Fig. 1: Multimodal framework for HRD detection from cfDNA in advanced prostate cancer.

From an initial cohort of 375 patients with prostate cancer with multiple sampling time points, we selected samples with elevated ctDNA levels from 106 patients for in-depth analysis. A tiered approach was applied to characterise both the causes and consequences of homologous recombination deficiency (HRD). Targeted panel sequencing was used to assess pathogenic variants in 18 HRR-related genes. Low-pass and high-coverage whole-genome sequencing (WGS) enabled the quantification of genomic instability and the extraction of fragmentomics and chromatin accessibility features. Whole-exome sequencing (WES) of matched tumour-normal cfDNA samples was performed in a subset to characterise HRD-associated mutational signatures. Downstream analyses integrated genomic alterations, genomic instability scores, mutational signatures, fragment length patterns, end motifs, and transcription factor binding site (TFBS) accessibility to derive classical and alternative HRD biomarkers from plasma. Created in BioRender. Heitzer, E. (2025) https://BioRender.com/zhwwhzq.