Evaluating sensitivity of NGS-based mutation detection across diverse sample types in prostate cancer

Prostate cancer (PCa) is one of the most common malignancies affecting men, with primary treatments involving surgery, radiotherapy, and hormonal therapy. The introduction of precision medicine and next-generation sequencing (NGS) has profoundly influenced the clinical management of PCa, particularly by enabling the assessment of genetic alterations that guide treatment decisions. Liquid biopsy using diverse sample types, including plasma, urine, and semen, offers non-invasive alternatives to tissue biopsies. This study sought to compare the performance of NGS-based mutation detection across various sample types in PCa patients.

Thirty-seven PCa patients, diagnosed with intermediate to advanced stages (II-IV), were enrolled. All collected samples, including tissues (n = 34), plasma (n = 37), urine (n = 32), and seminal fluids (n = 9), underwent targeted NGS of 437 cancer-related genes. The detection sensitivity, mutational landscape, and maximum variant allele frequencies (MVAFs) were compared across different sample types.

Tissue samples, serving as the gold standard, achieved a 100% mutation detection rate. Plasma and urine samples demonstrated high detection sensitivities, reaching 67.6% and 65.6%, respectively, while semen samples showed a lower detection rate of 33.3%. Mutations in FOXA1, SPOP, and TP53 were commonly detected across most sample types with comparable prevalence. AR mutations were observed with similar frequencies in plasma and semen samples, but were absent in tissue and urine samples. The average MVAFs were at similar levels among tissue, plasma, urine, and semen, although urine sediment samples exhibited the lowest MVAFs. Advanced disease stages correlated with increased circulating tumor DNA (ctDNA) detection in both plasma and urine samples. No significant survival advantage associated with ctDNA negativity was observed, likely due to the small sample size.

This study validates the utility of urine and plasma samples as non-invasive and sensitive liquid biopsy options for PCa, showing comparable ctDNA detection rates. Seminal fluid samples also demonstrate potential, despite current sampling challenges. These findings offer insights into the advantages of different sampling methods for PCa detection and reinforce the clinical utility of liquid biopsies in PCa management.