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-HNSCC there was a “Discovery Cohort” release.  Images associated with these cases can be downloaded using the following links:

• CPTAC-HNSCC Radiology Discovery Cohort
• CPTAC-HNSCC 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 (be they 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number of days between a subject’s longitudinal imaging studies are accurately preserved when more than one study has been archived while still meeting HIPAA requirements.

We would like to acknowledge the individuals and institutions that have provided data for this collection:

• International Institute for Molecular Oncology, Poznań, Poland - Special thanks to Maciej Wiznerowicz MD, PhD and Jan Lubiński MD PhD; Heliodor Święcicki Clinical Hospital, Poznań, Poland; Witold Szyfter MD, PhD, Malgorzata Wierzbicka MD, PhD., Ewelina Kalinowicz MD and Joanna Napierała
• BioPartners, CA - Special thanks to Alexander Gasparian, PhD.  from the Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, Kakhaber Zaalishvili, MD  Medical Advisor and Staff Pathologist at BioPartners, LLC, Milla Gorodnia,  President of BioPartners, Inc., Victoria Christensen, Global Business Development/Project Coordination Manager, Oksana Havryliuk, MD. Chief of Research department of radiodiagnostics of NCI (Ukraine), Marianna Gredil’, Director of BioPartners, LLC, and  Anna Legenka Chief of the Data Department at BioPartners, LLC.
• Beaumont Health System, Royal Oak, MI - Special thanks to George D. Wilson, PhD from the Department of Radiation Oncology Research, Barbara Pruetz of the Biobank, Debra Kapczynski, MHSA, CIIP, RT(R)(CT) and Rachel Deyer from the Department of Diagnostic Radiology.
• Boston Medical Center, Boston, MA - Special thanks to Chris D. Andry M.Phil, PhD from the Department of Pathology and Laboratory Medicine, Margaret Lavoye, Artem Kaliaev, Wilson Chavez, Stephan Anderson, Jorge Soto, and Mitchell Horn from the Department of Radiology, Elizabeth Duffy, MA and Cheryl Spencer, MA of the Biobank.
• University of Calgary, Alberta, Canada - Special thanks to Oliver Bathe, MD, FRCS(C) from the Departments of Surgery/Oncology, Marina Salluzzi, PhD and Nicole Blenkin from the Department of Radiology, Calgary Image Processing and Analysis Centre (CIPAC), and Jennifer Koziak and Elleine Allapitan from the Department of Surgery.
• Washington University in St. Louis, Saint Louis, MO - Special thanks to Sidharth V Puram, MD, PhD, Fudong Wang, PhD, Thomas Barrett, MD, Salma Ramadan, MD,  and Sophie Gerndt, MD from the Department of Otolaryngology-Head and Neck Surgery.
• University of Kansas Medical Center – Special thanks to Andrew K. Godwin, PhD and Rashna Madan, MBBS from the Department of Pathology and Laboratory Medicine and Monica Mays, Lauren DiMartino, and Alex Webster from the University of Kansas Cancer Center.
• University of Oklahoma– Special thanks to Kar-Ming Fung, MD, PhD, Director of Anatomic Pathology, David Brown, Assistant Director of Clinical Trials Office, Biospecimen Core Lab, Shawnton Long, Manager of Clinical Trials Office, Tissue Lab, Biospecimen Core Lab, and Myria Reed, RHIA, Project Manager of Clinical Trials Office, Biospecimen Core Lab.
• H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL - Special thanks to John Koomen, Ph.D. from the Department of Molecular Oncology, and Edward R. Seijo, MS and Olya Stringfield, PhD.

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.

TCIA encourages the community to publish your analyses of our datasets. Below is a list of such third party analyses published using this Collection:

• Crowds Cure Cancer: Data collected at the RSNA 2018 annual meeting (Crowds-Cure-2018)
• Annotations for The Clinical Proteomic Tumor Analysis Consortium Head and Neck Squamous Cell Carcinoma Collection (CPTAC-HNSCC-Tumor-Annotations)

Version 14: Updated 2023/10/05

Version 13: Updated 2023/08/18

Added DICOM imaging.

Version 12: Updated 2023/02/24

Radiology modality data cleanup to remove extraneous scans.

Version 11: Updated 2023/02/16

added radiology cases from 4  sites

Version 10: Updated 2020/09/03

Changed to new Aspera download link for histopathology slides.

Version 9: Updated 2020/06/23

Added imaging for 3 radiological imaging participants.

Version 8: Updated 2020/03/31

Added 8 new radiology subjects.

Version 7: Updated 2019/12/19

Added 20 new radiology subjects.

Version 6: Updated 2019/09/30

added new subjects.

Version 5: Updated 2019/06/30

Added Subjects

Version 4: Updated 2019/03/31

Added new subjects

Version 3: Updated 2018/10/24

Added new subjects

Version 2: Updated 2018/06/30

Added new subjects

Version 1: Updated 2018/04/25

Version 15: Updated 2024/01/11

Added 9 ID to radiology download:C3L-05553, C3L-05511, C3L-05514, C3L-10001, C3L-10461, C3L-10463, C3L-10464, C3L-10466, C3L-10467.