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Summary

The Cancer Genome Atlas-Head-Neck Squamous Cell Carcinoma (TCGA-HNSC) data collection is part of a larger effort to enhance TCGA's data set with characterized radiological images. The Cancer Imaging Program (CIP) with the cooperation of several of the TCGA tissue-contributing institutions are working to archive a large portion of the radiological images of the genetically-analyzed HNSC cases.

Clinical, genetic, and pathological data resides in the TCGA data portal, while the radiological data is stored on The Cancer Imaging Archive (TCIA). The data utilizes the same TCGA patient identifiers in both repositories, allowing researchers to explore the correlations between tissue genotype and radiological phenotype. This collection within TCIA is related to the HNSC disease type within TCGA.


Note: Per TCGA Guidelines, formal permission requests are still required for publications using TCGA-HNSC data. More info about TCGA Publication Policies can be found on the Data Usage Policies and Restrictions page.

CIP TCGA Radiology Initiative

The CIP has begun multiple projects to collaborate with the academic community to encourage cross disciplinary research, which utilizes the data provided in these resources. More can be learned about this effort on the TCGA Head-Neck Phenotype Research Group page.

How to Retrieve the Images from TCIA

Imaging Data

You can view and download these images on TCIA by logging in and selecting the TCGA-HNSC collection. A full listing of the available imaging studies/series for each patient can be found in this spreadsheet: TCGA-HNSC.XLSX

Collection Statistics

Updated 2014/05/19

Modalities

computed tomography (CT)

magnetic resonance (MR)

positron emission tomography (PET)

Number of Patients

128

Number of Studies

180

Number of Series

795

Number of Images

78,351

If you are unsure how to download this ollection, please view Searching by Collection or refer to TCIA's User's Guide for more detailed instructions on using the site.

Related Data

The TCGA data portal has extensive clinical and genomic data, which can be matched to the patient identifiers on the images here in TCIA.

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.
  • 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).

Acknowledgements

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

  • 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 SmithMD, Ph.D. and Shanah Kirk from the Department of Radiology.
  • MD Anderson Cancer Center, Houston TX - Special thanks to Rivka Colen, MD and Kimberly Garcia.
  • Vanderbilt University Medical Center, Nashville TN - Special thanks to Dominique Delbeke, MD, Ph.D. and Michelle Pham.
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