Sperm DNA Fragmentation in Native Semen: A Reflection of Apoptotic and Non-Viable Spermatozoa and Its Implications for Assisted Reproduction.

Sperm DNA fragmentation (SDF) is widely used as a biomarker of male fertility, although its predictive value for assisted reproductive technology (ART) outcomes remains controversial. We hypothesised that this discrepancy reflects the inclusion of non-viable spermatozoa in conventional SDF assessment of native semen. We retrospectively analysed semen samples from 1394 men to evaluate associations between DNA fragmentation index (DFI), sperm vitality, motility, and concentration. In addition, the viability-gated sperm chromatin structure assay (SCSA) was performed in a prospective cohort of 11 samples, and DFI was assessed before and after density gradient centrifugation, swim-up, microfluidic selection, and magnetic-activated cell sorting. Native semen DFI showed significant negative correlations with sperm vitality, motility, and concentration. Viability-gated analysis demonstrated a 3.5-fold lower mean DFI in viable spermatozoa than in the total ejaculate (11.27% vs. 39.64%, p < 0.001). All sperm preparation methods significantly reduced DFI while enriching motile and viable spermatozoa. These findings suggest that a substantial proportion of SDF detected in native semen originates from non-viable spermatozoa and that native semen DFI may not fully represent the DNA integrity of the fertilisation-competent sperm fraction, providing a potential biological explanation for its limited predictive value in ART.