Validation of QuANTUM-derived tumor cell fraction for molecular testing in high-grade serous tubo-ovarian carcinoma

Tumor cell fraction (TCF) estimation is an essential step in homologous recombination deficiency (HRD) testing of tubo-ovarian high-grade serous carcinoma (HGSC). However, it is prone to variability and observer dependence. Here, we assess the reliability of the QuANTUM computational pipeline for TCF estimation (cTCF) in HGSC samples. 70 HGSC cases were retrospectively collected and the AmoyDx HRD Focus Panel was employed for DNA extraction and sequencing. TCF estimates were obtained from multiple pathologists, along with the TCF calculated by the proprietary AmoyDx algorithm. The QuANTUM pipeline-derived cTCF and a manually calculated ground truth (GT) were obtained on the same slides, and concordance analyses were performed. Weighted kappa (Wk) values for the agreement among the various pathologists ranged from 0.28 to 0.63, reflecting low to substantial concordance. The QuANTUM algorithm showed substantial and better agreement with the GT and the AmoyDx tool (Wk = 0.73 and 0.63, respectively) as compared to the pathologists' estimates. No significant differences were observed between QuANTUM, the GT and the AmoyDx tool in identifying cases with tumor cellularity above or below the method-defined 30% cutoff. Considering its high reliability, the QuANTUM algorithm may serve as a robust tool for ensuring adequate TCF evaluation in HGSC.