Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: updated citation formats and buttons, all underlying ata is untouched.

Summary

Excerpt

The Cancer Genome Atlas Glioblastoma Multiforme (TCGA-GBM) 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 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., 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 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 to Lisa Scarpace and  and Tom Mikkelsen, MD from  from the Department of Neurosurgery, Hermelin Brain Tumor Center.
  • University of California, San Francisco, CA - Special thanks to to Soonmee Cha, MD from  from the Department of Neurological Surgery, Brain Tumor Research Center.
  • MD Anderson Cancer Center, Houston, TX - Special thanks to to Sujaya Rao and  and Sangeeta Tekchandani from  from the Office of Translational/Clinical Research.
  • Emory University, Atlanta, GA - Special thanks to to David Gutman, MD, PhD and Ph.D. and Joel Saltz, MD, PhD from Ph.D. from the Center for Comprehensive Informatics.
  • Mayo Clinic, Rochester, MN - Special thanks to Bradley J. Erickson, MD, PhD from the Department of Radiology, Mayo Medical School.
  • Thomas Jefferson University, Philadelpha, PA  - Special thanks to to Nancy Pedano and  and Adam E. Flanders, MD from  from the Department of Radiology, Jefferson Medical College.
  • CWRU School of Medicine, Cleveland, OH - Special thanks to to Jill Barnholtz-Sloan, PhD and Ph.D. and Quinn Ostrom, MA, MPH from  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.

...

CIP TCGA Radiology Initiative

The Cancer Imaging Program 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.

Data Access

Imaging Data

Info

You can view and download these images on The Cancer Imaging Archive by logging in to TCIA 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_series_descriptions.csv

Collection Statistics

(updated 2/15/2013)

Modalities

MR

Number of Patients

279

Number of Studies

958

Number of Series

9,084   

Number of Images

671,743

If you are unsure how to download this Collection please view our quick guide on Searching by Collection or refer to our The Cancer Imaging Archive User's Guide for more detailed instructions on using the site.

Metadata

...

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. Below is a snapshot of clinical data extracted on 1/5/2016:

...

  • zip  ( NOTE: this is just a representative sample of

...

  • what's available. Visit the GDC Data Portal to obtain the latest/complete data set)

Explanations of the clinical data

...

bcr_patient_barcode,additional_chemo_therapy,additional_drug_therapy,additional_hormone_therapy,additional_immuno_therapy,additional_pharmaceutical_therapy,additional_radiation_therapy,age_at_initial_pathologic_diagnosis,
anatomic_organ_subdivision,chemo_therapy,days_to_birth,days_to_death,days_to_initial_pathologic_diagnosis,days_to_last_followup,days_to_tumor_progression,days_to_tumor_recurrence,drugs,gender,histological_type,hormonal_therapy,
immuno_therapy,informed_consent_verified,initial_pathologic_diagnosis_method,person_neoplasm_cancer_status,pretreatment_history,prior_glioma,radiation_therapy,radiations,targeted_molecular_therapy,tumor_tissue_site,vital_status,
year_of_initial_pathologic_diagnosis

...

...

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).




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.