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Summary

The Cancer Genome Atlas-Breast Cancer (TCGA-BRCA) data collection is part of a larger effort to enhance the TCGA 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 BRCA 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 BRCA disease type within TCGA.

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 Breast Phenotype Research Group page.

Acknowledgements

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

  • Mayo Clinic, Rochester, MN - Special thanks to Wilma Lingle, MD and Bradley J. Erickson, MD, Ph.D. from the Department of Radiology, Mayo Medical School.
  • University of Pittsburgh/UPMC, Pittsburgh, PA - Special thanks to  Margarita L Zuley, MD and Rose Jarosz.
  • Roswell Park, Buffalo, NY - Special thanks to Ermelinda Bonaccio, MD and Joe Filippini from the Department of Diagnostic Radiology.

  • University of Miami, Miller School of Medicine, Miami, FL - Special thanks to Jose M. NetMD and Len Levi.

  • Memorial Sloan-Kettering Cancer Center/MSKCC, New York, NY - Special thanks to Elizabeth A Morris MDGloria Guman Figler, and Pierre Elnajjar.

  • University of North Carolina, Chapel Hill, NC - Special thanks to J. Keith SmithMD, Ph.D. and Shanah Kirk from the Department of Radiology.
  • University of Chicago, Chicago, IL – Special thanks to Maryellen Giger, MD, and Nick Gruszauskas, PhD, from the Department of Radiology.

 

 

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 TypeDownload all or Query/Filter
Images (DICOM, 88.1GB) 
Clinical Data (TXT)
Genomics (web)

Click the Versions tab for more info about data releases.

Detailed Description

Image Statistics

 Updated 12/30/2014

Modalities

MR, mammography (MG)

Number of Patients

139

Number of Studies

164

Number of Series

1,877

Number of Images

230,167

Images Size (GB)88.1

TCGA Data Portal - Clinical and Genomic 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.  Below is a snapshot of clinical data extracted on 1/5/2016.

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.
  • 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 

TCGA collections have special publication embargoes which must be followed in addition to our normal data usage policies. See the TCGA 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:

TCGA-BRCA Citation

DOI coming soon.

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

See the TCGA-BRCA section on our Publications page for other work leveraging this collection. If you have a publication you'd like to add please contact the TCIA Helpdesk.

 

Version 2 (Current): Updated 2016/01/05

Data TypeDownload all or Query/Filter
Images (DICOM, 88.1GB) 
Clinical Data (TXT)
Genomics (web)

Extracted latest release of clinical data (TXT) from the TCGA Data Portal.

Version 1: Updated 2014/12/30

Data TypeDownload all or Query/Filter
Images (DICOM, 88.1GB) 
Clinical Data (TXT)
Genomics (web)

 

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