Summary
The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (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. CPTAC’s progress in proteogenomics enabled expansion to radiogenomics aimed at deepening our understanding of emerging fields.
Radiological imaging here associated with these data are part of a larger effort to build a research community connecting cancer phenotypes to genotypes by providing clinical images matched to subjects from The Cancer Genome Atlas (TCGA). Clinical, genetic, and pathological data resides in the Genomic Data Commons (GDC) Data Portal while the radiological data is stored on The Cancer Imaging Archive (TCIA).
Matched CPTAC-patient identifiers allow researchers to explore the CPTAC/TCIA databases for correlations between tissue genotype, radiological phenotype and patient outcomes. Tissues were collected from many sites. For this reason the image data sets are also extremely heterogeneous in terms of scanner modalities, manufacturers and acquisition protocols. In most cases the images were acquired as part of routine care and not as part of a controlled research study or clinical trial.
CIP TCGA Radiology Initiative
Imaging Source Site (ISS) Groups are being populated and governed by participants from institutions that have provided imaging data to the archive for a given cancer type. Modeled after TCGA analysis groups, ISS groups are given the opportunity to publish a marker paper for a given cancer type per the guidelines in the table above. This opportunity will generate increased participation in building these multi-institutional data sets as they become an open community resource. Learn more about the TCGA Bladder Phenotype Research Group.
Acknowledgements
We would like to acknowledge the individuals and institutions that have provided data for this collection:
- University of Calgary - Special thanks to Oliver Bathe, MD from the Department of .
- Beaumont Health Biobank - Special thanks to George Wilson, MD from the Department of __.
- St. Joseph's Hospital and Medical Center and Barrow Neurological Institute - Cathy Seiler, PhD.
- IIMO
Data Access
Choosing the Download option will provide you with a file to launch the TCIA Download Manager to download the entire collection. If you want to browse or filter the data to select only specific scans/studies please use the Search By Collection option.
| Data Type | Download all or Query/Filter |
|---|---|
| Images (DICOM, 32.9GB) | |
| Tissue Slide Images (web) |
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| Clinical Data (CSV) |
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| Genomics (web) |
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Click the Versions tab for more info about data releases.
Detailed Description
Image Statistics |
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|---|---|
Modalities | CT, MR, PT |
Number of Patients | 17 |
Number of Studies | 123 |
Number of Series | 782 |
Number of Images | 69,481 |
| Images Size (GB) | 32.9 |
CPTAC Data Portal - All data is freely available to the public, subject to the Data Use Agreement (link is external). Reference mass spectral peptide libraries resulting from these studies may also be downloaded freely from the NIST Peptide Library (link is external).
CPTAC Antibody Portal
CPTAC Assay Portal
CPTAC Software Tools
Clinical and Genomic Data
The GDC Data Portal has extensive clinical and genomic data, which can be matched to the patient identifiers on the images here in TCIA. Below is a snapshot of clinical data extracted on 1/27/2016.
Explanations of the clinical data can be found on the Biospecimen Core Resource Clinical Data Forms linked below:
A Note about TCIA and TCGA Subject Identifiers and Dates
Subject Identifiers: a subject with radiology images stored in TCIA is identified with a Patient ID that is identical to the Patient ID of the same subject with demographic, clinical, pathological, and/or genomic data stored in TCGA. For each TCGA case, the baseline TCGA imaging studies found on TCIA are pre-surgical.
Dates: TCIA and TCGA handle dates differently, and there are no immediate plans to reconcile:
- TCIA Dates: dates (be they birth dates, imaging study dates, etc.) in the Digital Imaging and Communications in Medicine (DICOM) headers of TCIA radiology images have been offset 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.
- CPTAC tissue Dates:
Citations & Data Usage Policy
CPTAC collections have special publication embargoes which must be followed in addition to our normal data usage policies. See the CPTAC section within TCIA's Data Usage Policies and Restrictions for additional details. After the publication embargo period ends these collections are freely available to browse, download, and use for commercial, scientific and educational purposes as outlined in the Creative Commons Attribution 3.0 Unported License. Questions may be directed to help@cancerimagingarchive.net. Please be sure to acknowledge both this data set and TCIA in publications by including the following citations in your work:
Data Citation
Authors. (2017). Radiology Data from The CPTAC-GBM collection. The Cancer Imaging Archive. http://doi.org/data_DOI
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. The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, December, 2013, pp 1045-1057. (paper)
Other Publications Using This Data
TCIA maintains a list of publications which leverage our data. At this time we are not aware of any manuscripts based on this data. If you have a manuscript you'd like to add please contact the TCIA Helpdesk.