Summary
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The Cancer Genome Atlas -Urothelial Bladder Endothelial Carcinoma (TCGA-BLCA) 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 BLCA 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 resides in the TCGA data portal |
, while the radiological data is stored on The Cancer Imaging Archive (TCIA). |
Matching 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 BLCA disease type within TCGA.
CIP TCGA Radiology Initiative
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 The CIP is supporting multiple projects within the academic community to encourage cross disciplinary research, which utilizes the data provided in these resources. However, at this time, there is no TCGA Bladder Phenotype Research Group.
Acknowledgements
We would like to acknowledge the individuals and institutions that have provided data for this collection:
- University of North Carolina- Special thanks to J. Keith Smith, M.D., Ph.D. and Shanah Kirk from the Department of Radiology.
- Barretos Cancer Hospital, Barretos, São Paulo, Brazil – Special Thanks to Fabiano Rubião Lucchesi, MD and Natália Del Angelo Aredes
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title | Detailed Description |
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| Detailed Description | |
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Modalities | CT, MR | Number of Patients | 19 | Number of Studies | 29 | Number of Series | 148 | Number of Images | 17,617 | Images Size (GB) | 9.4 |
TCGA Data Portal - Clinical and Genomic DataThe 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 DatesSubject 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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title | Citations & Data Usage Policy |
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| 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: Info |
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| 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 DataTCIA maintains a list of publications which leverage our data. At this time we are not aware of any manuscripts based on this data. If you have a manuscript you'd like to add please contact the TCIA Helpdesk. |
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| Version 1: Updated 2014/12/09Data Type | Download all or Query/Filter |
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Images (DICOM, 9.4GB) |
| Clinical Data (TXT) | | Genomics (web) | |
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