Y Microdeletion Analysis

Y microdeletion analysis is an advanced genetic screening method that detects regional losses of the Y chromosome that can lead to male infertility. By identifying molecular deficiencies that affect spermatogenesis, this analysis guides the diagnostic process and contributes to planning appropriate treatment.

Evaluation of the AZF region, in Y microdeletion analysis, allows prediction of possible clinical outcomes by classifying specific gene losses that impair sperm production. This approach reveals in detail the genetic background that influences treatment success.

In genetic investigations of infertility, Y microdeletion analysis has prognostic value with regard to TESE success and the feasibility of assisted reproductive techniques. The test provides critical data that support the individualization of reproductive treatment roadmaps.

Laboratory-based molecular methods provide high sensitivity in Y microdeletion analysis through PCR-based confirmation procedures. These methods constitute a reliable diagnostic framework for assessing carrier risk and the probability of transmission to future generations.

What Is Y Microdeletion Analysis?

Y microdeletion analysis is a molecular genetic test performed to detect genetic deletions (microdeletions) on the Y chromosome that can cause infertility in men. This test is especially used in men with impaired sperm production. Deletions in the AZF regions (AZFa, AZFb, AZFc) can directly affect sperm production. The results are of great importance for determining treatment options and for genetic counseling.

How Do the Y Chromosome and Y Microdeletions Affect Sperm Production?

In humans, sex is determined by the X and Y chromosomes. Men have one X and one Y chromosome (XY). The Y chromosome carries the SRY gene, which enables a person to develop as male, as well as genes that control male-specific characteristics and sperm production.

A large part of the Y chromosome (about 95%) is called the “Male-Specific Region” (MSY). This region is passed directly from father to son without recombination. The “control center” of sperm production (spermatogenesis) is located in this region. This control center is called the Azoospermia Factor (AZF).

Sperm production depends on the flawless functioning of the genes in this AZF region on the Y chromosome. Losses of genetic material in this region, that is, Y microdeletions, are like a malfunction that stops or severely slows the operation of the sperm factory.

Why Do These Genetic Losses Called Y Microdeletions Occur?

The AZF region of the Y chromosome unfortunately has a structurally “fragile” or “unstable” genetic architecture. The reason is that this region is full of repetitive and highly similar DNA sequences (amplicons) and mirror-image genetic blocks called “palindromes”.

During sperm production, when cells divide, these highly similar sequences can sometimes make an error. This can be compared to the teeth of a zipper misaligning while closing it. This misalignment can cause the genetic material to form a loop and break, leading to permanent loss of a DNA segment spanning millions of bases.

This is not a random error but a risk inherent in the structural properties of the Y chromosome itself. As a result, genes that are critical for sperm production are lost, and this condition is called a Y chromosome microdeletion.

What Is the AZF Region and How Do Y Microdeletions Affect It?

AZF is the main region on the long arm of the Y chromosome (Yq11) where the genes that control sperm production are clustered. This region is divided into three main subregions, each of which plays a different role in sperm production:

The basic functions of the AZF subregions in sperm production are:

• AZFa (Initiation and Stem Cell Stage)
• AZFb (Growth and Maturation)
• AZFc (Final Shaping and Completion)

Gene loss in these regions causes production to stop at that stage or not to start at all.

• AZFa Region

This region contains the genes that control the earliest “stem cell” (spermatogonia) stage of sperm production. The most important genes here are known as USP9Y and DDX3Y. When the entire AZFa region is lost, sperm stem cells cannot develop at all. Examination of the testicular tissue (histology) reveals a picture in which there are no primary sperm-producing cells and only supporting cells (Sertoli cells) are present. This is called “Sertoli-Cell-Only Syndrome” (SCOS). Men in this situation are always azoospermic (no sperm in the semen).

• AZFb Region

This region contains the genes required for sperm cells to grow and complete the maturation stage known as meiosis. When the entire AZFb region is lost, sperm stem cells exist and production begins, but meiosis cannot be completed. Production stops at the maturation stage of the sperm cell (usually at the spermatocyte stage). This condition is called “Maturation Arrest”. Men with this pattern are also always azoospermic.

• AZFc Region

This region is genetically the most dynamic and the site where deletions are most frequently seen. It contains critical genes for the last stage of sperm production, “spermiogenesis”, where sperm cells acquire a tail and become fully mature sperm. The most critical gene family here is the DAZ genes, which are present in four copies.

Unlike the other regions, the outcome of AZFc loss is variable. The testicular pattern can be SCOS or Maturation Arrest, but sometimes “Hypospermatogenesis” (all stages are present but production is severely reduced) may be seen. Therefore, some men with AZFc deletions are azoospermic, whereas a significant proportion are severely oligospermic (with very low but present sperm counts in the semen). Even in azoospermic men, small “foci of production” may remain within the testicles.

How Many Clinical Types of Y Microdeletions Exist?

Y microdeletions are clinically classified into three main groups according to the location and size of the loss.

• Complete (Full) Deletions

These are conditions in which an entire AZF region is lost.

Complete AZFa deletion (Rare)

Complete AZFb deletion (Rare)

Complete AZFc deletion (the most common type, accounting for 70–80% of all Y microdeletions)

• Combined Deletions

Sometimes the genetic error is larger and covers more than one region.

AZFbc deletion (the second most common type)

AZFabc deletion (loss of all regions, very rare)

• Partial Deletions

In this case, not the entire AZF regions but only part of them is lost.

gr/gr deletion

The “gr/gr deletion”, the most common partial loss, is a deletion of part of the AZFc region. This does not necessarily cause absolute infertility, but is considered an important genetic risk factor for impaired sperm production. Men with this deletion can have a normal sperm count, but can also be azoospermic.

How Common Is Y Microdeletion in Men with Infertility Problems?

The frequency of this genetic condition is directly related to the severity of infertility. In men with normal sperm counts who are able to father children, Y microdeletion is almost absent (approximately 1 in 4000).

However, in men presenting with infertility, this rate increases rapidly. Among men with severe oligospermia (sperm count below 5 million per milliliter), the frequency of Y microdeletions ranges between 3% and 7%.

The highest rates are seen in men with non-obstructive azoospermia, in whom no sperm is found in the semen. In this group, the reported frequency of Y microdeletions ranges between 8% and 20%, depending on the study. These figures clearly show that Y microdeletions are the second most common genetic cause of male infertility after Klinefelter syndrome.

Who Should Be Tested for Y Microdeletions?

Y microdeletion testing is not a routine test performed on every man with infertility. To be cost-effective and clinically meaningful, it should be applied to specific patient groups in whom the risk is high.

The main international urology and andrology societies (AUA – American Urological Association and EAU/EAA – European Urology/Andrology Associations) have clear recommendations on this topic:

• Situations in which Y microdeletion testing is strongly recommended:
• Azoospermia (no sperm in the semen)
• Severe oligospermia (sperm count below 5 million per milliliter)

While the European guidelines generally use the <5 million threshold, the American guidelines, based on more recent data, particularly recommend testing in men with azoospermia or sperm counts below 1 million.

There are also situations in which the test is generally NOT REQUIRED:

• Azoospermia due to obstruction of the ducts (obstructive azoospermia)
• Infertility due to hormonal disorders (hypogonadotropic hypogonadism)
• Mild or moderate reductions in sperm count (sperm count above 5 million/mL)
• Presence of another known cause of infertility (e.g., genetic diseases, previous operations)

How Is the Diagnosis of Y Microdeletion Made?

These losses on the Y chromosome are “micro” in scale; although they may involve millions of base pairs, they are too small to be seen in a standard chromosome analysis (karyotype).

The diagnosis is made using a molecular test performed on DNA obtained from a blood sample. The “gold standard” method is called Multiplex PCR (Polymerase Chain Reaction).

The principle of this method is quite simple. Special DNA markers called “Sequence Tagged Sites” (STS), whose positions in the AZFa, AZFb and AZFc regions of the Y chromosome are well known, are used. DNA extracted from the patient’s blood is subjected to PCR amplification using these STS markers.

This can be likened to calling specific addresses (STS markers) on the Y chromosome by telephone. If the address we are calling (the gene region) is present, the phone rings (PCR gives a signal). If the address has been deleted, that is, if a Y microdeletion is present, the line does not connect (no signal is obtained).

Organizations such as the European Academy of Andrology (EAA) recommend a two-step confirmation (basic screening and extended analysis) to ensure the reliability of the test. This is done both to detect the deletion and to clearly delineate its boundaries.

How Does the Y Microdeletion Test Result Affect Our Chances of Finding Sperm?

The most important clinical value of this test goes beyond diagnosis: it provides a strong prediction (prognosis) about the patient’s future. The test result gives almost definitive information about the likelihood of finding sperm in the testes by surgical methods (micro-TESE). This prevents couples from undergoing unnecessary surgeries and allows them to start treatment with realistic expectations.

According to the type of deletion, the chances of finding sperm with surgery (micro-TESE) are as follows:

Complete AZFa Deletion

This is the most severe situation.

• Sperm stem cells never develop (Sertoli-Cell-Only Syndrome).
• There are no primary sperm-producing cells in the testes.
• The chance of finding sperm with a micro-TESE operation is 0%.
• Unnecessary, costly and painful surgery is not recommended for these couples.
• Complete AZFb or Combined AZFbc Deletion

This is also a very severe picture.

• Sperm production starts but stops at the maturation stage (Maturation Arrest).
• No mature sperm cells can be found in the testes.
• The chance of finding sperm with micro-TESE is almost zero (0%).

In this situation, surgery is likewise not recommended.

Complete AZFc Deletion

This is the most common and prognostically most variable type.

• Some of these men have a small number of sperm in their semen (severe oligospermia).
• In those who have no sperm in the semen (azoospermia), small focal areas of production may remain within the testes.
• A micro-TESE operation is required to locate these foci of production.
• The chance of finding sperm with a micro-TESE operation ranges between 50% and 70%.

For this reason, micro-TESE is strongly recommended in azoospermic patients with AZFc deletions.

In short, the Y microdeletion test effectively says “Stop, do not have surgery” for AZFa and AZFb deletions, while it says “Proceed, your chance of finding sperm with surgery is high” for AZFc deletions.

How Are IVF and ICSI Performed in the Presence of a Y Microdeletion?

When this genetic condition is present, regardless of the number of sperm found (whether very few in the semen or obtained from the testes by micro-TESE), pregnancy is not possible by natural means or by insemination.

The only solution is In Vitro Fertilization (IVF) and, specifically, Intracytoplasmic Sperm Injection (ICSI). ICSI is the procedure in which a single healthy sperm cell is injected directly into the egg under the microscope in the laboratory. This method enables fertilization regardless of how low the sperm count or quality is.

Although some studies have reported that, due to the genetic load of sperm obtained from men with AZFc deletions, fertilization rates after ICSI may be somewhat lower than in other causes of infertility, ICSI remains the only effective method that allows these couples to have biological children.

What Preventive Measures Should Be Taken for Men with Y Microdeletions?

This is one of the most critical points in clinical management. In men with AZFc deletions who still have a small amount of sperm in their semen (severe oligospermia), sperm production may progressively deteriorate over time.

In other words, a patient whose sperm count is 1 million per milliliter today may become completely azoospermic after a few years. If he wishes to have children in the future, finding sperm for ICSI may then only be possible through a micro-TESE operation.

To eliminate this risk, all men with AZFc deletions who still have sperm in their semen should be advised to undergo sperm freezing (cryopreservation) without delay. Sperm banking protects the fertility potential of these patients as a “preventive” measure and may spare them from needing surgery in the future.

Are There Any Other Options If No Sperm Is Found with Micro-TESE in Y Microdeletion Cases?

For a couple diagnosed with a Y microdeletion, the treatment process may sometimes not lead to the desired outcome. Alternative paths come into consideration in the following situations:

The patient has a complete AZFa or AZFb/bc deletion (surgical chance is 0).

The patient has a complete AZFc deletion, has undergone a micro-TESE operation, but no sperm has been found.

The couple, after genetic counseling, decides that they do not wish to pass this genetic condition on to the next generation.

In these scenarios, another effective route to parenthood is sperm donation (treatment with sperm from a sperm bank) or adoption. These options should be discussed in detail with the couple during genetic counseling.

If Y Microdeletion Is Genetic, Will Our Child Inherit It?

This is the most important question asked by every couple diagnosed with Y microdeletion and forms the basis of genetic counseling. The answer is very clear, because the Y chromosome is transmitted from the father only to male offspring.

What Is the Situation for Daughters?

Daughters (XX) do not receive a Y chromosome from their father; they receive his X chromosome.

Daughters are affected by this condition in 0% of cases.

They do not genetically carry this condition and do not transmit it to their own children.

What Is the Situation for Sons?

Sons (XY) must receive the Y chromosome from their father.

The father’s Y microdeletion is transmitted to his son with 100% certainty.

These male children will very likely have the same genetic loss as their father.

It is almost certain that they will encounter the same infertility problems in adulthood.

Patients often ask, “If this condition did not come from my father (since he had children naturally), how did it develop in me?” The great majority of Y microdeletions are “de novo”, that is, new genetic errors that occur for the first time in that individual within the family. However, through ICSI, this “new” error is consciously transmitted to the next generation.

Why Is Genetic Counseling Mandatory for Couples Diagnosed with Y Microdeletions?

IVF technology allows a situation that nature would normally not permit (a man who is infertile becoming a father) and thereby enables the transmission of this genetic condition to the next generation. While this is a major medical achievement, it also brings with it a serious ethical responsibility.

Couples must fully understand this situation in all its aspects before starting any treatment. Genetic counseling is not carried out to impose a decision on the couple, but to provide them with complete and accurate information so that they can make the decision that best aligns with their own values.

During counseling, the following points are clearly explained to the couple:

• What the diagnosis means
• That the cause of infertility is this genetic loss
• Their chances of finding sperm (prognosis)
• Treatment options (ICSI, TESE)
• Alternative options (donation, adoption)
• That transmission to a son is 100% (inheritance)
• That the son will also be infertile in the future

Studies show that the vast majority of couples diagnosed with AZFc deletions (almost 80%) choose to have their own biological children despite knowing that they will pass this condition on to their sons. This is a personal decision for the couple, and the role of the healthcare team is to ensure that they make this decision with the most accurate and complete information possible.

Frequently Asked Questions