Fig. 2: Performance of the 10-gene methylated marker panel in detecting positive lymph nodes in women with breast cancer using the GeneXpert Prototype BCDA.

FNA was collected from lymph nodes intraoperatively during SLNB for cytology and molecular analysis prior to assessment by histology. a FNA collection schema of the prospective study sample set. b Box plots show the median cumulative methylation of FNA from malignant lymph nodes versus benign lymph nodes by histology. For the box plot, the whiskers are Tukey, the box is 25th and 75th percentiles, and the center bar is the median. c Receiver operating characteristic (ROC) analysis of the area under the curve (AUC) indicates the discriminatory power of the 10-gene marker panel at a threshold for benign at 8.5 CM units. d Performance of BCDA compared to the gold standard of histopathology of the sentinel lymph node removed at surgery. NPV and PPV of BCDA are presented. e Performance of cytology compared to histopathology. For cytology comparisons, two FNA samples of malignant lymph node and four samples of benign lymph node which were of indeterminate cytology (yellow bars) were removed from the analysis. NPV and PPV of cytology are presented. f Histogram plots indicate the percent methylation (colored segment) in each gene and cumulative methylation of the 10-gene marker panel by BCDA in each patient sample. g A heat map of LN-FNA samples positive (red) and negative (green) for methylation by BCDA compared to histopathology, and cytology. Yellow bars: indeterminate by cytology. BCDA breast cancer detection assay, CM cumulative methylation units, NPV negative predictive value, PPV positive predictive value, RUO research use only.