Assessing the Detection Power of Genome-Wide Copy Number Variation Profiles in Prostate Cancer Using Simulated Shallow Whole-Genome Sequencing Data.

[PURPOSE] Shallow whole-genome sequencing (sWGS) is a cost-effective approach for detecting genome wide copy number profiles in tumor samples. In metastatic castration-resistant prostate cancer (mCRPC), recognizing homologous recombination deficiency (HRD) and tandem duplication (TD) genomic profiles may contribute to improved treatment choices such as poly (ADP-ribose) polymerase inhibitors. This study aims to determine the minimum sequencing depth and tumor content (TC) required to accurately identify these clinically significant genomic profiles using sWGS.

[MATERIALS AND METHODS] Whole-genome sequencing (WGS) data from 168 tumor and matched normal biopsies from 155 patients with mCRPC were mixed in silico to generate a set of 3,360 mixtures with varying TCs (original, 20%, 10%, 5%, 3%) and sequencing depths (original, 5×, 2×, 1×, 0.1×). Copy number variations (CNVs) were analyzed using ichorCNA and WisecondorX at different window sizes.

[RESULTS] An average sequencing depth of 1× at 20% TC was found to be sufficient to detect CNVs with high sensitivity (>0.85) and high specificity (>0.95). For HRD and TD profile detection, ichorCNA at a 50 Kb window size was optimal and a reliable detection of HRD profiles was achieved with a very strong correlation of R = 0.88 ( < 2.2e-16). Detection of TD profiles also remained accurate at these parameters with a strong correlation of R = 0.72 ( < 2.2e-16), although the median length of duplication events increased at lower depths. TC estimation by ichorCNA strongly correlated with full-depth WGS of diploid genomes.

[CONCLUSION] In this study, through in silico simulations of WGS data, we demonstrate that the genomic scars of two druggable genomic profiles, HRD and TD, can be reliably detected in mCRPC with 1× average sequencing depth and ≥20% TC. Further research is required to correlate these markers with outcome of specific treatments using sWGS.