TCGA-BRCA
The Cancer Genome Atlas Breast Invasive Carcinoma Collection
Pre-surgical breast MRI and a few mammograms of 139 women with invasive breast carcinoma from seven US centers, matched by patient ID to the TCGA clinical, genomic and pathology data for radiogenomics research.
Overview
TCGA-BRCA is the radiology part of The Cancer Genome Atlas project on breast invasive carcinoma, hosted by The Cancer Imaging Archive. Patient IDs match those in the NCI Genomic Data Commons, which holds the clinical, genomic and histopathology data of the same women. Researchers use this link to relate the imaging appearance of a breast tumor to its genotype and to patient outcome. The first series went public in 2011, and the current version 3 dates from May 2020.
Composition
The collection holds 139 patients with 164 imaging studies, 1,877 DICOM series and 230,167 images, about 88 GB. Nearly all of it is breast MRI: 137 patients have MR, five have mammography, and three of those five have both. All patients are recorded as female in the DICOM headers. The baseline studies of each case were taken before surgery. The collection page offers a 2016 snapshot of the TCGA clinical data together with the case report forms that define its fields.
Acquisition
Seven US institutions supplied images: Mayo Clinic, University of Pittsburgh/UPMC, Roswell Park, University of Miami, Memorial Sloan-Kettering Cancer Center, University of North Carolina and University of Chicago. Exams come from routine clinical care rather than a research protocol, so scanners, sequences and contrast timing vary. GE systems appear for 108 patients, Siemens for 16 and Philips for 15; the mammograms come from GE and LORAD units. Some series are derived images from the Confirma CADstream software. DICOM dates are shifted back by a random offset that is fixed per site, so intervals between a patient's studies are kept.
Annotations
The image collection carries no labels of its own. Data derived from it by other groups are published as separate TCIA analysis results, among them TCGA-Breast-Radiogenomics, LuminalB-Breast-MR-Enhancement and DICOM-SR-Breast-Clinical.
Known limitations
- Sequences, contrast phases and scanners differ between sites and patients, and no acquisition details are curated.
- Only five patients have mammography, so the collection is in practice an MRI cohort.
- TCIA and TCGA store dates differently, so imaging dates cannot be aligned directly with clinical event dates.
- The modality, vendor and sex counts here were counted from the public TCIA metadata API, not from a publication.
Cohort
Aggregate numbers from the sources below. Bars are relative to the 139 subjects.
Sex
- Female 139 100%
Modality
subjects
- MRI 137 99%
- Mammography 5 4%
Scanner vendor
subjects
- GE HealthCare 108 78%
- Siemens Healthineers 16 12%
- Philips 15 11%
- Other 2 1%
License and access
Our reading of the license, not legal advice. Before you use the data, read the original license and confirm that your use is allowed. We take no responsibility for how you use a dataset. Full disclaimer
Download without an account
Images download with the TCIA Data Retriever. Clinical, genomic and histopathology data for the same patient IDs are held in the NCI Genomic Data Commons.
Creative Commons Attribution 3.0 Unported
Older version of CC BY. Use, share and adapt the data for any purpose, including commercial use, as long as you credit the creators.
What you can do
- Yes
- Yes
- Yes
- Yes
What you can share
- Yes
- Yes
- Yes
What you must do
- Yes
- Share alike No
- No
- No
- Manuscript review No
- Release code No
- Return results No
- Delete after use No
Limits
- No
- Location limits No
Citation
Lingle W, Erickson BJ, Zuley ML, Jarosz R, Bonaccio E, Filippini J, Net JM, Levi L, Morris EA, Figler GG, Elnajjar P, Kirk S, Lee Y, Giger M, Gruszauskas N. (2016). The Cancer Genome Atlas Breast Invasive Carcinoma Collection (TCGA-BRCA) (Version 3) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.AB2NAZRP
All numbers
Every number on this page, as stored in stats.csv, with its source.
| Measure | Breakdown | Value | Source |
|---|---|---|---|
| Subjects | total | 139 | tcia-tcga-brca Data Access table |
| Studies | total | 164 | tcia-tcga-brca Data Access table |
| Scans | total DICOM series | 1,877 | tcia-tcga-brca Data Access table |
| Images | total DICOM images (slices) | 230,167 | tcia-tcga-brca Data Access table |
| Subjects | modality=MR | 137 | tcia-api-tcga-brca-series Modality; PatientID |
| Subjects | modality=MG | 5 | tcia-api-tcga-brca-series Modality; PatientID |
| Studies | modality=MR | 157 | tcia-api-tcga-brca-series Modality; StudyInstanceUID |
| Studies | modality=MG | 7 | tcia-api-tcga-brca-series Modality; StudyInstanceUID |
| Scans | modality=MR DICOM series | 1,858 | tcia-api-tcga-brca-series Modality |
| Scans | modality=MG DICOM series | 19 | tcia-api-tcga-brca-series Modality |
| Subjects | sex=female DICOM header value | 139 | tcia-api-tcga-brca-patients PatientSex |
| Subjects | vendor=ge patients with at least one GE series (MR or MG) | 108 | tcia-api-tcga-brca-series Manufacturer; PatientID |
| Subjects | vendor=siemens patients with at least one Siemens series | 16 | tcia-api-tcga-brca-series Manufacturer; PatientID |
| Subjects | vendor=philips patients with at least one Philips series | 15 | tcia-api-tcga-brca-series Manufacturer; PatientID |
| Subjects | vendor=other LORAD mammography units | 2 | tcia-api-tcga-brca-series Manufacturer; PatientID |
Sources
The keys used in the table above.
- tcia-tcga-brca TCIA TCGA-BRCA collection page (version 3, updated 2020/05/29) website
- tcia-api-tcga-brca-series TCIA public NBIA API, series list of TCGA-BRCA (open, no login, CC BY 3.0), MR and MG series counted per PatientID, Modality, StudyInstanceUID and Manufacturer; the 164 SR series of DICOM-SR-Breast-Clinical excluded computed
- tcia-api-tcga-brca-patients TCIA public NBIA API, patient list of TCGA-BRCA (open, no login), counted per PatientSex computed