Research indicates that sperm with high-levels of DNA fragmentation have a lower probability of producing a successful pregnancy. A review of data on hundreds of semen samples show that patients with a DNA fragmentation level of greater than 30% are likely to have significantly-reduced fertility potential, including a significant reduction in term pregnancies and a doubling of miscarriages. Sperm that appears to be normal by traditional semen analysis parameters (motile, morphologically normal sperm) may even have extensive DNA fragmentation. In an effort to achieve the most effective measurement of male fertility potential, the SCSA reports the percentage of the following four major populations of sperm present in a semen sample:

• Sperm with a low level DNA fragmentation
• Sperm with increased susceptibility to DNA denaturation classified into a moderate and a high level of defragmentation
• Sperm with immature chromatin due to less chromatin condensation, allowing for a higher degree of DNA stainability

The SCSA is performed using an instrument called a flow cytometer in which cells that have been stained with a fluorescent dye are sent through a glass channel in liquid suspension. The cells pass through a laser beam and the light from the beam causes the dye to emit fluorescent light of a certain color. When performing an SCSA, the colors measured are red and green; green fluorescing sperm have very low levels of fragmented DNA and red fluorescing sperm have moderate to high levels of fragmented DNA.

While the semen analysis has been the standard for male fertility analysis in the past, the introduction of the SCSA offers many advantages over existing clinical assays for a number of reasons. First of all, the SCSA can measure 5000 individual sperm in just seconds and the data provides both a diagnostic and prognostic evaluation of the male's potential for subfertility or infertility. Another advantage of note is the fact that the data are from objective, machine-defined criteria rather than from biased human eye measurements as with a standard semen analysis. In addition to having a higher level of repeatability than that of any other semen parameter, the SCSA randomly measures all cell types in the semen sample as opposed to evaluation of only washed samples.

In a study of 700 in vitro fertilization (IVF) cases in which intracytoplasmic sperm injection (ICSI) was performed, pregnancy occurred in less than 1% of the cases when the percentage of sperm with damaged DNA was greater than thirty. Another study confirmed greater than 30% DFI (% sperm with damaged DNA) as a significant lack of fertility potential, 15-30% DFI as reasonable potential and less than 15% DFI as high fertility potential. In this study, 84% of men who fell into the "high fertility potential" category with a DFI of 15% or lower conceived within the first three months.

There are a number of factors that may help explain why a certain individual has high DNA fragmentation in the sperm, resulting in low fertility potential. When examining SCSA studies, length of sexual abstinence, age (significant increase in DFI after age 46), smoking history and exposure to high levels of air pollution all factor into significant variations in results. Sperm chromatin structure is also compromised in patients with leukocytospermia, febrile illness and testicular cancer. Significant exposure to prolonged heat in the testicles can also contribute to high levels of fragmentation; for example, excessive hot tubbing, truck driving and avid cycling are all key factors in poor SCSA results. Drug use, exposure to chemicals or radiation and testicular trauma are other potential causes of abnormal results. The SCSA is also helpful in identifying men who may have a varicocele, a tangle of veins surrounding the testicle. Surgical correction of varicocles significantly restores fertility potential in about two-thirds of the cases.