Accessing CPTAC publication cohorts

All CPTAC cohorts are released as either a single combined cohort, or split into Discovery and Confirmatory where applicable. In the case of CPTAC-UCEC there was a “Discovery Cohort” release.  Images associated with these cases can be downloaded using the following links:

• CPTAC-UCEC Radiology Discovery Cohort
• CPTAC-UCEC Pathology Discovery Cohort

Accessing the Proteomic & Genomic Clinical Data

To access/download the clinical data on the Proteomic Data Commons (PDC) and Genomic Data Commons (GDC), once you have identified the data of your interest, move to the ‘Clinical’ tab on the browse page. Select the checkbox to select a specific row, all rows on the page or all pages and click the export clinical manifest button in CSV or TSV format on the GDC, or TSV or JSON format on the PDC.

A Note about TCIA and CPTAC Subject Identifiers and Dates

Subject Identifiers:

A subject with radiology and pathology images stored in TCIA is identified with a de-identified project Patient ID that is identical to the Patient ID of the same subject with clinical, proteomic, and/or genomic data stored in other CPTAC databases and web sites.

Dates:

The radiology imaging data is in DICOM format. To provide temporal context information aligned with events in the clinical data set for each patient, TCIA has inserted information in DICOM tag (0012,0050) Clinical Trial Time Point ID. This DICOM tag contains the number of days from the date the patient was initially diagnosed pathologically with the disease to the date of the scan. E.g. a scan acquired 3 days before the diagnosis would contain the value -3. A follow up scan acquired 90 days after diagnosis would contain the value 90.

The DICOM date tags (i.e. birth dates, imaging study dates, etc.) are modified per TCIA’s standard process which offsets them by a random number of days. The offset is a number of days between 3 and 10 years prior to the real date that is consistent for each TCIA image-submitting site and collection, but that varies among sites and among collections from the same site. Thus, the number of days between a subject’s longitudinal imaging studies are accurately preserved when more than one study has been archived while still meeting HIPAA requirements.

Publications by the Dataset Authors

The authors recommended this paper as the best source of additional information about this dataset:

• Y. Dou, L. Katsnelson, M.A. Gritsenko, Y. Hu, B. Reva, R. Hong, Y-T. Wang, I. Kolodziejczak, R.J-H. Lu, C-F Tsai, W. Bu, W. Liu, X. Guo, E. An, R.C. Arend, J. Bavarva, L. Chen, R.K. Chu, A. Czekański, T. Davoli, E.G. Demicco, D. DeLair, K. Devereaux, S.M. Dhanasekaran, P. Dottino, B. Dover, T.L. Fillmore, McK. Foxall, C.E. Hermann, T. Hiltke, G. Hostetter, M. Jędryka, S.D. Jewell, I. Johnson, A.G. Kahn, A.T. Ku, C. Kumar-Sinha, P. Kurzawa, A.J. Lazar, R. Lazcano, J.T. Lei, Y. Li, Y. Liao, T-S.M. Lih, T-T. Lin, J.A. Martignetti, R.P. Masand, R. Matkowski, W. McKerrow, M. Mesri, Matthew E. Monroe, J. Moon, R.J. Moore, M.D. Nestor, C. Newton, T. Omelchenko, G.S. Omenn, S.H. Payne, V.A. Petyuk, A.I. Robles, H. Rodriguez, K.V. Ruggles, D. Rykunov, S.R. Savage, A.A. Schepmoes, T. Shi, Z. Shi, J. Tan, M. Taylor, M. Thiagarajan, J.M. Wang, K.K. Weitz, B. Wen, C.M. Williams, Y. Wu, M.A. Wyczalkowski, X. Yi, X.Zhang, R. Zhao, D. Mutch, A.M. Chinnaiyan, R.D. Smith, A.I. Nesvizhskii, P. Wang, M. Wiznerowicz, Li Ding, D.R. Mani, H. Zhang, M.L. Anderson, K.D. Rodland, B. Zhang, T. Liu, D. Fenyö , and the Clinical Proteomic Tumor Analysis Consortium. (2023)  Proteogenomic insights suggest druggable pathways in endometrial carcinoma. Cancer Cell. https://doi.org/10.1016/j.ccell.2023.07.007

No publications by dataset authors were found.

Research Community Publications

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

Version 10: Updated 2023/02/24

Radiology modality data cleanup to remove extraneous scans.

Version 9: Updated 2020/09/03

Changed to new Aspera download link for histopathology slides.

Version 8: Updated 2020/03/31

Added 14 radiology subjects

Version 7: Updated 2019/09/30

Added new subjects

Version 6: Updated 2019/06/30

Added Subjects

Version 5: Updated 2019/01/23

Added links to clinical and proteomic data from CPTAC Discovery Study (first 100 patients)

Version 4: Updated 2018/10/29

Added new subjects.

Version 3: Updated 2018/06/30

Added new subjects.

Version 2: Updated 2018/04/26

Added new subjects.

Version 1: Updated 2018/01/10

Version 11: Updated 2023/08/18

Added cases new DICOM imaging.