Journal Article

Analytical validation of a homologous recombination deficiency signature (HRDsig) in pan-tumor tissue samples

Schrock, Alexa B., Li, Wenshu, Elvin, Julia A., Wang, Shuoguo, Sokol, Ethan, Decker, Brennan, Patel, Nimesh, Chen, Kuei-Ting, Dennis, Lucas, Walker, Louisa, Ritterhouse, Lauren L., Hughes, Jason, Frampton, Garrett, Leibowitz, Jeffrey A., Yilmazel, Bahar, Xu, Chang

2025

Overview

Homologous recombination repair (HRR) is a cellular pathway for high-fidelity double strand DNA break repair that uses the sister chromatid as a guide to ensure chromosomal integrity and cell viability. Deficiency in the HRR pathway (HRD) can sensitize tumors to poly (ADP-ribose) polymerase inhibitors (PARPi) and platinum-based chemotherapy, offering an avenue to identify patients who may benefit from targeted therapies. HRD signature (HRDsig) is a pan-solid-tumor biomarker on the FoundationOne®CDx (F1CDx®) assay that employs a DNA scar-based approach to calculate a score based on copy number features (e.g., segment size, oscillation patterns, and breakpoints per chromosome arm) and does not rely on HRR gene alterations, enabling detection of genomic and epigenetic mechanisms of HRD. After finalizing the HRDsig algorithm, analytical validation was conducted in a CAP-accredited, CLIA-certified laboratory on 278 solid tumor and normal tissue specimens. HRDsig results were compared with an independent HRD biomarker, defined by the presence of a reversion mutation restoring HRR gene function. In this evaluation, 100 HRD-positive and 126 HRD-negative samples showed a positive percent agreement of 90.00% and a negative percent agreement of 94.44%. The limit of detection (LoD) was estimated at 23.04% tumor purity, with the limit of blank (LoB) confirmed as zero in 60 normal tissue replicates. Reproducibility testing on 11 positive and 11 negative samples across multiple labs, reagent lots, and sequencers yielded agreement in 99.49% of positive and 99.73% of negative replicates. HRDsig status remained consistent in the presence of interfering substances, demonstrating 100% concordance in spiked samples. These validation results underscore the high analytical concordance, low false-positive rate, and overall robustness of HRDsig for reliable assessment of homologous recombination deficiency.

• Publisher: Public Library of Science,PLOS,Public Library of Science (PLoS)
• Subject: Adenosine diphosphate / Algorithms / Analysis / Biology and Life Sciences / Biomarkers / Biomarkers, Tumor - genetics / Breakpoints / Breast cancer / Cell viability / Chemotherapy / Chromosomes / Copy number / Deoxyribonucleic acid / DNA / DNA damage / DNA repair / Engineering and Technology / Epigenetics / Genes / Genetic testing / Genomes / Genotype & phenotype / Homologous Recombination / Homologous recombination repair / Humans / Medicine and Health Sciences / Methods / Mutation / Neoplasms - genetics / Neoplasms - pathology / Ovarian cancer / Platinum / Prostate / Quality control / Reagents / Recombinational DNA Repair - genetics / Reversion / Ribose / Samples / Scars / Sister chromatid exchange / Solid tumors / Tumors / Validation studies / Validity