204564 0.885565934HALLMARK_IL2_STAT5_SIGNALING 0.703781314 0.887906098HALLMARK_FATTY_ACID_METABOLISM 0.717154925 0.887906098HALLMARK_P53_PATHWAY 0.746258372 0.902451985HALLMARK_HYPOXIA 0.770993075 0.911173634HALLMARK_G2M_CHECKPOINT 0.824588226 0.952857506HALLMARK_MYC_TARGETS_V1 0.853475994 0.96479895HALLMARK_INTERFERON_ALPHA_RESPONSE 0.904727096 0.968350969HALLMARK_MITOTIC_SPINDLE 0.913879961 0.968350969HALLMARK_UV_RESPONSE_UP 0.92300621 0.968350969HALLMARK_REACTIVE_OXIGEN_SPECIES_PATHWAY 0.943799376 0.968350969HALLMARK_IL6_JAK_STAT3_SIGNALING 0.952125237 0.968350969HALLMARK_ADIPOGENESIS 0.968350969 0.968350969 Supplementary Table 4. Single Sample Immune Response In Silico Gene Set Enrichment Analysis of Germline BRCA Mutated Cases versus Matched Controls   Signature T.test_Pvalue FDR_PvalueGSE22886_NEUTROPHIL_VS_DC 0.052923328 0.992449816GSE22886_NAIVE_VS_IGM_MEMORY_BCELL 0.054589297 0.992449816GSE22886_NEUTROPHIL_VS_DC_UP 0.067489042 0.992449816GSE22886_IGG_IGA_MEMORY_BCELL_VS_BM_PLASMA_CELL_UP 0.082740987 0.992449816GSE22886_NAIVE_VS_IGM_MEMORY_BCELL_UP 0.084395373 0.992449816GSE22886_IGM_MEMORY_BCELL_VS_BM_PLASMA_CELL_UP 0.10910867 0.992449816GSE22886_DAY0_VS_DAY7_MONOCYTE_IN_CULTURE_UP 0.11180083 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_NKCELL 0.123627711 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_MONOCYTE_UP 0.155678174 0.992449816GSE22886_NAIVE_BCELL_VS_MONOCYTE_DN 0.158466133 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_MONOCYTE_DN 0.159572469 0.992449816GSE22886_NAIVE_BCELL_VS_MONOCYTE_UP 0.159743287 0.992449816GSE22886_IGA_VS_IGM_MEMORY_BCELL 0.163567329 0.992449816GSE22886_DC_VS_MONOCYTE_DN 0.163684792 0.992449816GSE22886_IGA_VS_IGM_MEMORY_BCELL_DN 0.169889527 0.992449816GSE22886_DAY0_VS_DAY1_MONOCYTE_IN_CULTURE_DN 0.196352045 0.992449816GSE22886_NAIVE_TCELL_VS_MONOCYTE_DN 0.196617726 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_MONOCYTE_DN 0.202673149 0.992449816GSE22886_NAIVE_VS_IGM_MEMORY_BCELL_DN 0.208200895 0.992449816GSE22886_DC_VS_MONOCYTE 0.210527101 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_NKCELL_DN 0.213687281 0.992449816GSE22886_IGG_IGA_MEMORY_BCELL_VS_BLOOD_PLASMA_CELL_DN 0.215485743 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_48H_ACT_TH2_UP 0.236004937 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_NKCELL_UP 0.242888831 0.992449816GSE22886_IGM_MEMORY_BCELL_VS_BLOOD_PLASMA_CELL_UP 0.258253176 0.992449816GSE22886_TH1_VS_TH2_48H_ACT 0.261509237 0.992449816GSE22886_NAIVE_BCELL_VS_BLOOD_PLASMA_CELL_DN 0.266970882 0.992449816GSE22886_IGM_MEMORY_BCELL_VS_BLOOD_PLASMA_CELL_DN 0.269544809 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_MEMORY_TCELL_DN 0.270795456 0.992449816GSE22886_DAY1_VS_DAY7_MONOCYTE_IN_CULTURE_UP 0.27225891 0.992449816GSE22886_IGG_IGA_MEMORY_BCELL_VS_BM_PLASMA_CELL 0.276167255 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_DC_DN 0.278824442 0.992449816GSE22886_NAIVE_TCELL_VS_NKCELL 0.290298865 0.992449816GSE22886_NAIVE_BCELL_VS_NEUTROPHIL_DN 0.300482633 0.992449816GSE22886_NAIVE_TCELL_VS_NKCELL_DN 0.301222491 0.992449816GSE22886_CD8_VS_CD4_NAIVE_TCELL 0.305766133 0.992449816GSE22886_IGM_MEMORY_BCELL_VS_BM_PLASMA_CELL 0.307041001 0.992449816GSE22886_CD8_VS_CD4_NAIVE_TCELL_DN 0.307268086 0.992449816GSE22886_NAIVE_BCELL_VS_DC_DN 0.309211881 0.992449816GSE22886_TH1_VS_TH2_48H_ACT_DN 0.315130595 0.992449816GSE22886_DAY0_VS_DAY7_MONOCYTE_IN_CULTURE_DN 0.321778593 0.992449816GSE22886_NAIVE_BCELL_VS_NEUTROPHIL 0.330739403 0.992449816GSE22886_IGG_IGA_MEMORY_BCELL_VS_BLOOD_PLASMA_CELL_UP 0.331489827 0.992449816GSE22886_NAIVE_TCELL_VS_DC_DN 0.348013355 0.992449816GSE22886_TH1_VS_TH2_48H_ACT_UP 0.351564905 0.992449816GSE22886_NEUTROPHIL_VS_MONOCYTE_DN 0.365753413 0.992449816GSE22886_IL2_VS_IL15_STIM_NKCELL_DN 0.37124705 0.992449816GSE22886_NAIVE_VS_IGG_IGA_MEMORY_BCELL_DN 0.371404648 0.992449816GSE22886_NAIVE_VS_MEMORY_TCELL_DN 0.371950576 0.992449816GSE22886_DAY0_VS_DAY1_MONOCYTE_IN_CULTURE_UP 0.374706168 0.992449816GSE22886_UNSTIM_VS_IL2_STIM_NKCELL_UP 0.376114361 0.992449816GSE22886_UNSTIM_VS_STIM_MEMORY_TCELL_UP 0.385321281 0.992449816GSE22886_DAY0_VS_DAY7_MONOCYTE_IN_CULTURE 0.392327887 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_MONOCYTE_UP 0.393498184 0.992449816GSE22886_IL2_VS_IL15_STIM_NKCELL 0.45367746 0.992449816GSE22886_DAY1_VS_DAY7_MONOCYTE_IN_CULTURE 0.481577593 0.992449816GSE22886_CD8_VS_CD4_NAIVE_TCELL_UP 0.482146879 0.992449816GSE22886_NAIVE_TCELL_VS_NKCELL_UP 0.485796745 0.992449816GSE22886_TH1_VS_TH2_12H_ACT_DN 0.494942278 0.992449816GSE22886_IGA_VS_IGM_MEMORY_BCELL_UP 0.498654962 0.992449816GSE22886_TH1_VS_TH2_12H_ACT_UP 0.525123151 0.992449816GSE22886_NEUTROPHIL_VS_MONOCYTE 0.533564006 0.992449816GSE22886_UNSTIM_VS_IL2_STIM_NKCELL 0.545351067 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_MEMORY_TCELL_DN 0.556298937 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_12H_ACT_TH1_UP 0.569691311 0.992449816GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP 0.570420024 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_DC_DN 0.571127765 0.992449816GSE22886_NAIVE_TCELL_VS_DC 0.584264304 0.992449816GSE22886_TCELL_VS_BCELL_NAIVE_UP 0.58536891 0.992449816GSE22886_NAIVE_BCELL_VS_BLOOD_PLASMA_CELL_UP 0.593875382 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_DC 0.598457546 0.992449816GSE22886_NAIVE_TCELL_VS_MONOCYTE 0.607512536 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_NKCELL_DN 0.610157911 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_NKCELL_UP 0.617108649 0.992449816GSE22886_DAY0_VS_DAY1_MONOCYTE_IN_CULTURE 0.620046659 0.992449816Supplementary Table 4. (cont)  GSE22886_DAY1_VS_DAY7_MONOCYTE_IN_CULTURE_DN 0.627523773 0.992449816GSE22886_NAIVE_VS_MEMORY_TCELL 0.631563883 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_MEMORY_TCELL_UP 0.63579439 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_12H_ACT_TH2_UP 0.643180147 0.992449816GSE22886_NAIVE_VS_IGG_IGA_MEMORY_BCELL 0.646914836 0.992449816GSE22886_IL2_VS_IL15_STIM_NKCELL_UP 0.669628092 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_MONOCYTE 0.673784239 0.992449816GSE22886_CD8_TCELL_VS_BCELL_NAIVE_UP 0.680313357 0.992449816GSE22886_TH1_VS_TH2_12H_ACT 0.681063091 0.992449816GSE22886_NEUTROPHIL_VS_DC_DN 0.683949548 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_MEMORY_TCELL 0.693579173 0.992449816GSE22886_CD8_TCELL_VS_BCELL_NAIVE_DN 0.699570967 0.992449816GSE22886_NEUTROPHIL_VS_MONOCYTE_UP 0.714083125 0.992449816GSE22886_NAIVE_BCELL_VS_BM_PLASMA_CELL_UP 0.715192421 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_12H_ACT_TH1_DN 0.721106028 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_48H_ACT_TH2_DN 0.727423558 0.992449816GSE22886_NAIVE_BCELL_VS_BLOOD_PLASMA_CELL 0.731413105 0.992449816GSE22886_NAIVE_BCELL_VS_MONOCYTE 0.731770105 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_NEUTROPHIL_DN 0.740628765 0.992449816GSE22886_UNSTIM_VS_IL15_STIM_NKCELL_UP 0.757275457 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_12H_ACT_TH2_DN 0.765163601 0.992449816GSE22886_CD4_TCELL_VS_BCELL_NAIVE_DN 0.771227266 0.992449816GSE22886_UNSTIM_VS_STIM_MEMORY_TCELL_DN 0.774770783 0.992449816GSE22886_CD4_TCELL_VS_BCELL_NAIVE_UP 0.777955657 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_DC_UP 0.785145413 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_DC_UP 0.79313471 0.992449816GSE22886_UNSTIM_VS_IL15_STIM_NKCELL 0.79621323 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_48H_ACT_TH2 0.800036298 0.992449816GSE22886_IGG_IGA_MEMORY_BCELL_VS_BM_PLASMA_CELL_DN 0.801434496 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_MEMORY_TCELL 0.813146865 0.992449816GSE22886_NAIVE_BCELL_VS_DC 0.815379961 0.992449816GSE22886_UNSTIM_VS_IL2_STIM_NKCELL_DN 0.815887739 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_NEUTROPHIL 0.819524958 0.992449816GSE22886_DC_VS_MONOCYTE_UP 0.824702796 0.992449816GSE22886_CTRL_VS_LPS_24H_DC_DN 0.826549419 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_NEUTROPHIL_UP 0.828791945 0.992449816GSE22886_TCELL_VS_BCELL_NAIVE_DN 0.828868233 0.992449816GSE22886_TCELL_VS_BCELL_NAIVE 0.830486634 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_NEUTROPHIL_UP 0.83478815 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_NEUTROPHIL 0.841330774 0.992449816GSE22886_NAIVE_VS_IGG_IGA_MEMORY_BCELL_UP 0.841825266 0.992449816GSE22886_UNSTIM_VS_IL15_STIM_NKCELL_DN 0.845942673 0.992449816GSE22886_NAIVE_BCELL_VS_DC_UP 0.854049994 0.992449816GSE22886_CTRL_VS_LPS_24H_DC 0.856014845 0.992449816GSE22886_NAIVE_BCELL_VS_BM_PLASMA_CELL 0.857654173 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_MEMORY_TCELL_UP 0.867467039 0.992449816GSE22886_NAIVE_TCELL_VS_NEUTROPHIL 0.872201142 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_DC 0.887160376 0.992449816GSE22886_CTRL_VS_LPS_24H_DC_UP 0.887367677 0.992449816GSE22886_IGM_MEMORY_BCELL_VS_BM_PLASMA_CELL_DN 0.899821898 0.992449816GSE22886_NAIVE_TCELL_VS_DC_UP 0.901902106 0.992449816GSE22886_IGM_MEMORY_BCELL_VS_BLOOD_PLASMA_CELL 0.902617 0.992449816GSE22886_NAIVE_TCELL_VS_NEUTROPHIL_DN 0.902995724 0.992449816GSE22886_IGG_IGA_MEMORY_BCELL_VS_BLOOD_PLASMA_CELL 0.906117199 0.992449816GSE22886_NAIVE_TCELL_VS_NEUTROPHIL_UP 0.910470695 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_NKCELL 0.912287352 0.992449816GSE22886_NAIVE_CD8_TCELL_VS_NEUTROPHIL_DN 0.912333886 0.992449816GSE22886_UNSTIM_VS_STIM_MEMORY_TCELL 0.917427863 0.992449816GSE22886_NAIVE_BCELL_VS_NEUTROPHIL_UP 0.931295021 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_48H_ACT_TH1_UP 0.944653849 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_12H_ACT_TH1 0.96506936 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_MONOCYTE 0.970876549 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_48H_ACT_TH1 0.976378034 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_12H_ACT_TH2 0.976935003 0.992449816GSE22886_NAIVE_VS_MEMORY_TCELL_UP 0.981892419 0.992449816GSE22886_NAIVE_BCELL_VS_BM_PLASMA_CELL_DN 0.982458439 0.992449816GSE22886_CD8_TCELL_VS_BCELL_NAIVE 0.989432627 0.992449816GSE22886_CD4_TCELL_VS_BCELL_NAIVE 0.991033676 0.992449816GSE22886_NAIVE_CD4_TCELL_VS_48H_ACT_TH1_DN 0.992449816 0.992449816

Matched cohort study of germline BRCA mutation carriers with triple negative breast cancer in brightness

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Matched cohort study of germline BRCA mutation carriers with triple negative breast cancer in brightness

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