Fig. 5

The three-dimensional tumor mass was investigated using PHLI-seq. a A total of 177 cell clusters were isolated and analyzed from 7 consecutive tissue sections from a triple-negative breast tumor. Before the isolation, cancer cells with various phenotypes were identified by histopathological evaluation from H&E and IHC (AR, CK5/6, Ki-67, and p53; see Additional file 1: Figure S7) sections. Based on the phenotypic information, the 177 cell clusters were selected to discover genetic heterogeneity in tumor cells with various phenotypes. Seven consecutive tissue sections had a 700-μm interval between each section. b Whole-genome sequencing of the 177 cell clusters in the tumor discovered three subclones. The in situ clones 1 and 2 shared CNAs in chromosomes 1 and X. On the other hand, the invasive clone had considerably more amplifications in chromosomes 1 and X, and additional amplifications in chromosomes 5, 7, 8, and 10. c Whole-exome sequencing of the selected samples from each subclone. The subclonal mutations are labeled in the corresponding color to demonstrate shared and unique mutations. d In situ clone 1 included DCIS and benign usual ductal hyperplasia, whereas in situ clone 2 included DCIS and ADH. Histopathologic evaluation of the invasive clone showed that every cell clusters in this subclone were IDC