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  • HER2 and trastuzumab treatment response H&E slides with tumor ROI annotations (HER2 tumor ROIs)

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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 182 samples (90 HER2- and 92 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.


Localtab Group


Localtab
activetrue
titleData Access

Data Access

Data TypeDownload all or Query/FilterLicense

Tissue Slide Images and ROI annotation spreadsheet (SVS, XML, 40GB)


Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex/public/package?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjUyMSIsInBhc3Njb2RlIjoiMGViODRmNzU4ODhmYTUzNDNlYTI3NjliZjEyZmM1ZjU1ZmU1MTJmMSIsInBhY2thZ2VfaWQiOiI1MjEiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjczOSIsInBhc3Njb2RlIjoiNzEwNmUzNDFjMDY4MjljNjBkMmM0ZjcxYTBhMTE1ODcxNGIzZWNjNSIsInBhY2thZ2VfaWQiOiI3MzkiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0=



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labelSearch
urlhttps://pathdb.cancerimagingarchive.net/imagesearch?f[0]=collection:her2_roi


 

(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) 


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Clinical data (XLSX, 15 kB)


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urlhttps://wiki.cancerimagingarchive.net/download/attachments/119702524/Yale_trastuzumab_response_cohort_metadata_clean.xlsx?api=v2



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Nci_crdc additional resources

  • 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 182 samples (90 HER2- and 92 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. To download the slides, GDC recommends the following: “The TCGA case (patient) barcode can be extracted from the first 12 characters of the file names in the manifest (i.e. TCGA-BH-A0EE, TCGA-D8-A27W etc.) which can be used to match the data in the clinical files to the slide images.” Contact https://gdc.cancer.gov/support with any questions about downloading the corresponding slides.


Localtab
titleDetailed Description

Detailed Description


Pathology Image Statistics

Modalities

Pathology

Number of Patients

273

Number of Images

273

Images Size (GB)40




Localtab
titleCitations & Data Usage Policy

Citations & Data Usage Policy

Tcia limited license policy

Info
titleData 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 3) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/E65C-AM96


Info
titlePublication Citation

Farahmand, S., Fernandez, A. I., Ahmed, F. S., Rimm, D. L., Chuang, J. H., Reisenbichler, E., & Zarringhalam, K. (2022). Deep learning trained on hematoxylin and eosin tumor region of Interest predicts HER2 status and trastuzumab treatment response in HER2+ breast cancer. In Modern Pathology (Vol. 35, Issue 1, pp. 44–51). Elsevier BV. https://doi.org/10.1038/s41379-021-00911-w


Info
titleTCIA 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. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository. In Journal of Digital Imaging (Vol. 26, Issue 6, pp. 1045–1057). Springer Science and Business Media LLC. https://doi.org/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 TCIA's Helpdesk.


Localtab
titleVersions

Version 3 (Current): Updated 2022/08/01

Data TypeDownload all or Query/FilterLicense

Tissue Slide Images and ROI annotation spreadsheet (SVS, XML, 40GB)


Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex?context=eyJyZXNvdXJjZSI6InBhY2thZ2VzIiwidHlwZSI6ImV4dGVybmFsX2Rvd25sb2FkX3BhY2thZ2UiLCJpZCI6IjUyMSIsInBhc3Njb2RlIjoiMGViODRmNzU4ODhmYTUzNDNlYTI3NjliZjEyZmM1ZjU1ZmU1MTJmMSIsInBhY2thZ2VfaWQiOiI1MjEiLCJlbWFpbCI6ImhlbHBAY2FuY2VyaW1hZ2luZ2FyY2hpdmUubmV0In0=



Tcia button generator
labelSearch
urlhttps://pathdb.cancerimagingarchive.net/imagesearch?f[0]=collection:her2_roi



(Download and apply the IBM-Aspera-Connect plugin to your browser to retrieve this faspex package) 


Tcia cc by 4

Clinical data (XLSX)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/119702524/Yale_trastuzumab_response_cohort_metadata_clean.xlsx?api=v2



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changes made:

macros removed from all SVS images. older versions of the data no longer available for download.

Version 2: Updated 2022/06/28

Data TypeDownload all or Query/FilterLicense

Tissue Slide Images and ROI annotation spreadsheet (SVS, XML, 40GB)


Tcia cc by 4

Clinical data (XLSX)


Tcia button generator
urlhttps://wiki.cancerimagingarchive.net/download/attachments/119702524/Yale_trastuzumab_response_cohort_metadata_clean.xlsx?api=v2



Tcia cc by 4

changes made: 

5 files were removed ("TCGA-A2-AOEQ-01Z-00-DX1", "TCGA-AO-AOJG-01Z-00-DX1", "TCGA-B6-A019-01Z-00-DX1”, "TCGA-EW-A1OZ-01Z-00-DX1.svs" & TCGA_BRCA_Filtered/meta.txt), 2 files were cleaned up and replaced (gdc_manifest.2022-0420.txt & HER2_TCGA.csv) and 1 file was added (case&annotation_counts_clean.xlsx). The 'HER2 Yale cohort' paragraph was updated to correct patient counts (99 negative & 93 positive for a total of 192 cases). The 'TCGA HER2 cohort' paragraph was updated to correct patient counts (92 positive & 90 negative for a total of 182 cases). The metadata CSV file was replaced with an updated XLSX file to remove duplicate patient rows.

Version 1: Updated 2022/03/25

Data TypeDownload all or Query/FilterLicense

Tissue Slide Images and ROI annotation spreadsheet (SVS, XML, 40GB)


Tcia cc by 4

Clinical data (CSV)

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older versions of the data no longer available for download.


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