At the time of our study, 108 cases with breast MRI data were available in the TCGA-BRCA collection. In order to minimize variations in image quality across the multi-institutional cases we included only breast MRI studies acquired on GE 1.5 Tesla magnet strength scanners (GE Medical Systems, Milwaukee,Wisconsin, USA) scanners, yielding a total of 93 cases. We then excluded cases that had missing images in the dynamic sequence (1 patient), or at the time did not have gene expression analysis available in the TCGA Data Portal (8 patients). After these criteria, a dataset of 84 breast cancer patients resulted, with MRIs from four institutions: Memorial Sloan Kettering Cancer Center, the Mayo Clinic, the University of Pittsburgh Medical Center, and the Roswell Park Cancer Institute. The resulting cases contributed by each institution were 9 (date range 1999-2002), 5 (1999-2003), 46 (1999-2004), and 24 (1999-2002), respectively. The dataset of biopsy proven invasive breast cancers included 74 (88%) ductal, 8 (10%) lobular, and 2 (2%) mixed. Of these, 73 (87%) were ER+, 67 (80%) were PR+, and 19 (23%) were HER2+. Various types of analyses were conducted using the combined imaging, genomic, and clinical data. Those analyses are described within several manuscripts created by the group (cited abovebelow).
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- Image Data: DICOM – Save/open this file to initiate our Java Web Start download manager to begin your download
- Radiologist Annotations/Markup: Please contact the TCIA Helpdesk to request access
- Computer-extracted image phenotypes: Please contact the TCIA Helpdesk to request access
- tcga breast radiologist reads.xls
- 3D Lesion Segmentations & Quantitative Radiomic Features
- Note: With regards to the naming structure, *S2-1.les: S2 means DCE-MRI sequence 2, lesion #1. Sometimes, there are multiple DCE-MRI sequences on TCIA data, and so the team used the sequence that corresponded to the one on which the radiologists annotated the truth.
- Note: please reference these data extracted using version V2010 of the UChicago MRI Quantitative Radiomics workstation
- Multi-gene assays including MammaPrint, Oncotype DX, and PAM50: Please contact the TCIA Helpdesk to request access Perou TCGA BRCA MRIs+PAM50+GHI21+NKI70 MAILED.xlsx
- TCGA Clinical Data (from TCGA Data Portal, archived in case of subsequent updates made by TCGA): Please contact the TCIA Helpdesk to request access brca-clinicalforwiki.xls