Flow diagram outlining the study cohort, genomic procedures, and analysis performed on all samples. The cohort comprised HGSOC patients with advanced disease, high tumor burden, and carcinosis disseminated throughout the entire peritoneal cavity and in some cases in the paracardiac and pleural cavities. Tumors were collected from the entire peritoneal and extraperitoneal cavity, such as the upper abdomen (spleen, lesser sac, celiac trunk, diaphragm/Morison’s pouch, liver capsule, retroperitoneal pelvic, and paraortic lymph nodes), the bowel, mesentery, parietal and visceral peritoneum, and pleura and paracardiac lymph nodes, where present. Each tumor sample collected was split for nucleotide extraction for subsequent genomic analysis and primary tumor cell culture. SNP array genotyping was performed on 305 primary and relapsed tumor samples and matched germline samples. These data were used to generate genome-wide allele-specific CN profiles, which in turn were used to reconstruct the clonal evolution of disease for each patient in the cohort. Patterns of clonal evolution were catalogued across the cohort, and associations between genomic heterogeneity and phenotypes, proteomic profiles, and anatomical heterogeneity were explored. CNA, copy-number aberration; CNEventDist, copy-number aberration event distance; PDS, primary debulking surgery; RPPA, reverse phase protein array.
