Fig. 2

Variant identification in sorted cell populations (stromal and tumor) from primary EAC and chest metastases. a Relevant variants in the sorted pure populations of tumor (red), stromal (blue) cells and unsorted fractions (violet). Numeric values represent the alternative allele frequency. Table cells with gray background highlight positions with very low coverage. b BAF plot obtained using WES data of the primary EAC and a control female individual (WES performed on genomic DNA derived from peripheral blood). In the tumor track, the green lines highlight the positions of genes with putative LOH events detected using the OncoSeek panel. While the control profile shows a flat signal centered around 50%, as expected for a normal germline DNA, EAC tumor profile highlights several consistent regions with abnormal allele frequency, describing putative copy-number altered regions. Given the high variability of allele frequency, due to the relative low coverage in WES, a local smoothing on 20 Mb-long regions, represented by red dots, was calculated specifically to mitigate the frequency variability and to give a sharper idea of copy-number alterations at genome-level. c Her-2 fold-change in all sorted pure populations (stromal and tumor). Histogram of CNV differences in the primary EAC and metastases. * = p < 0.05,** = p < 0.001, NS = not significant (ANOVA test). d Her-2 Copy-number analysis using EAC WES data on unsorted material. e (i) Histological appearance and Her-2-immunoreactivity in the primary EAC (i-ii), M1 (iii-iv) and M2 (v-vi) metastases. f Her2 cluster amplification detected by Ventana’s Her2 SISH test in primary EAC (i), M1 (ii) and M2 (iii) metastases. Clusters are represented by black areas in the nuclei (normal signal: black dots)