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PTRC-HGSOC

The Cancer Imaging Archive

PTRC-HGSOC | Proteogenomic analysis of chemo-refractory high grade serous ovarian cancer

DOI: 10.7937/6RDA-P940 | Data Citation Required | Image Collection

Location Species Subjects Data Types Cancer Types Size Supporting Data Status Updated
Ovary Human 174 Histopathology High grade serous ovarian cancer 120.5GB Clinical Public, Complete 2023/08/03

Summary

In our study, we have generated proteomic and genomic (RNA sequencing and whole genome sequencing) profiles from high grade serous ovarian cancer (HGSOC) tumor biopsies. All biospecimens are formalin-fixed, parrafin-embedded (FFPE) tissues and annotated for patient sensitivity to platinum chemotherapy (refractory or sensitive). For all 174 tumors that were analyzed, we have H&E-stained and imaged the first and last sections (“bookend”) cut from each FFPE block to allow study of tumor pathology. These H&E pathology images are uploaded in this dataset. The 174 tumors represented 158 unique patients (imaging was performed on two FFPE blocks for a small subset of patients where additional tumor mass was required for proteomic analysis). The bookend FFPE slides were cut at 4 μm thickness using a microtome and mounted on glass slides (Leica Biosystems Cat# 3800040) for H&E staining. Digital images of the H&E slides were recorded using a ScanScope AT Slide Scanner (Leica Aperio Technologies, Vista, CA, USA) under 20X objective magnification (0.5 μm resolution). Images were analyzed by HALO Image Analysis Platform software (Indicta Labs, Albuquerque, New Mexico, USA).

The following clinical data are also provided for these subjects: 

  • Image file name (combination of Image Name and Image ID) and corresponding sample IDs
  • Chemotherapy response status: (sensitive/refractory; refractory is defined in our study as clinical ovarian cancer that progresses while on platinum-based therapy or within 4 weeks)
  • neo-adjuvant treatment (yes/no)
  • Tumor location
  • Tumor grade, stage, substage
  • Patient age
  • Patient ethnicity
  • Patient race
  • Age of sample

The goals of the study were to understand mechanisms of platinum resistance in epithelial ovarian cancers (EOCs) in order to: i) predict EOCs that will respond to DNA-damaging platinum therapy, and ii) identify potential new drug targets in resistant disease to point to desperately needed new therapeutic approaches. The ability to predict platinum-resistant/refractory disease would be clinically impactful by enabling the immediate triage of patients with refractory disease to clinical trials of experimental therapies, avoiding use of ineffective standard of care chemotherapy and helping to identify novel treatments. In this study, we generated proteomic and genomic (RNA sequencing and whole genome sequencing) profiling datasets and H&E images from high grade serous ovarian cancer (HGSOC) tumor biopsies representing platinum-sensitive and platinum-refractory disease.

Data Access

Clinical Data notes:

A note about the values in CSV spreadsheet “PTRC-HGSOC_List_clinical_data” Patient Age column, there are some ages that were anonymized in accordance with TCIA policy, that is, to bin any age over 89 into a common age group “90+”. Please be aware that some of these are not actual ages of patients.

Version 1: Updated

Title Data Type Format Access Points Subjects Studies Series Images License
Tissue Slide Images Histopathology SVS 158 348 CC BY 4.0
Clinical data CSV CC BY 4.0

Citations & Data Usage Policy

Data Citation Required: Users must abide by the TCIA Data Usage Policy and Restrictions. Attribution must include the following citation, including the Digital Object Identifier:

Data Citation

Chowdhury, S., Kennedy, J. J., Ivey, R. G., Murillo, O., Hosseini, N., Song, X., Petralia, F., Calinawan, A., Voytovich, U. J., Savage, S. R., Berry, A., Reva, B., Ozbek, U., Krek, A., Ma, W., da Veiga Leprevost, F., Ji, J., Yoo, S., Lin, C., … Paulovich, A. G. (2023). Proteogenomic analysis of chemo-refractory high grade serous ovarian cancer (PTRC-HGSOC) (Version 1) [dataset]. The Cancer Imaging Archive. https://doi.org/10.7937/6RDA-P940

Detailed Description

Clinical Data notes:

A note about the values in CSV spreadsheet “PTRC-HGSOC_List_clinical_data” Patient Age column, there are some ages that were anonymized in accordance with TCIA policy, that is, to bin any age over 89 into a common age group “90+”. Please be aware that some of these are not actual ages of patients.

Other Publications Using this Data

TCIA maintains a list of publications which leverage TCIA data.  If you have a manuscript you’d like to add please contact TCIA’s Helpdesk.

Publication Citation

Chowdhury, S., Kennedy, J. J., Ivey, R. G., Murillo, O. D., Hosseini, N., Song, X., Petralia, F., Calinawan, A., Savage, S. R., Berry, A. B., Reva, B., Ozbek, U., Krek, A., Ma, W., da Veiga Leprevost, F., Ji, J., Yoo, S., Lin, C., Voytovich, U. J., … Paulovich, A. G. (2023). Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer. In Cell (Vol. 186, Issue 16, pp. 3476-3498.e35). Elsevier BV. https://doi.org/10.1016/j.cell.2023.07.004

TCIA Citation

Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., & Prior, F. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. In Journal of Digital Imaging (Vol. 26, Issue 6, pp. 1045–1057). Springer Science and Business Media LLC. https://doi.org/10.1007/s10278-013-9622-7