Cancer cell lines are frequently used as in vitro tumor models. Recent molecular profiles of hundreds of cell lines from the Cancer Cell Line Encyclopedia (CCLE) and thousands of tumor samples from The Cancer Genome Atlas (TCGA) now allow a systematic genomic comparison of cell lines and tumors. We analyzed a panel of 47 ovarian cancer cell lines and identified those that have the highest genetic similarity to ovarian tumors. Our comparison of copy-number changes, mutations and mRNA expression profiles revealed pronounced differences in molecular profiles between commonly used ovarian cancer cell lines and high-grade serous ovarian cancer tumor samples. We identified several rarely used cell lines that more closely resemble cognate tumor profiles than commonly used cell lines, and we propose these lines as the most suitable models of ovarian cancer. Our results indicate that the gap between cell lines and tumors can be bridged by genomically informed choices of cell line models for all tumor types. The genomic profiles of these ovarian cancer cell lines and tumor samples can be explored and analyzed via the cBioPortal for Cancer Genomics (

Citation Format: Nikolaus Schultz. Cell lines as ovarian cancer models: Insights from molecular profiles in TCGA and CCLE. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr IA2.