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.Clinical, genetic, and pathological data reside 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 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
magnetic resonance (MR)
Number of Patients
Number of Studies
Number of Series
Number of Images
The TCGA data portal has extensive clinical and genomic data, which can be matched to the patient identifiers of the images here in TCIA. Here is a snapshot of the data obtained from the data portal on 2/6/2014:
- TCGA-GBM clinical data-2014-02-06.xls (NOTE: this is just a representative sample of what's available. Visit the TCGA data portal to obtain the latest/complete data set)
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).
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.
|03-01-2013||Subjects reduced from 279 to 240 because some cases were found to not to have TCGA data available.|