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Yale trastuzumab response cohort: The response 85 response cohort cases were identified also by retrospective search of the Yale Pathology electronic database. Cases included those patients with a pre-treatment breast core biopsy with HER2 positive invasive breast carcinoma who then received neoadjuvant targeted therapy with trastuzumab +/- pertuzumab prior to definitive surgery. HER2 positivity was defined as previously described for the HER2 negative/positive cohort. The response to targeted therapy was obtained from the pathology reports of the surgical resection specimens and dichotomized into responders or non-responders. Those with a complete pathologic response, defined as no residual invasive, lymphovascular invasion or metastatic carcinoma, were designated as responders (n=36). Cases with only residual in situ carcinoma were included in the responder category. Those cases with any amount of residual invasive carcinoma, lymphovascular invasion or metastatic carcinoma were categorized as non-responders (n=49).

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.

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Localtab active true title Data Access Data Access Data Type Download all or Query/Filter License Tissue Slide Images (SVS,40GB) ROI Annotations (XML) Tcia button generator url https://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/278?passcode=4ee5d71f5adb4f116b72e3cab18abc6c4a037e5b (Download requires Aspera) Tcia cc by 4 Clinical data (CSV)Image Removed Tcia cc by 4 Click the Versions tab for more info about data releases. Additional Resources Genomic Data Commons: The 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. Click the Versions tab for more info about data releases. Please contact help@cancerimagingarchive.net  with any questions regarding usage. Localtab title Detailed Description Detailed Description Image Statistics Modalities Pathology Number of Patients 273 Number of Images 273 Images Size (GB) 40 Localtab title Citations & Data Usage Policy Citations & Data Usage Policy Tcia limited license policy Info title Data Citation 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 Info title Publication Citation 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 Info title TCIA Citation 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 Data TCIA maintains a list of publications which leverage TCIA data. If you have a manuscript you'd like to add please contact the TCIA Helpdesk. Localtab title Versions Version 1 (Current): Updated 2022/03/25 Data Type Download all or Query/Filter License Tissue Slide Images (SVS,40GB) ROI Annotations (XML) Tcia button generator url https://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/278?passcode=4ee5d71f5adb4f116b72e3cab18abc6c4a037e5b (Download requires Aspera) Tcia cc by 4 Clinical Data data (CSV) Image Modified Tcia cc by 4