Whole Genome Sequencing Data of High Grade Serous Ovarian Cancer

Longitudinal whole genome sequencing data to study chemoresponse in ovarian cancer. These samples belong to an ongoing sample collection and the data already includes hundreds of samples from over 200 patients. Samples are from primary and metastatic tissues and ascites. All patients have been treated with platinum-taxane based chemotherapy and majority of them are diagnosed with high-grade serous ovarian cancer.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

21 Datasets 10 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001009738	Whole genome sequencing data of 5 High-grade serous carcinoma (HGSC) patients (6 samples) sequenced with BGI.	unspecified	6
EGAD00001009791	Whole genome sequencing data of 8 High-grade serous carcinoma (HGSC) patients (20 samples) sequenced with HiSeq X Ten.	HiSeq X Ten	20
EGAD00001009888	Whole genome sequencing data of 9 high-grade serous carcinoma (HGSC) patients (55 samples) sequenced with HiSeq X Ten.	HiSeq X Ten	55
EGAD00001010019	Sequencing data of 10 high-grade serous carcinoma (HGSC) patients (58 samples including blood derived normal samples as germline controls, fresh frozen tissue samples as tissue controls and organoids) sequenced with HiSeq X Ten / BGISEQ-500 / MGISEQ-2000.	HiSeq X Ten unspecified	58
EGAD00001010029	Whole genome sequencing data of 19 high-grade serous carcinoma (HGSC) patients (47 samples) sequenced with HiSeq X Ten.	HiSeq X Ten	78
EGAD00001010066	Whole genome sequencing data of 7 high-grade serous carcinoma (HGSC) patients (32 samples) sequenced with HiSeq X Ten.	HiSeq X Ten	-
EGAD00001010202	Whole genome sequencing data of 31 high-grade serous carcinoma (HGSC) patients (101 samples) sequenced with HiSeq X Ten and BGISEQ-500	HiSeq X Ten unspecified	90
EGAD00001010845	Whole genome sequencing data of 36 high-grade serous carcinoma (HGSC) patients (89 samples) sequenced with HiSeq X Ten.	unspecified	77
EGAD00001011086	Whole genome sequencing data of 21 high-grade serous carcinoma (HGSC) patients (59 samples) sequenced with MGISEQ-2000.	unspecified	59
EGAD00001011304	Whole genome sequencing data of 26 high-grade serous carcinoma (HGSC) patients (87 samples) sequenced with MGISEQ-2000 and HiSeq X Ten.	HiSeq X Ten unspecified	84
EGAD00001011353	Whole genome sequencing data of 6 high-grade serous carcinoma (HGSC) patients (11 samples) sequenced with MGISEQ-2000	unspecified	11
EGAD00001011368	Whole genome sequencing data of 35 high-grade serous carcinoma (HGSC) patients (112 samples) sequenced with Illumina Novoseq 6000	Illumina NovaSeq 6000	112
EGAD50000000177	Whole genome sequencing data of 19 high-grade serous carcinoma (HGSC) patients (48 samples) sequenced with MGISEQ-2000	unspecified	48
EGAD50000000211	Whole genome sequencing data of 25 high-grade serous carcinoma (HGSC) patients (65 samples) sequenced with Illumina Novoseq 6000	Illumina NovaSeq 6000	65
EGAD50000000275	Whole genome sequencing data of 56 high-grade serous carcinoma (HGSC) patients (208 samples) sequenced with Novoseq 6000	Illumina NovaSeq 6000	208
EGAD50000000313	The dataset contains whole genome sequencing data of 23 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 89 samples are either fresh frozen tumour samples or blood samples. The files provided are paired fastq files.	Illumina NovaSeq 6000	89
EGAD50000000441	The dataset contains whole genome sequencing data of 17 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 46 samples are either fresh frozen tumour samples or blood samples. The files provided are paired fastq files.	Illumina NovaSeq 6000	46
EGAD50000000442	The dataset contains whole genome sequencing data of 32 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 82 samples are either fresh frozen tumour samples or blood samples. The files provided are paired fastq files.	Illumina NovaSeq 6000	82
EGAD50000000507	The dataset contains whole genome sequencing data of 42 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 100 samples are either fresh frozen tumour samples or blood samples. The files provided are paired fastq files.	Illumina NovaSeq 6000	100
EGAD50000000526	The dataset contains whole genome sequencing data of 8 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 16 samples are either fresh frozen tumour samples or blood samples. The files provided are paired fastq files.	Illumina NovaSeq 6000	16
EGAD50000000777	The dataset contains whole genome sequencing data of 58 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 144 samples are either fresh frozen tumour samples or blood samples. The files provided are paired fastq files.	Illumina NovaSeq 6000	144

Publications	Citations
Optimized detection of homologous recombination deficiency improves the prediction of clinical outcomes in cancer. Perez-Villatoro F, Oikkonen J, Casado J, Chernenko A, Gulhan DC, Tumiati M, Li Y, Lavikka K, Hietanen S, Hynninen J, Haltia UM, Tyrmi JS, Laivuori H, Konstantinopoulos PA, Hautaniemi S, Kauppi L, Färkkilä A. NPJ Precis Oncol 6: 2022 96	31
Functional Homologous Recombination Assay on FFPE Specimens of Advanced High-Grade Serous Ovarian Cancer Predicts Clinical Outcomes. Pikkusaari S, Tumiati M, Virtanen A, Oikkonen J, Li Y, Perez-Villatoro F, Muranen T, Salko M, Huhtinen K, Kanerva A, Koskela H, Tapper J, Koivisto-Korander R, Joutsiniemi T, Haltia UM, Lassus H, Hautaniemi S, Färkkilä A, Hynninen J, Hietanen S, Carpén O, Kauppi L. Clin Cancer Res 29: 2023 3110-3123	21
H&E image analysis pipeline for quantifying morphological features. Ariotta V, Lehtonen O, Salloum S, Micoli G, Lavikka K, Rantanen V, Hynninen J, Virtanen A, Hautaniemi S. J Pathol Inform 14: 2023 100339	4
Genome-wide quantification of copy-number aberration impact on gene expression in ovarian high-grade serous carcinoma. Jamalzadeh S, Dai J, Lavikka K, Li Y, Jiang J, Huhtinen K, Virtanen A, Oikkonen J, Hietanen S, Hynninen J, Vähärautio A, Häkkinen A, Hautaniemi S. BMC Cancer 24: 2024 173	8
Deciphering cancer genomes with GenomeSpy: a grammar-based visualization toolkit. Lavikka K, Oikkonen J, Li Y, Muranen T, Micoli G, Marchi G, Lahtinen A, Huhtinen K, Lehtonen R, Hietanen S, Hynninen J, Virtanen A, Hautaniemi S. Gigascience 13: 2024 giae040	3
Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics. Lavikka K, Maarala AI, Oikkonen J, Hautaniemi S. Bioinformatics 41: 2025 btaf091	0
DiffInvex identifies evolutionary shifts in driver gene repertoires during tumorigenesis and chemotherapy. Khalil A, Supek F. Nat Commun 16: 2025 4209	0
Joint inference of mutational signatures from indels and single-nucleotide substitutions reveals prognostic impact of DNA repair deficiencies. Ferrer-Torres P, Galván-Femenía I, Supek F. Genome Med 17: 2025 76	0
Decoding the Genomic and Functional Landscape of Emerging Subtypes in Ovarian Cancer. Micoli G, Lavikka K, Li Y, Pirttikoski A, Afenteva D, Senkowski W, Marchi G, Vähärautio A, Muranen TA, Joutsiniemi T, Hietanen S, Virtanen A, Wennerberg K, Hynninen J, Oikkonen J, Hautaniemi S. Cancer Discov 15: 2025 2262-2277	0
Multi-omics analysis reveals the attenuation of the interferon pathway as a driver of chemo-refractory ovarian cancer. Afenteva D, Yu R, Rajavuori A, Salvadores M, Launonen IM, Lavikka K, Zhang K, Pirttikoski A, Marchi G, Jamalzadeh S, Isoviita VM, Li Y, Micoli G, Erkan EP, Falco MM, Ungureanu D, Lahtinen A, Oikkonen J, Hietanen S, Vähärautio A, Sur I, Virtanen A, Färkkilä A, Hynninen J, Muranen TA, Taipale J, Hautaniemi S. Cell Rep Med 6: 2025 102316	0