Purpose: Ovarian cancer is heterogeneous with multiple histological subtypes and a wide range of genetic aberrations. While high-grade serous ovarian carcinoma (HGSOC) is the most common, clear cell ovarian carcinoma (CCOC) is the most challenging to treat and exhibits low response rates to standard therapies. However, efforts to understand CCOC and develop new therapies have been limited because it represents a minority of ovarian cancers in the U.S. and Europe. In contrast, CCOC accounts for approximately 30% of all ovarian cancer in Japan. To improve the survival of patients with CCOC, a deeper understanding of the molecular features that define available model systems is needed. Our goal is to comprehensively characterize a panel of CCOC lines using next generation sequencing and functional in vitro and in vivo experiments to define the lines that are most faithful to CCOC and are tractable for subsequent in vivo drug discovery. Method: We obtained 9 CCOC cells from ATCC, Riken Cell Bank, and University of Miami (ES-2, TOV21G, OVTOKO, OVMANA, OCI-C5x, JHOC-5, JHOC-7, JHOC-9, and OVISE). Genomic DNA, RNA, and protein were isolated and subjected to whole exome DNA-seq, RNA-seq, and reverse phase protein array (RPPA), respectively. We performed in vitro MTT assays to test the sensitivity of these lines to chemotherapies. Tumorigenicity was evaluated by injecting 5 million cells of luciferized CCOC lines into NSG female mice using both the subcutaneous route and the intraperitoneal route. Imaging was performed weekly using the In Vivo Imaging System. Results: ARID1A mutation, the most prevalent mutation in CCOC, is present in 8 of the 9 cell lines (TOV21G, OVTOKO, OVMANA, OCI-C5x, JHOC-5, JHOC-7, JHOC-9, and OVISE), whereas the second common mutation in CCOC (PIK3CA) is detected in 5 lines (TOV21G, OVMANA, OCI-C5x, JHOC-7, and OVISE). The ES-2 cell line has both TP53 and BRAF mutations and its genomic profile is not typical of CCOC. Principal component analysis of RPPA showed distinct groups between the 9 CCOC lines and the 6 HGSOC lines. Interestingly, we also observed two distinct clusters within the CCOC lines. Consistent with our genomic analysis, the ES-2 cell line correlated more closely with the HGSOC lines based on RPPA data. In our in vitro drug studies, OVTOKO and OCI-C5x exhibited resistance to Carboplatin/Paclitaxel. In xenograft study, 4 cell lines (ES-2, TOV21G, OVTOKO, and OCI-C5x) formed measurable tumor within a month. In contrast, OVMANA, JHOC-7, JHOC-9, and OVISE took over 100 days to form tumors. Conclusion: Our data suggests that there may exist two functionally distinct groups within CCOC that warrants further study. In vitro and in vivo studies identified 4 cell lines that represent tractable models for rigorous therapeutic studies: ES-2, TOV21G, OVTOKO, and OCI-C5x. However, ES-2 appears to cluster more closely with HGSOC and may not represent the CCOC histotype. Citation Format: Yasuto Kinose, Dorothy Hallberg, Kai Doberstein, Gordon Mills, Tan Ince, Victor Velculescu, Fiona Simpkins, Ronny Drapkin. Comprehensive molecular and experimental characterization of ovarian clear cell carcinoma cell lines for in vivo drug development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1065.