README.md

TCGA-PRAD Biochemical Recurrence Dataset

This dataset was curated as part of a research project aimed at predicting biochemical recurrence (BCR) in prostate cancer directly from H&E-stained prostatectomy specimens.
Based on the TCGA Prostate Adenocarcinoma (TCGA-PRAD) cohort, we provides curated labels for biochemical recurrence along with packed diagnostic whole-slide images and corresponding tissue masks.

📂 Repository Structure

The dataset is organized into the following folders and files:

whole-slide-images/

• Packed WSIs for the 298 TCGA-PRAD patients included in our study in .tif format

tissue-masks/

• Corresponding binary tissue segmentation masks, also in .tif format (0 = background, 1 = tissue)

biotab-xml/

• Original case-specific biotab XML files for 403 TCGA-PRAD patients with at least one diagnostic slide.
• Used for extracting BCR status and metadata.

metadata.csv

• metadata prased from biotab XML files for all the 403 TCGA-PRAD patients with diagnostic slides.

bcr.csv

• Curated biochemical recurrence labels for the 298 TCGA-PRAD patients included in our study
  • case_id: TCGA case ID
  • event: 1 if biochemical recurrence occurred, 0 otherwise
  • follow_up_y: Time to event (if event=1) or time to last follow-up (if event=0), in years

🧬 Label Curation Process

Biochemical recurrence labels were curated from the biotab XML files, based on the following logic:

• Event = 1 (Biochemical Recurrence):

  • biochemical_recurrence_indicator = YES, using days_to_biochemical_recurrence_first as time to event.
  • OR new_tumor_event_type = "Biochemical evidence of disease" with available new_tumor_event_dx_days_to.

• Event = 0 (No Recurrence):

  • biochemical_recurrence_indicator = NO and no tumor event indicating recurrence.
  • Time to last follow-up taken from last_contact_days_to.

Patients with incomplete or contradictory information were excluded (105 patients).

🧾 Citation

If you use this dataset in your research, please cite:

to be added soon

🔒 License

This dataset is derived from TCGA, which is distributed under the TCGA Data Use Certification.

Redistribution of image data is permitted for academic and non-commercial research purposes only.

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tags: - medical - histology - tcga size_categories: - n<1K