Ovarian cancer organoid biobank - EGA European Genome-Phenome Archive

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Dataset ID	Description	Technology	Samples
EGAD00001004387	WGS of ovarian cancer organoids, tumor samples and blood references. Ovarian cancer (OC) is a heterogeneous disease usually diagnosed at a late stage. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of OC are limited and hard to establish. We present a novel protocol that enables efficient derivation and long-term expansion of OC organoids. Utilizing this protocol, we have established 56 organoid lines from 32 patients, representing the spectrum of ovarian neoplasms, including non-malignant borderline tumors, as well as mucinous, clear-cell, endometrioid, low- and high-grade serous carcinomas. OC organoids recapitulate histological and genomic features of the pertinent lesion from which they were derived, illustrating intra- and inter-patient heterogeneity, and can be genetically modified. We show that OC organoids can be used for drug screening assays and capture different tumor subtype responses to the gold standard platinum-based chemotherapy, including acquisition of chemoresistance in recurrent disease. Finally, OC organoids can be xenografted, enabling in vivo drug sensitivity assays. Taken together, this demonstrates their potential application for research and personalized medicine.	HiSeq X Ten	111
EGAD00001004509	Ovarian cancer (OC) is a heterogeneous disease usually diagnosed at a late stage. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of OC are limited and hard to establish. We present a novel protocol that enables efficient derivation and long-term expansion of OC organoids. Utilizing this protocol, we have established 56 organoid lines from 32 patients, representing the spectrum of ovarian neoplasms, including non-malignant borderline tumors, as well as mucinous, clear-cell, endometrioid, low- and high-grade serous carcinomas. OC organoids recapitulate histological and genomic features of the pertinent lesion from which they were derived, illustrating intra- and inter-patient heterogeneity, and can be genetically modified. We show that OC organoids can be used for drug screening assays and capture different tumor subtype responses to the gold standard platinum-based chemotherapy, including acquisition of chemoresistance in recurrent disease. Finally, OC organoids can be xenografted, enabling in vivo drug sensitivity assays. Taken together, this demonstrates their potential application for research and personalized medicine.	NextSeq 500	50
EGAD00001005476	WGS Nanopore nanopore sequencing of organoid line HGS-3.1 and matching blood reference HGS-3	MinION	2
EGAD00001005707	WGS of more samples in the ovarian cancer organoid biobank dataset.	HiSeq X Ten	23

Publications	Citations
An organoid platform for ovarian cancer captures intra- and interpatient heterogeneity. Kopper O, de Witte CJ, Lõhmussaar K, Valle-Inclan JE, Hami N, Kester L, Balgobind AV, Korving J, Proost N, Begthel H, van Wijk LM, Revilla SA, Theeuwsen R, van de Ven M, van Roosmalen MJ, Ponsioen B, Ho VWH, Neel BG, Bosse T, Gaarenstroom KN, Vrieling H, Vreeswijk MPG, van Diest PJ, Witteveen PO, Jonges T, Bos JL, van Oudenaarden A, Zweemer RP, Snippert HJG, Kloosterman WP, Clevers H. Nat Med 25: 2019 838-849	318
Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients. Valle-Inclan JE, Stangl C, de Jong AC, van Dessel LF, van Roosmalen MJ, Helmijr JCA, Renkens I, Janssen R, de Blank S, de Witte CJ, Martens JWM, Jansen MPHM, Lolkema MP, Kloosterman WP. Genome Med 13: 2021 86	9
Primary human organoids models: Current progress and key milestones. Calà G, Sina B, De Coppi P, Giobbe GG, Gerli MFM. Front Bioeng Biotechnol 11: 2023 1058970	4