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

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

Summary

Excerpt

Image AddedThe current standard of care for many patients with HER2-positive breast cancer is neoadjuvant chemotherapy in combination with anti-HER2 agents, based on HER2 amplification as detected by in situ hybridization (ISH) or protein immunohistochemistry (IHC). However, hematoxylin & eosin (H&E) tumor stains are more commonly available, and accurate prediction of HER2 status and anti-HER2 treatment response from H&E would reduce costs and increase the speed of treatment selection. Computational algorithms for H&E have been effective in predicting a variety of cancer features and clinical outcomes, including moderate success in predicting HER2 status. We trained a CNN classifier on 188 H&E whole slide images (WSIs) manually annotated for tumor regions of interest (ROIs) by our pathology team. Our classifier achieved an area under the curve (AUC) of 0.90 in cross-validation of slide-level HER2 status and 0.81 on an independent TCGA test set. Moreover, we trained our classifier on pre-treatment samples from 187 HER2+ patients that subsequently received trastuzumab therapy. Our classifier achieved an AUC of 0.80 in a five-fold cross validation. Our work provides an H&E-based algorithm that can predict HER2 status and trastuzumab response in breast cancer at an accuracy that may benefit clinical evaluations. Here, we are providing the datasets used in the study to facilitate development of other HER2+ diagnosis and trastuzumab response applications.

...

Localtab Group


Localtab
activetrue
titleData Access

Data Access

Data TypeDownload all or Query/Filter
Tissue Slide Images (SVS,40GB)


Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/278?passcode=4ee5d71f5adb4f116b72e3cab18abc6c4a037e5b


(Download requires Aspera)

Clinical data (CSV)

Click the Versions tab for more info about data releases.

Please contact help@cancerimagingarchive.net  with any questions regarding usage.


Localtab
titleDetailed Description

Detailed Description

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 license 4 international

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


Info
titlePublication 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
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. 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
titleVersions

Version 1 (Current): Updated 2022/03/25

Data TypeDownload all or Query/Filter
Images (SVS, 40GB)


Tcia button generator
urlhttps://faspex.cancerimagingarchive.net/aspera/faspex/external_deliveries/278?passcode=4ee5d71f5adb4f116b72e3cab18abc6c4a037e5b



(Download requires Aspera)

Clinical Data (CSV)



...