SummaryThe Cancer Genome Atlas Head-Neck Squamous Cell Carcinoma (TCGA-HNSC) data collection is part of a larger effort to build a research community focused on 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 TCGA patient identifiers allow researchers to explore the TCGA/TCIA databases for correlations between tissue genotype, radiological phenotype and patient outcomes. Tissues for TCGA were collected from many sites all over the world in order to reach their accrual targets, usually around 500 specimens per cancer type. 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 Head-Neck Phenotype Research Group.
We would like to acknowledge the individuals and institutions that have provided data for this collection:
- Ontario Cancer Institute/University Health Network, Toronto, Ontario - Special thanks to Fei-Fei Liu (MD), Kenneth Yip (Ph.D.), Katrina Rey-McIntyre (BSc.), Scott Bratman (MD, Ph.D.) and John Waldron (MD, MSc.).
- University of Pittsburgh/UPMC, Pittsburgh, PA - Special thanks to Margarita L Zuley, MD and Rose Jarosz.
- University of North Carolina, Chapel Hill, NC - Special thanks to J. Keith Smith, MD, Ph.D. and Shanah Kirk from the Department of Radiology.
- MD Anderson Cancer Center, Houston TX - Special thanks to Rivka Colen, MD, Kimberly Garcia, and Bowman Willams.
- Vanderbilt University Medical Center, Nashville TN - Special thanks to Dominique Delbeke, MD, Ph.D. and Michelle Pham.
- Johns Hopkins University - Special thanks to Paul Nagy, PhD, FSIIM and Gorkem Sevinc
- University of Miami, Miller School of Medicine- Special thanks to Jose M. Net, MD
- Barretos Cancer Hospital, Barretos, São Paulo, Brazil – Special Thanks to Fabiano Rubião Lucchesi, MD and Natália Del Angelo Aredes.
Click the Download button to save a ".tcia" manifest file to your computer, which you must open with the NBIA Data Retriever. Click the Search button to open our Data Portal, where you can browse the data collection and/or download a subset of its contents.
|Data Type||Download all or Query/Filter|
|Images (DICOM, 130GB)|
|Tissue Slide Images (web)|
|Clinical Data (TXT)|
Click the Versions tab for more info about data releases.
computed tomography (CT)
magnetic resonance (MR)
positron emission tomography (PET)
RTDOSE, RTPLAN, RTSTRUCT
Number of Patients
Number of Studies
Number of Series
Number of Images
|Images Size (GB)||129.6|
Total Cases by Site
|MDA (TSS code "-CV-")||78|
|UNC (TSS code "-BA-")||22|
|UPMC (TSS code "-CN-")||5|
|Vanderbilt (TSS code "-CR-")||51|
|JHU (TSS code "-BB-")||15|
|Miami (TSS code "-IQ-")||5|
|Barretos (TSS code "-UF-")||16|
|UHN (TSS code "-CQ-")||35|
Total Cases by Modality and Site
GDC Data Portal - Clinical and Genomic Data
The Genomic Data Commons (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 1/5/2016:
Case report forms for the clinical data collected by TCGA can be found on the Biospecimen Core Resource Clinical Data Forms linked below:
The contents of the clinical_patient file as of June 29, 2014, for cases whose imaging are archived on TCIA are here.
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.
- TCGA Dates: the patient demographic and clinical event dates are all the number of days from the index date, which is the actual date of pathologic diagnosis. So all the dates in the data are relative negative or positive integers, except for the “days_to_pathologic_diagnosis” value, which is 0 – the index date. The years of birth and diagnosis are maintained in the distributed clinical data file. The NCI retains a copy of the data with complete dates, but those data are not made available.With regard to other TCGA dates, if a date comes from a HIPAA “covered entity’s” medical record, it is turned into the relative day count from the index date. Dates like the date TCGA received the specimen or when the TCGA case report form was filled out are not such covered dates, and they will appear as real dates (month, day, and year).
Citations & Data Usage Policy
This collection is freely available to browse, download, and use for commercial, scientific and educational purposes as outlined in the Creative Commons Attribution 3.0 Unported License. See TCIA's Data Usage Policies and Restrictions for additional details. Questions may be directed to email@example.com.
Please be sure to include the following attribution and citations in your work if you use this data set:
Zuley, M. L., Jarosz, R., Kirk, S., Lee, Y., Colen, R., Garcia, K., … Aredes, N. D. (2016). Radiology Data from The Cancer Genome Atlas Head-Neck Squamous Cell Carcinoma [TCGA-HNSC] collection. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2016.LXKQ47MS
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.
Version 4 (Current): Updated 2018/08/30
Added new DICOM images.
Version 3: Updated 2017/03/30
Added new DICOM images.
Version 2: Updated 2016/01/05
Extracted latest release of clinical data (TXT) from the GDC Data Portal.
Version 1: Updated 2014/11/26
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