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Summary


Excerpt

This collection contains subjects from the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium Head-and-Neck cancer (CPTAC-HNSCC) cohort. CPTAC is a national effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis, or proteogenomics. Radiology and pathology images from CPTAC patients are being collected and made publicly available by The Cancer Imaging Archive to enable researchers to investigate cancer phenotypes which may correlate to corresponding proteomic, genomic and clinical data.

Imaging from each cancer type will be contained in its own TCIA Collection, with the collection name "CPTAC-cancertype".  Radiology imaging is collected from standard of care imaging performed on patients immediately before the pathological diagnosis, and from follow-up scans where available.  For this reason the radiology image data sets are heterogeneous in terms of scanner modalities, manufacturers and acquisition protocols. Pathology imaging is collected as part of the CPTAC qualification workflow.  

All CPTAC cohorts are released as either a single combined cohort, or split into Discovery and Confirmatory where applicable.  There are two main types of proteomic studies: discovery proteomics and targeted proteomics. The term "discovery proteomics" is in reference to "untargeted" identification and quantification of a maximal number of proteins in a biological or clinical sample. The term “targeted proteomics” refers to quantitative measurements on a defined subset of total proteins in a biological or clinical sample, often following the completion of discovery proteomics studies to confirm interesting targets selected. Commonly used proteomic technologies and platforms are different types of mass spectrometry and protein microarrays depending on the needs, throughput and sample input requirement of an analysis, with further development on nanotechnologies and automation in the pipeline in order to improve the detection of low abundance proteins, increase throughput, and selectively reach a target protein in vivo.  Once the protein targets of interest are identified, high-throughput targeted assays are developed for confirmatory studies: tests to affirm that the initial tests were accurate. A summary of CPTAC imaging efforts can be found on the CPTAC Imaging Proteomics page. 

CPTAC Imaging Special Interest Group

You can join the CPTAC Imaging Special Interest Group to be notified of webinars & data releases, collaborate on common data wrangling tasks and seek out partners to explore research hypotheses!  Artifacts from previous webinars such as slide decks and video recordings can be found on the CPTAC SIG Webinars page.

Acknowledgements

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 from the Department of Surgery.


Localtab Group



Localtab
activetrue
titleData Access

Data Access

Tcia head license access

Data TypeDownload all or Query/FilterLicense

Images (DICOM, 51 GB)



Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/37224639/TCIA-CPTAC-HNSCC_v9_20200630.tcia?version=1&modificationDate=1592933696538&api=v2



Tcia button generator
labelSearch
urlhttps://www.cancerimagingarchive.net/nbia-search/?CollectionCriteria=CPTAC-HNSCC



(Download requires the NBIA Data Retriever)

Tcia restricted license

Tissue Slide Images (SVS, 97 GB)


Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/25?passcode=9907cd5111477f668c1abb9d7e6baa260ec550ef



Tcia button generator
labelSearch
urlhttps://pathdb.cancerimagingarchive.net/eaglescope/dist/?configurl=/system/files/collectionmetadata/202208/cptac_metadata_page_0.json&filterState=[{"id":"Tumor","title":"Tumor","field":"Tumor","operation":"eq","values":"HNSCC"}]



(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) 

Tcia cc by 3

Click the Versions tab for more info about data releases.

Nci_crdc additional resources


Third Party Analyses of this Dataset

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




Localtab
titleDetailed Description

Detailed Description



Radiology Image Statistics

Pathology Image Statistics

Modalities

CT, SC, MR

Pathology

Number of Participants

64

112

Number of Studies

71

N/A

Number of Series

529

N/A

Number of Images

 95,839

390
Images Size (GB)5197

Accessing CPTAC publication cohorts

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

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.




Localtab
titleCitations & Data Usage Policy

Citations & Data Usage Policy 

Tcia limited license policy

Info
titleData Citation

National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2018). The Clinical Proteomic Tumor Analysis Consortium Head and Neck Squamous Cell Carcinoma Collection (CPTAC-HNSCC) (Version 10) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.UW45NH81


Info
titleAcknowledgement

The CPTAC program requests that publications using data from this program include the following statement: “Data used in this publication were generated by the National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC).”


Info
titleTCIA 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


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 the TCIA Helpdesk.




Localtab
titleVersions

Version 10 (Current): 2020/09/03

Data TypeDownload all or Query/Filter
Images (DICOM, 51 GB)

 

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/37224639/TCIA-CPTAC-HNSCC_v9_20200630.tcia?version=1&modificationDate=1592933696538&api=v2


    


Tcia button generator
labelSearch
urlhttps://www.cancerimagingarchive.net/nbia-search/?CollectionCriteria=CPTAC-HNSCC




(Requires NBIA Data Retriever.)

Tissue Slide Images (SVS, 97 GB)


Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/25?passcode=9907cd5111477f668c1abb9d7e6baa260ec550ef



 

Tcia button generator
labelSearch
urlhttps://cancerimagingarchive.net/datascope/cptac/home/?filter={%22Image_Available%22:%5B%22Yes%22%5D,%22Tumor%22:%5B%22HNSCC%22%5D}



Clinical Data API (JSON -  more info


Tcia button generator
urlhttps://clinicalapi-cptac.esacinc.com/api/tcia/clinical_data/tumor_code/HNSCC



Proteomics (web)


Tcia button generator
labelSearch
urlhttps://proteomics.cancer.gov/data-portal



Changed to new Aspera download link for histopathology slides.

Version 9: Updated 2020/06/23

Data TypeDownload all or Query/Filter
Images (DICOM, 51 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/37224639/TCIA-CPTAC-HNSCC_v9_20200630.tcia?version=1&modificationDate=1592933696538&api=v2


   


Tcia button generator
labelSearch
urlhttps://www.cancerimagingarchive.net/nbia-search/?CollectionCriteria=CPTAC-HNSCC



(Requires NBIA Data Retriever.)

Tissue Slide Images (SVS, 97 GB)


Tcia button generator
urlhttps://pathology.cancerimagingarchive.net/download/HNSCC/



 

Tcia button generator
labelSearch
urlhttps://cancerimagingarchive.net/datascope/cptac/home/?filter={%22Image_Available%22:%5B%22Yes%22%5D,%22Tumor%22:%5B%22HNSCC%22%5D}



Clinical Data API (JSON -  more info


Tcia button generator
urlhttps://clinicalapi-cptac.esacinc.com/api/tcia/clinical_data/tumor_code/HNSCC



Proteomics (web)


Tcia button generator
labelSearch
urlhttps://proteomics.cancer.gov/data-portal



Added imaging for 3 radiological imaging participants.


Version 8: Updated 2020/03/31


Data TypeDownload all or Query/Filter
Images (DICOM, 48 GB)

 

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/37224639/TCIA-CPTAC-HNSCC_v8_20200331.tcia?version=1&modificationDate=1585671577266&api=v2



   

(Requires NBIA Data Retriever.)

Tissue Slide Images (SVS, 97 GB)


Tcia button generator
urlhttps://pathology.cancerimagingarchive.net/download/HNSCC/



 

Clinical Data API (JSON -  more info


Tcia button generator
urlhttps://clinicalapi-cptac.esacinc.com/api/tcia/clinical_data/tumor_code/HNSCC



Proteomics (web)


Tcia button generator
labelSearch
urlhttps://proteomics.cancer.gov/data-portal




Added 8 new radiology subjects.

Version 7: Updated 12/19/2019


Data TypeDownload all or Query/Filter
Images (DICOM, 46 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/37224639/TCIA_CPTAC-HNSCC-v7-Dec2019.tcia?version=1&modificationDate=1576770855188&api=v2


  

(Requires NBIA Data Retriever.)

Tissue Slide Images (SVS, 97 GB)


Tcia button generator
urlhttps://pathology.cancerimagingarchive.net/download/HNSCC/



 

Tcia button generator
labelSearch
urlhttps://cancerimagingarchive.net/datascope/cptac/home/?filter={%22Image_Available%22:%5B%22Yes%22%5D,%22Tumor%22:%5B%22HNSCC%22%5D}



Clinical Data (web)

Coming soon

Proteomics (web)


Tcia button generator
labelSearch
urlhttps://proteomics.cancer.gov/data-portal




Added 20 new radiology subjects.

Version 6 : Updated 2019/09/30


Data TypeDownload all or Query/Filter
Images (DICOM, 30.5 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/37224639/TCIA_CPTAC-HNSCC-v6-Sep2019.tcia?version=2&modificationDate=1569608141421&api=v2


  

(Requires NBIA Data Retriever.)

Tissue Slide Images (SVS, 97 GB)


Tcia button generator
urlhttps://pathology.cancerimagingarchive.net/download/HNSCC/



Clinical Data (web)

Coming soon

Proteomics (web)


Tcia button generator
labelSearch
urlhttps://proteomics.cancer.gov/data-portal




added new subjects.

Version 5 : Updated 2019/06/30


Data TypeDownload all or Query/Filter
Images (DICOM, 24.8 GB)

 

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/37224639/TCIA_CPTAC-HNSCC-batch6-June2019.tcia?version=1&modificationDate=1561766319233&api=v2


   

(Requires NBIA Data Retriever.)

Tissue Slide Images (SVS, 94.7 GB)


Tcia button generator
urlhttps://pathology.cancerimagingarchive.net/download/HNSCC/



Clinical Data (web)

Coming soon

Proteomics (web)


Tcia button generator
labelSearch
urlhttps://proteomics.cancer.gov/data-portal




Added Subjects

Version 4 : Updated 2019/03/31


Data TypeDownload all or Query/Filter
Images (DICOM, 11.8 GB)

 

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/37224639/CPTAC-HNSCC_batch5_Mar2019.tcia?version=1&modificationDate=1554003156327&api=v2




(Requires NBIA Data Retriever.)

Tissue Slide Images (web)


Tcia button generator
labelSearch
urlhttps://cancerimagingarchive.net/datascope/cptac/home/?filter={%22Image_Available%22:%5B%22Yes%22%5D,%22Tumor%22:%5B%22HNSCC%22%5D}



Clinical Data (web)

Coming soon

Proteomics (web)


Tcia button generator
labelSearch
urlhttps://proteomics.cancer.gov/data-portal




Added new subjects

Version 3 : Updated 2018/10/24


Data TypeDownload all or Query/Filter
Images (DICOM, 11.8 GB)

 

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/37224639/TCIA_CPTAC-HNSCC-Batch4-2018-10-24.tcia?version=1&modificationDate=1540999434051&api=v2


   

(Requires NBIA Data Retriever.)

Tissue Slide Images (web)


Tcia button generator
labelSearch
urlhttps://cancerimagingarchive.net/datascope/cptac/home/?filter={%22Image_Available%22:%5B%22Yes%22%5D,%22Tumor%22:%5B%22HNSCC%22%5D}



Proteomics (web)


Tcia button generator
labelSearch
urlhttps://proteomics.cancer.gov/data-portal




Added new subjects

Version 2: Updated 2018/06/30


Data TypeDownload all or Query/Filter
Images (DICOM, 5.2GB)

 

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/37224639/TCIA_CPTAC-HNSCC-2018-06-30-doiJNLP-ASLqxnz6.tcia?version=1&modificationDate=1534787060623&api=v2


   

(Requires NBIA Data Retriever.)

Tissue Slide Images (web)


Tcia button generator
labelSearch
urlhttps://cancerimagingarchive.net/datascope/cptac/?filter={%22Image_Available%22:%5B%22Yes%22%5D,%22Tumor%22:%5B%22HNSCC%22%5D}



Proteomics (web)


Tcia button generator
labelSearch
urlhttps://proteomics.cancer.gov/data-portal




Added new subjects

Version 1: Updated 2018/04/25


Data TypeDownload all or Query/Filter
Images (DICOM, 2.0 GB)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/37224639/TCIA_CPTAC-HNSCC-B2-2018-05-01-doiJNLP-OLj7A5xk.tcia?version=1&modificationDate=1534787061526&api=v2



(Requires NBIA Data Retriever.)

Tissue Slide Images (web)


Tcia button generator
labelSearch
urlhttps://cancerimagingarchive.net/datascope/cptac/?filter={%22Image_Available%22:%5B%22Yes%22%5D,%22Tumor%22:%5B%22HNSCC%22%5D}



Proteomics (web)


Tcia button generator
labelSearch
urlhttps://proteomics.cancer.gov/data-portal