Fig. 1

Tissue collection in DCIS with distinct HER2 status. a Workflow diagram for laser capture microdissection (LCM) Smart-3SEQ/WGS. Consecutive breast tissue sections were cut for H&E staining, LCM, and HER2-FISH. RNA and DNA were extracted from LCM-collected DCIS cells and subjected to Smart-3SEQ and WGS. b HER2-IHC staining for DCIS possessing different degrees of HER2 amplification with strongly stained ducts (purple arrows) and weakly stained ducts (orange arrows) at 200×. c Representative images of H&E (10×), LCM (10×), and HER2-FISH (400×) taken from consecutive sections of DCIS with different degrees of HER2 amplification. d Correlation between HER2 variance stabilizing transformation (VST)-normalized gene counts from Smart-3SEQ data and the HER2 copy number/cell from HER2-FISH results in DCIS. The HER2 copy number/cell is the absolute number of HER2-FISH signals/cell. It is calculated by averaging all detected cells in the DCIS duct