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Excerpt

The Cancer Genome Atlas - Glioblastoma Multiforme (TCGA-GBM) 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 has archived a large portion of the radiological images of the genetically-analyzed GBM cases.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

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resides in the Genomic Data Commons (GDC) Data Portal while the radiological data is stored on The Cancer Imaging Archive (TCIA). 

Matched The data utilizes the same TCGA patient identifiers in both repositories, allowing allow researchers to explore the TCGA/TCIA databases for correlations between tissue genotype and , radiological phenotype . This collection within TCIA is related to the GBM disease type within TCGA.

CIP TCGA Radiology Initiative

The CIP is supporting multiple projects within the academic community to encourage cross disciplinary research, which utilizes the data provided in these resources. Much more can be learned about this effort on the TCGA Glioma Phenotype Research Group page.

How to retrieve the images from TCIA

Imaging Data

Info

You can view and download these images on TCIA by logging in, clicking Search Images, and selecting the TCGA-GBM collection.

A full listing of the available imaging studies/series for each patient can be found in this spreadsheet: TCGA-GBM.XLSX..

Collection Statistics

(updated 05/08/2014)

Modalities

magnetic resonance (MR)

Number of Patients

260

Number of Studies

570

Number of Series

5,370  

Number of Images

474,831

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

Related Data

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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 Glioma Phenotype Research Group.

Acknowledgements

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

  • Henry Ford Hospital, Detroit, MI - Special thanks to Lisa Scarpace and Tom Mikkelsen, MD from the Department of Neurosurgery, Hermelin Brain Tumor Center.
  • University of California, San Francisco, CA - Special thanks to Soonmee Cha, MD from the Department of Neurological Surgery, Brain Tumor Research Center.
  • MD Anderson Cancer Center, Houston, TX - Special thanks to Sujaya Rao and Sangeeta Tekchandani from the Office of Translational/Clinical Research.
  • Emory University, Atlanta, GA - Special thanks to David Gutman, MD, Ph.D. and Joel Saltz, MD, Ph.D. from the Center for Comprehensive Informatics.
  • Thomas Jefferson University, Philadelpha, PA  - Special thanks to Nancy Pedano and Adam E. Flanders, MD from the Department of Radiology, Jefferson Medical College.
  • CWRU School of Medicine, Cleveland, OH - Special thanks to Jill Barnholtz-Sloan, Ph.D. and Quinn Ostrom, MA, MPH from Case Comprehensive Cancer Center.
  • Duke University School of Medicine, Durham, NC - Special thanks to Daniel Barboriak, MD and Laura J Pierce.
  • Fondazione IRCCS Instituto Neuroligico C. Besta, Milan, Italy - Special thanks to Domenico Aquino and Alessandro Perin MD.


Localtab Group



Localtab
activetrue
titleData Access

Data Access

Data TypeDownload all or Query/Filter
Images (DICOM, 73.5GB)

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/1966258/TCIA_TCGA-GBM_09-16-2015.tcia?api=v2

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

(Download requires the NBIA Data Retriever)

Tissue Slide Images (web)

Tcia button generator
exttrue
labelSearch
urlhttps://portal.gdc.cancer.gov/legacy-archive/search/f?filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_format%22,%22value%22:%5B%22SVS%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.program.name%22,%22value%22:%5B%22TCGA%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:%5B%22TCGA-GBM%22%5D%7D%7D%5D%7D

Clinical Data (TXT)

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/1966258/gdc_download_clinical_gbm.tar.gz?api=v2

Biomedical Data (TXT)

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/1966258/gdc_download_biomedical_gbm.tar.gz?api=v2

Genomics (web)

Tcia button generator
exttrue
labelSearch
urlhttps://portal.gdc.cancer.gov/projects/TCGA-GBM


Click the Versions tab for more info about data releases.

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


Image Statistics

Radiology

Modalities

CT,MR,DX

Number of Participants

262

Number of Studies

575

Number of Series

5,412

Number of Images

481,158

Images Size (GB)73.5


GDC Data Portal - Clinical and Genomic Data

The GDC Data Portal has extensive clinical and genomic data, which can be matched to the patient identifiers of the images here in TCIA.

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Below is a snapshot of

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clinical data extracted on 1/5/2016:

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  • Clinical Data.zip  ( NOTE: this is just a representative sample of what's available. Visit the

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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).

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Localtab
titleCitations & Data Usage Policy

Citations & Data Usage Policy 

Public collection license

Info
titleTCGA Attribution
"The results <published or shown> here are in whole or part based upon data generated by the TCGA Research Network: http://cancergenome.nih.gov/."


Info
titleData Citation

Scarpace, L., Mikkelsen, T., Cha, S., Rao, S., Tekchandani, S., Gutman, D., Saltz, J. H., Erickson, B. J., Pedano, N., Flanders, A. E., Barnholtz-Sloan, J., Ostrom, Q., Barboriak, D., & Pierce, L. J. (2016). Radiology Data from The Cancer Genome Atlas Glioblastoma Multiforme [TCGA-GBM] collection [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.RNYFUYE9


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. Journal of Digital Imaging, 26(6), 1045–1057. https://doi.org/10.1007/s10278-013-9622-7


 Other Publications Using This Data

See the TCIA Publications page for other work leveraging TCIA collections. If you have a manuscript you'd like to add please contact the TCIA Helpdesk.





Localtab
titleVersions

Version 4 (Current): Updated 2020/05/29

Data TypeDownload all or Query/Filter
Images (DICOM, 73.5GB)

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/1966258/TCIA_TCGA-GBM_09-16-2015.tcia?api=v2

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

(Download requires the NBIA Data Retriever)

Tissue Slide Images (web)

Tcia button generator
exttrue
labelSearch
urlhttps://portal.gdc.cancer.gov/legacy-archive/search/f?filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_format%22,%22value%22:%5B%22SVS%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.program.name%22,%22value%22:%5B%22TCGA%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:%5B%22TCGA-GBM%22%5D%7D%7D%5D%7D

Clinical Data (TXT)

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/1966258/gdc_download_clinical_gbm.tar.gz?api=v2

Biomedical Data (TXT)

Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/1966258/gdc_download_biomedical_gbm.tar.gz?api=v2

Genomics (web)

Tcia button generator
exttrue
labelSearch
urlhttps://portal.gdc.cancer.gov/projects/TCGA-GBM

Updated clinical data link with latest spreadsheets from GDC. Added new biomedical spreadsheets from GDC.

Version 3: Updated 2015/09/16


Data TypeDownload all or Query/Filter
Images (DICOM, 73.5GB)
Clinical Data (TXT)
Genomics (web)


 1 new subject added.

Version 2: Updated 2016/01/05


Data TypeDownload all or Query/Filter
Images (DICOM, 72.8GB)

Image Added

(Download requires the NBIA Data Retriever .)

Clinical Data (TXT)
Genomics (web)


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

Version 1: Updated 2014/12/30


Data TypeDownload all or Query/Filter
Images (DICOM, 72.8GB)
Clinical Data (TXT)
Genomics (web)


On 03-01-2013 available s ubjects in TCIA were reduced from 279 to 240 because some cases were subsequently excluded from the GDC Data Portal.

Acknowledgements

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

  • Henry Ford Hospital, Detroit, MI - Special thanks to Lisa Scarpace and Tom Mikkelsen, MD from the Department of Neurosurgery, Hermelin Brain Tumor Center.
  • University of California, San Francisco, CA - Special thanks to Soonmee Cha, MD from the Department of Neurological Surgery, Brain Tumor Research Center.
  • MD Anderson Cancer Center, Houston, TX - Special thanks to Sujaya Rao and Sangeeta Tekchandani from the Office of Translational/Clinical Research.
  • Emory University, Atlanta, GA - Special thanks to David Gutman, MD, Ph.D. and Joel Saltz, MD, Ph.D. from the Center for Comprehensive Informatics.
  • Mayo Clinic, Rochester, MN- Special thanks to Bradley J. Erickson, MD, Ph.D. from the Department of Radiology, Mayo Medical School.
  • Thomas Jefferson University, Philadelpha, PA  - Special thanks to Nancy Pedano and Adam E. Flanders, MD from the Department of Radiology, Jefferson Medical College.
  • CWRU School of Medicine, Cleveland, OH - Special thanks to Jill Barnholtz-Sloan, Ph.D. and Quinn Ostrom, MA, MPH from Case Comprehensive Cancer Center.
  • Duke University School of Medicine, Durham, NC - Special thanks to Daniel Barboriak, MD and Laura J Pierce.   

Change Log

DateComment
03-01-2013Subjects reduced from 279 to 240 because some cases were found to not to have TCGA data available.

 

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