Patient Education Center

The Sperm Chromatin Structure Assay (SCSA) and DNA Fragmentation:
What Is It and What Does It Mean?

This article about “Sperm Chromatin Structure Assay” is from a Resolve newsletter written by Dr. Werthman.

Until several years ago, the belief among most reproductive specialists (including myself) was that if a man had live sperm then they were suitable for use with IVF / ICSI, and if the female partner didn’t get pregnant or a miscarriage ensued then it was probably an egg quality issue. Several studies had implied that the conventional sperm parameters (count, motility and morphology) as measured on a routine semen analysis had no bearing on success when ICSI was used.

Many couples pursued egg donation after failed IVF attempts because the husband’s semen parameters were relatively normal and yet conception hadn’t occurred. Some of these same couples were still unable to conceive even with the “better quality” donor eggs leaving both the doctors and the couples frustrated and perplexed. Some couples then went on to use both egg donors and surrogates thinking it was both an egg quality and implantation issue, again without success. The only commonality was the husband’s sperm.

About a year and a half ago a relatively new concept was introduced to clinical practice; sperm quality was dependent on the amount of damage to the sperm DNA or DNA fragmentation.

Simply put, DNA is arranged in a double helix or ladder configuration with side rails and rungs. If the rungs are broken, then the ladder is unsteady and won’t function properly. What has recently been shown in several studies is very interesting and in some ways unexpected. Sperm DNA fragmentation has little or nothing to do with the parameters that we measure on the routine semen analysis. It has little to do with the shape of the sperm or whether the sperm are moving. It is a completely independent variable. Men with otherwise normal semen analyses can have a high degree of DNA damage and men with what was called very poor spermatazoa quality can have very little DNA damage.

More importantly, what has also been demonstrated is that the degree of DNA fragmentation correlates very highly with the inability of the sperm to initiate a birth regardless of the technology used to fertilize the egg such as insemination, IVF or ICSI. Spermatazoa with high DNA fragmentation may fertilize an egg and embryo development stops before implantation or may even initiate a pregnancy, but there is a significantly higher likelihood that it will result in miscarriage.

By testing for sperm DNA fragmentation, many cases of formerly “unexplained” infertility can now be explained. Many of those couples who have been previously unable to conceive with what would be considered extreme measures have been diagnosed with high sperm DNA fragmentation and treated. It is now very clear to see that having this information about the quality of the sperm can be tremendously helpful to couples and their physicians.

SCSA Testing

There are several ways to test for sperm DNA fragmentation; the most widely used and statistically robust test is called the Sperm Chromatin Structure Assay or SCSA.

The patient semen samples are frozen and shipped in a liquid nitrogen container to the SCSA reference laboratory in South Dakota. The sperm are thawed out and a stress is applied (low pH). The sperm are then labeled with a special orange colored dye that only attaches to the ends of broken DNA within the sperm cell. If the DNA is intact then no dye will attach to the spermatazoa.

A machine called a flow cytometer is used to analyze ten thousand sperm from the sample. The sperm are passed single file by a beam of light that hits the dye inside the sperm cell and reflects light at a specific wavelength causing the sperm to appear either orange (damaged) or green (normal). A computer counts the percentage of green versus orange-labeled sperm and software allows for creation of a graphic plot of the percent of damaged sperm giving an index known as the DNA fragmentation Index (DFI).

The data from thousands of patients has been analyzed and correlated with the patient’s clinical outcomes and reference ranges were compiled. A normal sample has less than 15% of the sperm with DNA damage. Men with poor fertility potential have greater than 30% of their sperm damaged. A DFI between 16% and 29% is considered good to fair fertility potential but becomes poorer as it approaches 27%.

These numbers are thresholds, meaning that above 30% the outcome for most couples was failure to have a birth even though only 30+ percent of the sperm were damaged. Under 15% most couples achieved success.

The logical questions that arose were: what about the rest of the undamaged spermatazoa in the sample? Why don’t those sperm work? What causes sperm DNA fragmentation? Can the DNA fragmentation be reduced and the sperm improved? If so, how?

DNA fragmentation can be thought of as a marker for other types of damage to the sperm. It is akin to seeing the tip of the iceberg. Apparently, in semen samples with greater than 30% DNA fragmentation, other abnormalities are occurring with the non-fragmented sperm that the SCSA doesn’t measure and that is why samples used with DFIs above this level do not usually result in births.

SCSA Causes

The causes of high DNA fragmentation are those same causes of male factor infertility that we have known about for years such as chemical/toxin exposure, heat exposure, varicocele, infection, age, smoking, testicular cancer, radiation, and anything that increases the free radical levels in the semen among a list of many other things.

It is very important to understand that sperm DNA fragmentation can change with time and it can be improved in many cases. The goal of a male factor evaluation is to seek out the causes of poor sperm quality and try to correct them so conception can occur naturally or to improve the sperm quality for IVF and maximize the chances of success.

In situations where DFI can’t be improved, there is evidence to suggest that removing the sperm directly from the testicle via biopsy and using it with ICSI may lead to better outcomes than using poor quality ejaculated spermatazoa. Other options include counseling patients regarding the use of donor sperm either by insemination or fertilizing a portion of the eggs harvested for ICSI with donor sperm and a portion with the patient’s sperm, once again to maximize odds.

The clinical utility of the SCSA is readily apparent. All men with an abnormal semen analysis are candidates for this test as well as men with normal semen analyses who have failed IVF for unexplained reasons. Those couples using egg donors or surrogates may also benefit from screening prior to going thru the procedures because the effort and costs are so great. Men with poor DFI should have a male factor evaluation including a physical examination by a male reproductive specialist.

These new concepts have a significant impact on how we practice and what we recommend to couples but we must bear in mind that this test does not have a predictive value of 100% as healthy babies have been born from men with high DFI, but this is fairly uncommon.

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