Pannoramic viewer software package

We used the IGC procedure for TMA construction and for sampling FFPE tissue blocks for RNA extraction (Fig. 1). Hematoxylin and eosin (H&E)-stained and FFPE blocks containing both tumor and normal epithelium breast tissue were selected. The H&E-stained slides were scanned by the whole-slide digital Pannoramic scanner (3D-Histech, Budapest, Hungary). Then, pathologists (E.-Y.O, A.H.B) annotated the digital images to indicate 4 circular regions of interest from each whole-slide digital image (1 for tumor in center, 1 for tumor in periphery, and the other 2 for normal epithelium and stroma) using the Pannoramic Viewer Software package (3D-Histech). Circles for the selected areas may range in size from 0.6 to 2 mm in diameter, based on the desired size of the sample core. We selected different color cores to indicate whether the core was targeting tumor or normal tissue. In this study, we used a 1 or 1.5 mm diameter coring needle. The annotated whole-slide digital image was overlaid onto an image of the corresponding FFPE block using the software provided by the TMA-Master (3D-Histech). After selecting 2 reference points, the 2 images (from slide and block) were aligned and a computer-guided robotic arm obtained the selected core from the FFPE block (Fig. 1).