Authors
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Morris, Elizabeth, Burnside, |
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Elizabeth, Whitman, Gary, Zuley, Margarita |
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, Bonaccio, Ermelinda |
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Ganott, |
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Marie, … Giger, Maryellen L. (2014). Using Computer-extracted Image Phenotypes from Tumors on Breast MRI to Predict Stage. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2014.8SIPIY6G |
Citations
Coming soon
Description
At the time of our study, 108 cases with breast MRI data were available in
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the TCGA-BRCA
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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
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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
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below).
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Download
- Image Data: DICOM – Save
Download
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- /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
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- : tcga breast radiologist reads.xls
- 3D Lesion Segmentations & Quantitative Radiomic Features
Readme instructions
- 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
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- Multi-gene assays including MammaPrint,
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- Oncotype DX, and PAM50
- Please contact the TCIA Helpdesk to request access
- : Perou TCGA BRCA MRIs+PAM50+GHI21+NKI70 MAILED.xlsx
- TCGA Clinical Data (
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- from TCGA Data Portal, archived in case of subsequent updates made by TCGA)
- <insert working copy of clinical data file(s)>
Source Shared List
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