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Study dataset

High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing

Single-cell and bulk RNA-seq of tumors from 7 treatment-naive Leuven patients.

Listed Apr 24, 2026

  • Single-cell
  • Transcriptomic
  • Ovarian
  • Fallopian tube

Overview

We identified 11 cancer and 32 stromal cell phenotypes in HGSTOC tumours. Of these, the relative frequency of myofibroblasts, TGF-β-driven cancer-associated fibroblasts, mesothelial cells and lymphatic endothelial cells predicted poor outcome, while plasma cells correlated with more favourable outcome.

The centerpiece of the study is a single-cell RNA sequencing dataset generated from 7 treatment-naive HGSTOC patients treated at University Hospitals Leuven. Key features.

Additional molecular data were generated on the same patient material:

  • Bulk RNA-seq: Performed on matched tumor tissue from the same biopsies using KAPA stranded mRNA-seq kits on HiSeq4000.
  • Low-coverage whole-genome sequencing (WGS): Performed on one patient (P1) to generate a copy number profile for validating tumor cell identity in the scRNA-seq data via correlation of segment copy number with gene expression.

Inside the dataset

  • Samples

    12 fresh tumor biopsies collected from multiple anatomical sites — primary ovarian tumor (n=3 biopsies), peritoneal metastases (n=7), and omental tissue (n=2). This multi-site sampling design was intentional, enabling comparison of stromal heterogeneity across disease locations.

  • Tissue processing

    Fresh biopsies (≥5mm) were digested to single-cell suspensions within 2 hours of resection, using a collagenase/dispase/DNAse protocol optimized to minimize dissociation-induced artifacts.

  • Sequencing platform

    10x Genomics Chromium 3' droplet-based scRNA-seq (targeting ~5,000 cells per library), sequenced on Illumina HiSeq4000, aligned to GRCh38 using Cell Ranger.

  • Final cell count

    After quality filtering (removing low-UMI barcodes, low-gene cells, high-mitochondrial cells, and doublets), 18,403 high-quality single cells were retained from the original 20,483 captured.

  • Clinical staging

    Patients ranged from FIGO stage IC1 to IVB; 6 were confirmed HGSTOC, and 1 (P3) presented with a mixed clear cell / high-grade serous carcinoma.

Publications