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Guide to Sperm DNA Fragmentation

What is sperm DNA fragmentation, and how does it affect fertility? How can we identify and treat DNA damage within sperm? Read on for our in-depth guide to sperm DNA fragmentation.


Table of contents

Why is the genetic health of sperm important?

Sperm DNA fragmentation-why the genetic health of sperm is important

What is sperm DNA fragmentation?

Sperm DNA fragmentation—double helix

Sperm DNA fragmentation: natural repair?

DNA damage is actually quite common in the human body, but most cells have the ability to identify and correct damage to their own genetic code. While immature sperm that are still in progress may have the ability to repair their own DNA to some extent, mature sperm do not.

Eggs can actually somewhat compensate for this, and upon fertilization, have their own processes to repair errors in sperm DNA. But if the damage is too extensive—or if the egg is less able to perform this repair, possibly due to age—the damage can endure to the embryo stage. The result may be the embryo’s failure to develop or implant (infertility), miscarriage (possibly recurring), or genetic abnormalities or illness within the offspring.


DNA fragmentation index

Understanding DNA fragmentation index

The term “DNA fragmentation index,” or DFI, refers to the percentage of sperm in a particular semen sample with fragmented DNA. A higher DFI means that a larger percentage of a man’s sperm contains genetic damage. While experts disagree on specific cut-off values, generally speaking, a DFI over 30–50% is considered high, and may impact fertility.

In some cases, subfertility may be experienced even among those with a DFI of 15–30%, especially if other abnormal semen parameters are present (such as low sperm count or poor motility or morphology), or the female partner is older, as older eggs are less able to correct the damaged DNA within sperm.

Sperm DNA fragmentation and other semen parameters

Research demonstrates that men who have high levels of sperm DNA fragmentation are also more likely to have other abnormal semen parameters, such as poor sperm motility or morphology. In one 2002 study of 88 infertile men, researchers found that the average level of DNA damage was significantly higher among those with other abnormal semen parameters. This was confirmed in a 2009 study, in which higher sperm DNA damage was correlated with poorer semen parameters (sperm concentration, motility, morphology). Patients with abnormal results in all three categories had higher levels of DNA fragmentation and were more likely to have high DFI (over 30%) than patients with normal semen parameters.

This can be seen even in studies of those with just one problem with their sperm. In a 2014 study of 196 semen samples, it was found that men with teratozoospermia—a high level of abnormally shaped sperm—had higher DFI than men with normal sperm morphology. That same year, another study of over a thousand infertile men with isolated sperm defects (meaning just poor motility, poor morphology, or low sperm count, and not a combination of the above) found that levels of sperm DNA fragmentation were significantly higher among men with poor sperm motility. Approximately 31% of those men had high sperm DNA fragmentation, defined in this study as over 30% DFI.

Why does this happen? It’s probable that the same underlying factors that contribute to abnormal semen parameters, such as advanced paternal age, smoking, or toxin exposure, also cause high levels of sperm DNA fragmentation. There may be other connections or mechanisms connecting these measures, as well.

This is important to understand because, as stated above, abnormal semen parameters can compound sperm DNA fragmentation issues. However, as we’ll explore below, high sperm DNA fragmentation can impact fertility even when not paired with other factors.

Sperm DNA fragmentation, semen parameters

Sperm DNA fragmentation and male fertility

First, a note: conception is absolutely possible for men with sperm DNA fragmentation. Even in studies that report lower pregnancy rates, longer time to conception, or higher miscarriage rates among men with a high DNA fragmentation index, researchers note that full-term pregnancies have been achieved.

That being said, studies demonstrate that men with high rates of sperm DNA fragmentation are at an increased risk for infertility. In one study, men presenting for infertility evaluation—who had not been able to achieve a pregnancy for a year or more—had, on average, over twice as many sperm with DNA fragmentation than fertile men (27.6% vs. 13.3%). In another, couples experiencing infertility or miscarriage were more likely to have a male partner with moderate or high levels of DNA fragmentation; researchers concluded that “spermatozoa with denatured DNA… were the best predictor for whether a couple would not achieve pregnancy.”


Sperm DNA fragmentation and fertility treatment

This trend—higher levels of DNA fragmentation within sperm correlating with lower live birth rates—holds true even for those being treated for infertility with in vitro fertilization (IVF). In one study of 360 couples undergoing IVF, higher sperm DNA fragmentation levels were associated with lower fertilization rates, embryo quality, and pregnancy rates. The couples who were not able to achieve pregnancy had an average of 51.7% sperm with DNA fragmentation, as opposed to 39.5% in the pregnant couples. The researchers concluded that DNA fragmentation “can predict ART [assisted reproductive technology] outcome.”

This study was especially valuable because, other than DNA fragmentation results, there were few significant differences between the group that achieved clinical pregnancy and the group that didn’t. The sperm count, motility, semen volume, and other parameters were all basically equivalent between the two study groups. This allows us to surmise that DNA fragmentation impacts fertility independently of other semen parameters.

Sperm DNA fragmentation and pregnancy rates

Sperm DNA fragmentation and embryo quality

Sperm DNA fragmentation and embryo quality

Sperm DNA fragmentation and miscarriage

Sperm DNA fragmentation and the health of the child

Because of the many factors that contribute to the development of disease, it’s complicated to conduct research into specific causes. Some experts believe that “loss of sperm DNA integrity not only impacts reproductive and psychological health of the infertile couple but also increases childhood disease burden,” and that healthy sperm DNA is essential for “the health and well being of the next generation.” But the links are difficult to make conclusively.

A strong correlation has been found between the development of retinoblastoma, a childhood eye cancer, and DNA damage in paternal sperm. Researchers found that DFI levels were significantly higher in the sperm of fathers of children with retinoblastoma. It’s also been shown that advanced paternal age has been associated with many conditions in offspring—including cleft palate, heart defects, schizophrenia, autism, and epilepsy—possibly due to increased sperm DNA fragmentation with age.


What causes sperm DNA fragmentation?

There are a few possible ways that sperms’ genetic material becomes damaged, and it can happen at several points in the process of producing and storing sperm.


How sperm gets damaged:

Sperm DNA fragmentation chromatin condensation

Errors or damage during “condensation”

During spermatogenesis (the sperm production process), the genetic material within sperm condenses. The DNA wraps around a few specific proteins to organize itself snugly in the sperm’s head. This allows large amounts of DNA to occupy a very small space, and—it’s theorized—may protect the DNA from damage.

But this process also has the potential to introduce damage. Firstly, it’s quite a large amount of genetic material that needs to be compacted tightly within the nucleus of the sperm; it’s possible that this twisting could cause physical breaks in the DNA. Additionally, if there are problems with the mechanisms that package this genetic material, such as a lack of the proteins required to facilitate the condensation process, DNA will be more susceptible to damage from outside forces.

Oxidative stress

Those “outside forces” include free radicals. Free radicals, also known as reactive oxygen species (ROS), are unstable molecules produced as natural byproducts of daily life. At low levels, ROS are not typically damaging and may even be useful to cells. But if left unchecked, free radicals can cause damage to other molecules inside our cells, such as DNA. This damage is known as “oxidative stress.”

Our bodies typically use compounds called antioxidants—produced naturally by our body and absorbed from food or supplements—to neutralize these molecules and prevent damage. In fact, semen is known to contain relatively high quantities of antioxidants such as vitamin E, vitamin C, and glutathione, to protect sperm from oxidative stress. Antioxidants are also produced in other parts of the male reproductive system, including the epididymis, where sperm is stored.

There are certain experiences or behaviors that can cause levels of free radicals to rise beyond what our body can typically handle: exposure to environmental toxins such as pesticides, heavy metals, or pollution; radiation; infections; smoking tobacco; and drinking alcohol are all known to increase the presence of ROS. On the other hand, if levels of antioxidants are too low, possibly due to a poor diet, they won’t be able to adequately counteract free radicals.

Any disruption of the delicate balance of free radicals and antioxidants can result in oxidative stress. Researchers believe that oxidative stress is the major cause of sperm DNA fragmentation. In research, it’s been shown that as oxidative stress increases, sperm exhibit elevated levels of DNA damage; at the highest levels of oxidative stress, high DFI is observed alongside a loss of sperm motility.

Abortive apoptosis

Apoptosis is programmed cell death that’s part of normal growth and development. Think of it as a “self-cleaning” mechanism that eliminates unnecessary, damaged, or infected cells from the body. Though apoptosis involves the death of cells, it’s beneficial and important for the health of the overall organism. A cell that’s been marked for “deletion” can be identified by the presence of a specific protein, Fas, that induces apoptosis.

If the body is constantly cleaning out faulty cells, how do sperm cells with DNA damage make it into the semen? It seems that, sometimes, the body can recognize sperm with DNA damage and “earmark” them with Fas, but the process gets interrupted somewhere along the way, and damaged sperm are able to escape. This is known as abortive apoptosis. Why this happens is not entirely clear, but we know it has an impact on fertility: in one study, men with abnormal sperm parameters display higher levels of Fas on their sperm.

These mechanisms work together

These mechanisms are interrelated. It’s likely that, as opposed to a single one of these processes causing sperm DNA fragmentation, it’s a series of failures that results in high levels of DNA damage. For example, if the DNA within sperm is not packaged correctly, it’s more vulnerable to oxidative stress. Too-low levels of antioxidants allow that oxidative stress to damage sperm, and finally, the body fails to completely eliminate these damaged cells.

Risk factors for sperm DNA fragmentation

Sperm DNA fragmentation by age


Cigarette smoking is a known cause of exposure to many damaging chemicals (such as cadmium and nicotine) as well as increased oxidative stress. Several studies have found that smokers have increased levels of sperm DNA fragmentation, and that the level of DNA damage is correlated with how long the patient has been a smoker and how many cigarettes they smoke.

In one study of infertility patients, researchers found that the percentage of sperm with abnormal DNA condensation was significantly higher among smokers than non-smokers, and that the abnormalities were proportional to both the number of cigarettes smoked per day and the duration of smoking.

In another study, researchers found that of four patient groups—a control group, an alcohol-drinking group, a cigarette-smoking group, and a drinking/smoking group—the two groups with smoking patients exhibited the highest average levels of sperm DNA fragmentation. Drinking did appear to have a small impact on DNA damage to sperm, but smoking appeared to be much more impactful with regards to sperm DNA fragmentation.

Illness or infection

Possibly because they increase oxidative stress, illness or infection—such as influenza, cancer, or sexually transmitted infections—are associated with increased sperm DNA fragmentation.

In a study of men with sexually transmitted infections from chlamydia or mycoplasma (a bacteria that causes inflammation in the urinary tract), patients had increased DFI compared to controls (an average of 35% compared to 11%).

In a case study of one patient with a fever illness, sperm DNA fragmentation testing revealed that DFI increased significantly in the month following the fever—by 24% in the 15 days following the fever and 36% in the 37 days following—reflecting the infection and fever’s impact on the sperm that were in production at the time of the illness. The DFI did not decrease to normal levels until approximately 2–3 months after the fever resolved, once again reflecting the duration of spermatogenesis (it takes approximately 70–90 days to produce sperm).

And, while cancer treatment is well known for its impact on fertility (more on that below), research is revealing that cancer itself may have a damaging effect on sperm DNA. In a study of pre-treatment cancer patients that compared them to fertile and infertile patients, cancer patients had higher levels of sperm DNA fragmentation than even infertile men, before even receiving any chemotherapy or radiation treatments.

Cancer treatment

Cancer treatments such as chemotherapy and radiation are life-saving, but may have the side effect of impacting fertility.

Chemotherapy works by using medications to identify fast-dividing cancer cells and kill them or prevent them from dividing. But because the medication is administered through the bloodstream to the entire body, it can also attack other cells, including sperm cells. Research in male rats demonstrates that the chemotherapy medications most often used for testicular cancer are associated with an increase in sperm DNA damage. A case study of a human cancer patient presented a similar impact, revealing a substantial increase in sperm DNA damage after 8 weeks of chemotherapy treatment for leukemia, and persisted nearly a year later.

Radiation therapy involves directing high-energy rays at the cancer, in hopes of killing those cells. But by extension, this treatment can also damage parts of the body surrounding the cancer as well, potentially slowing down or stopping sperm cell production. Some men who undergo radiation will experience a temporary drop in fertility that recovers in the years following treatment; for others who undergo higher doses of radiation, sperm production may stop permanently. It’s been demonstrated in lab experiments that exposure to radiation creates a dose-dependent increase in DNA damage in sperm.

Up to 75% of reproductive-age men who are diagnosed with cancer may face infertility as a result of treatment, according to Livestrong. That’s why it’s highly recommended that men diagnosed with cancer freeze their sperm prior to treatment. Learn more about sperm freezing.

Chemical, toxin, or radiation exposure

According to the CDC, exposure to a number of chemicals or heavy metals are known to cause DNA damage within sperm. Examples include phthalates and styrene (chemicals used in plastic production); pesticides/insecticides such as organophosphate, carbaryl, or fenvalerate; lead; or benzene, a chemical that’s widely used in manufacturing and also found in gasoline and tobacco smoke.

Radiation is also implicated in sperm DNA damage, with one study of healthcare workers exposed to ionizing radiation (used in X-rays) concluding that sperm DNA fragmentation levels were significantly higher among exposed men than among non-exposed men.

The most damaging long-term, repeated exposure is typically thanks to a man’s occupation. Healthcare workers, for example, have repeated long-term exposure to radiation, as illustrated above. Other occupations with exposure risk include jobs in manufacturing, agriculture, and the military.

How can sperm DNA fragmentation be tested?

Sperm DNA fragmentation is not tested as part of a typical semen analysis. There are several different tests that use different technologies to identify and quantify DNA damage within sperm:
  • Sperm chromatin dispersion (SCD) testing, in which sperm are carefully denatured—or chemically degraded—and examined under a high-powered microscope to identify the “halos” formed by loops of intact DNA. (Sperm with damage will not produce a halo.) See image below.
  • Single cell gel electrophoresis assay (SCGE), also known as the comet assay, a process in which the cell membrane around sperm is broken down. Fragmented strands of DNA form a “tail,” like that on a comet, the presence and size of which indicates damage to the genetic material.
  • Sperm chromatin structure assay (SCSA), in which sperm cells are stained and placed in the path of a laser beam. The laser will cause the dye to emit fluorescent light of a certain color: green indicates sperm with non-detectable levels of fragmented DNA, while yellow and red indicate moderate to high levels of fragmented DNA.
  • Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, in which an enzyme that attaches to broken DNA strands is “tagged” with fluorescent dye and added to sperm cells. Under the same laser light as used in SCSA, the cells with DNA damage will emit a different color than those with intact DNA.
These tests are typically performed in a speciality lab — even if you collect your semen sample at your clinic, it will be shipped to the lab for DNA fragmentation testing.

At-home sperm DNA fragmentation testing

Legacy has introduced the first and only easy mail-in sperm testing kit that can analyze sperm DNA fragmentation. Our labs use the Halosperm SCD technique to assess sperm genetic health. Testing SDF at home, early in the process, can be game-changing, allowing you to address abnormalities early or work with your doctor to choose the best treatment for you. Legacy’s test kit makes this more accessible, affordable, and approachable.

Order your at-home sperm DNA fragmentation analysis.

Sperm DNA fragmentation testing results

When should sperm DNA fragmentation be tested?

Historically, sperm DNA fragmentation hasn’t been tested until a couple has gone through one or more failed fertility treatments. But that’s beginning to change as researchers recognize the predictive power of DNA fragmentation index, and its impact on the health of offspring.

Now, experts are arguing that sperm DNA fragmentation should be tested universally, prior to starting any fertility treatments.

There’s really no time that’s too early for testing. Especially because sperm DNA fragmentation may be treatable with lifestyle interventions, testing earlier in the fertility process can ultimately save time, energy, and money, and prevent you from undergoing more invasive procedures.

Who should be tested for sperm DNA fragmentation?

  • All fertility patients, especially:
    • Patients with unexplained infertility.
    • Patients diagnosed with male-factor infertility of an unknown cause.
    • Patients with a history of miscarriages.
    • Patients with poor embryo quality during IVF treatment.
  • Men over 40.
  • Men with a history of cancer.
  • Men under treatment with prescription medications.
  • Men with lifestyle habits that may affect sperm health, such as smoking.
  • All men who want a more thorough understanding of their sperm health.


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