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TCGA HER2 cohort: A total of 668 TCGA-BRCA HER2+/- samples with available HER2 status were downloaded from the GDC portal (see "Additional Resources" below). Slides were visually inspected by our pathology team to exclude low quality samples with tissue folding or those that appeared to be from frozen tissue. A total of 187 samples (92 HER2- and 95 HER2+) were retained for use as independent test set. Information about which specific samples were retained can be found the TCGA_BRCA_Filtered folder of the dataset.
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active | true |
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title | Data Access |
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| Data AccessData Type | Download all or Query/Filter | License |
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Tissue Slide Images (SVS,40GB) ROI Annotations (XML) |
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url | https://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/278?passcode=4ee5d71f5adb4f116b72e3cab18abc6c4a037e5b |
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(Download requires Aspera) | | Clinical data (CSV) |
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url | https://wiki.cancerimagingarchive.net/download/attachments/119702524/HER2_ROI.csv?api=v2 |
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Click the Versions tab for more info about data releases. Additional ResourcesThe NCI Cancer Research Data Commons (CRDC) provides access to additional data and a cloud-based data science infrastructure that connects data sets with analytics tools to allow users to share, integrate, analyze, and visualize cancer research data. - Genomic Data Commons Legacy Archive (Tissue Slide Images)
- TCGA HER2 cohort: A total of 668 TCGA-BRCA HER2+/- samples with available HER2 status were downloaded from the GDC portal. Slides were visually inspected by our pathology team to exclude low quality samples with tissue folding or those that appeared to be from frozen tissue. A total of 187 samples (92 HER2- and 95 HER2+) were retained for use as independent test set. Information about which specific samples were retained from the GDC can be found the TCGA_BRCA_Filtered folder of the dataset. Contact https://gdc.cancer.gov/support with any questions about downloading the corresponding slides.
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title | Detailed Description |
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| Detailed DescriptionImage Statistics |
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Modalities | Pathology | Number of Patients | 273 | Number of Images | 273 | Images Size (GB) | 40 |
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title | Citations & Data Usage Policy |
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| Citations & Data Usage Policy Tcia limited license policy |
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| Farahmand, Saman, Fernandez, Aileen I, Ahmed, Fahad Shabbir, Rimm, David L., Chuang, Jeffrey H., Reisenbichler, Emily, & Zarringhalam, Kourosh. (2022). HER2 and trastuzumab treatment response H&E slides with tumor ROI annotations (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/E65C-AM96 |
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title | Publication Citation |
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| Farahmand, S., Fernandez, A.I., Ahmed, F.S. et al. Deep learning trained on hematoxylin and eosin tumor region of Interest predicts HER2 status and trastuzumab treatment response in HER2+ breast cancer. Mod Pathol (2021). https://doi.org/10.1038/s41379-021-00911-w |
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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. DOI: 10.1007/s10278-013-9622-7 |
Other Publications Using This DataTCIA maintains a list of publications which leverage TCIA data. If you have a manuscript you'd like to add please contact the TCIA Helpdesk. |
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| Version 1 (Current): Updated 2022/03/25Data Type | Download all or Query/Filter | License |
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Tissue Slide Images (SVS,40GB) ROI Annotations (XML) |
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url | https://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/278?passcode=4ee5d71f5adb4f116b72e3cab18abc6c4a037e5b |
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(Download requires Aspera) | | Clinical data (CSV) | | |
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