Tissue samples

Archival formalin-fixed and paraffin-embedded (FFPE) tissue sections of paired endoscopic biopsy and surgically resected specimens from the enrolled patients were used for DNA extraction. Thin tissue sections (4 μm) cut from an FFPE tissue block were placed on microscopic slides and stained with hematoxylin and eosin (H&E) for histological examination. Five unstained tissue sections (10 μm) were also continuously cut from the same tissue block and were placed on a glass slide. The tumor histology was confirmed by a pathologist specializing in gastrointestinal cancer (SF) based on a microscopic examination of the H&E-stained slides. For the endoscopic biopsy specimens, the entire biopsy specimen was manually microdissected after confirming that the ratio of tumor cells to whole cells was >20% on slides stained with H&E. For the surgically resected specimens, a tumor area with a small amount of stromal cells where the ratio of tumor cells to whole cells was >50% on slides stained with H&E was manually microdissected (Fig. 1). DNA extraction was performed using the heat-induced retrieval method, as described previously [19, 20].

Photomicrographs of a case harboring a PIK3CA mutation in both types of specimens (H1047R; Case No. 66). Paired endoscopic biopsy and surgically resected specimens show the same mutation. a The entire biopsy was manually microdissected (scale bar: 1 mm). b The tumor area in the surgically resected specimen was marked (indicated by the solid line) and manually microdissected (scale bar: 2 mm). High-power views of each specimen are shown in the right panels (scale bar: 100 μm)