When Sperm Retrieval Is Not the End of the Genetic Story: Y-Chromosome Microdeletions in TESE-ICSI

“When sperm are finally retrieved from the testis of a man with severe spermatogenic failure, has the genetic problem necessarily ended – or has another clinical question just begun?

For men with azoospermia or severe oligozoospermia, Y-chromosome microdeletions are more than a laboratory finding. They can help explain impaired spermatogenesis, provide information about the likelihood of sperm retrieval, and become directly relevant to genetic counselling when testicular sperm are used for assisted reproduction.

Why should Y-chromosome microdeletion be considered before TESE?

The long arm of the Y chromosome contains three clinically important azoospermia factor regions: AZFa, AZFb and AZFc. These regions are not completely independent, and AZFb and AZFc partially overlap. Deletions involving these regions can impair spermatogenesis, but the clinical consequences depend on the location and extent of the deletion.

The EAA/EMQN best-practice guideline identifies Y-chromosomal AZF testing as a key component of the diagnostic work-up of azoospermic and severely oligozoospermic men. It also emphasizes that identification of a complete AZF deletion can establish a genetic cause of the spermatogenic phenotype, provide information for genetic counselling and contribute to prognosis when TESE or medically assisted reproduction is being considered (Krausz et al., 2024).

The AUA/ASRM 2024 guideline recommends Y-chromosome microdeletion analysis in men with primary infertility and azoospermia or sperm concentration ≤1 million/mL when accompanied by elevated FSH, testicular atrophy or a diagnosis of impaired sperm production (AUA/ASRM, 2024).

The exact threshold for severe oligozoospermia is not completely uniform across international guidance. The EAA/EMQN guideline notes that the decision limit remains debated in the range of 1–5 million sperm/mL, reflecting differences between guideline frameworks and the relatively low prevalence of clinically relevant deletions at higher sperm concentrations.

This is important because not every man undergoing TESE has the same indication for Y-chromosome testing. The test is particularly relevant when the clinical picture indicates impaired sperm production, especially azoospermia or severe oligozoospermia, rather than infertility alone.

The test is molecular rather than microscopic. DNA is typically obtained from peripheral blood and analysed using PCR-based methods targeting sequence-tagged sites across the AZF regions. The EAA/EMQN guideline states that multiplex PCR followed by deletion-extension analysis remains the gold-standard methodology for detecting and interpreting clinically relevant AZF deletions. It also emphasizes appropriate marker selection, internal quality control and external quality assessment of laboratories performing the test (Krausz et al., 2024).

What does the deletion pattern tell us about sperm retrieval?

A positive Y-chromosome microdeletion result does not provide a single prognosis. The type and extent of deletion matter.

Complete AZFa, AZFb or AZFbc deletions are associated with severe spermatogenic failure and have an extremely poor prognosis for surgical sperm retrieval. The AUA/ASRM guideline reports that sperm have not been retrieved by micro-TESE in men with complete AZFa, AZFb, AZFab or AZFabc microdeletions (AUA/ASRM, 2024).

AZFc is clinically different. Men with isolated AZFc deletion may present with severe oligozoospermia or azoospermia, but residual spermatogenesis can persist. Consequently, an AZFc deletion does not automatically mean that testicular sperm retrieval is futile.

The AUA/ASRM guideline reports that, among azoospermic men with AZFc deletions, sperm may be retrieved by micro-TESE in approximately 50% of cases. However, a 2024 systematic review of 11 cohort studies involving 441 men with AZFc microdeletion-associated azoospermia reported an overall mTESE sperm-retrieval rate of 62.4%, with individual studies ranging from 25.0% to 85.7%. The authors emphasized substantial variation between studies and the need for further evidence regarding patient-level predictors (Jiao et al., 2024).

These figures should therefore be interpreted as population-level estimates rather than a prediction for an individual patient.

The distinction between complete and partial deletions is also important. Modern molecular diagnosis is not simply a matter of reporting ‘Y-microdeletion positive.’ The EAA/EMQN guideline has updated the recommended deletion-extension markers specifically because accurate characterization of deletion boundaries can affect interpretation and TESE prognosis (Krausz et al., 2024).

For the clinical team, this creates a practical sequence:

clinical phenotype – Y-chromosome testing – deletion characterization – sperm-retrieval counselling – TESE/micro-TESE decision.

The genetic result therefore has value before surgery, not only after sperm retrieval has failed.

If sperm are retrieved, what changes genetically?

Sperm retrieval answers one question: can spermatozoa be obtained for assisted reproduction?

It does not eliminate the underlying Y-chromosome deletion.

A man with a Y-chromosome microdeletion can therefore move from a sperm-retrieval problem to a reproductive-genetics discussion once sperm are obtained and ICSI is considered.

The reason is straightforward: a Y-chromosome deletion is carried on the paternal Y chromosome. If a spermatozoon carrying that Y chromosome contributes to a male embryo, the paternal Y chromosome can be transmitted to the son. The EAA/EMQN guideline therefore specifically highlights genetic counselling because an established Y-chromosome deletion is expected to be transmitted to male offspring when the affected Y chromosome is passed on (Krausz et al., 2024).

The established clinical concern is future male reproductive function. An inherited Y-chromosome microdeletion can be associated with impaired spermatogenesis in the next male generation; it is therefore more accurate to describe this as a risk of impaired spermatogenesis and future male infertility rather than stating that every son will necessarily be infertile.

A daughter does not inherit the paternal Y chromosome. Consequently, the paternal Y-linked deletion is not transmitted to a female embryo through the father’s Y chromosome.

This inheritance pattern is one reason why genetic counselling belongs within the TESE–ICSI pathway rather than being treated as a separate issue after treatment.

Can the embryology laboratory identify a genetically normal sperm?

Not by conventional morphology.

A spermatozoon may have apparently normal morphology and still carry a Y chromosome containing the paternal microdeletion. Conversely, selecting a spermatozoon with better morphology does not establish that its Y chromosome is free of the known deletion.

This is an important distinction between microscopic sperm selection and molecular genetic status.

ICSI changes the route by which a sperm enters the oocyte; it does not repair or remove a Y-chromosome deletion.

Likewise, PGT-A should not automatically be described as a test for AZF microdeletions. PGT-A is primarily designed to assess embryo chromosome copy number. It is not equivalent to a targeted molecular test for a specific Y-chromosome microdeletion.

Where a known paternal Y-chromosome deletion is present, reproductive genetic counselling is therefore essential before decisions about embryo testing or embryo selection are made. The precise reproductive options depend on the genetic finding, clinical circumstances, available testing, local practice and the couple’s preferences.

What does current ART evidence show for AZFc?

The evidence becomes more complex once the discussion moves beyond sperm retrieval.

A systematic review and meta-analysis by Colaco and Modi, published in Fertility and Sterility in 2024, evaluated ART outcomes in men with and without AZFc microdeletions. The analysis included data from 3,807 men. Sperm-retrieval rates were not statistically different between men with AZFc microdeletions and non-deleted controls.

However, significantly lower fertilization, clinical pregnancy, and live-birth rates were observed in the AZFc group. No statistically significant differences were observed in embryo cleavage, blastocyst formation, good-quality embryo rates, implantation or miscarriage in the primary analysis (Colaco and Modi, 2024).

After correction for female factors, the meta-analysis also found significantly lower fertilization, cleavage, clinical pregnancy and live-birth rates in the AZFc group.

These findings are clinically interesting but require careful interpretation.

They demonstrate an association, not proof that an AZFc deletion directly causes impaired embryo development. The authors themselves called for further studies to clarify the potential role of AZF genes in embryonic development.

Importantly, the same meta-analysis found that comparable case-control data for ART outcomes in men with AZFa and AZFb deletions were unavailable. Therefore, findings from AZFc should not simply be generalized to every type of Y-chromosome microdeletion.

This distinction between established evidence and emerging evidence is particularly important in the IVF laboratory.

The strongest clinical evidence supports three established roles for Y-chromosome microdeletion testing: diagnosis of severe spermatogenic failure, prognosis for sperm retrieval, and genetic counselling regarding transmission to male offspring. Evidence concerning downstream ART and embryonic outcomes is more limited and remains an area for further investigation.

For the embryology team, the genetic result therefore does not end when sperm are found. Instead, it connects several stages of care:

genetic diagnosis – sperm-retrieval prognosis – TESE/micro-TESE – ICSI – embryo assessment – reproductive genetic counselling.

Y-chromosome microdeletion testing is consequently not simply a preoperative laboratory test. In appropriately selected men, it is information that can influence the clinical conversation before TESE, the interpretation of sperm-retrieval prospects and the genetic counselling that follows successful ICSI.”

Written by Saadat Hassan
Senior Clinical Embryologist/IVF and Embryology
BSc (Hons) Medical Laboratory Technology
King Edward Medical University, Lahore, Pakistan

References

Title: EAA/EMQN best practice guidelines for molecular diagnosis of Y-chromosomal microdeletions: State of the art 2023

Authors: Csilla Krausz, Paulo Navarro-Costa, Martina Wilke, Frank Tüttelmann

You can read the Full Article in Andrology.

Title: Diagnosis and Treatment of Infertility in Men: AUA/ASRM Guideline

Authors: Peter N. Schlegel, Mark Sigman, Barbara Collura, Christopher J. De Jonge, Michael L. Eisenberg, Dolores J. Lamb, John P. Mulhall, Craig Niederberger, Jay I. Sandlow, Rebecca Z. Sokol, Steven D. Spandorfer, Cigdem Tanrikut, Armand Zini; amendment panel: Robert E. Brannigan, Cigdem Tanrikut.

You can read the Full Article in the American Urological Association (AUA)/American Society for Reproductive Medicine (ASRM), 2024.

Title: Sperm retrieval rate and patient factors in azoospermia factor c microdeletion azoospermia: a systematic review

Authors: Zhong-Yu Jiao, Mao-Ran Li, Lin Zhuo, Yang-Yi Fang, Jia-Yuan Pan, Kai Hong

You can read the Full Article in BJU International.

Title: Azoospermia factor c microdeletions and outcomes of assisted reproductive technology: a systematic review and meta-analysis

Authors: Stacy Colaco, Deepak Modi

You can read the Full Article in Fertility and Sterility.

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