What Genetic Testing Is Done for IVF?

Genetic testing during IVF falls into two broad categories: tests performed on the prospective parents before embryos are created, and tests performed on the embryos themselves before transfer to the uterus. The most common embryo-level tests are preimplantation genetic testing for aneuploidy (PGT-A), for monogenic disorders (PGT-M), and for structural chromosomal rearrangements (PGT-SR). Newer and more experimental options, including polygenic risk scoring and non-invasive testing from culture media, are also entering the conversation. Which tests apply depends on the couple’s medical history, family genetics, and what they hope to learn.

Carrier Screening Before the Cycle Starts

Genetic testing in IVF often begins before a single embryo exists. Expanded carrier screening (ECS) is a blood or saliva test given to one or both prospective parents to find out whether they carry recessive variants for serious childhood conditions. A person can carry a variant for a disease like cystic fibrosis or spinal muscular atrophy without having symptoms. The risk emerges when both partners happen to carry a variant on the same gene, making them an “at-risk couple” whose children have a meaningful chance of being affected.

Panels for these screens typically follow criteria set by professional organizations and focus on conditions that are severe, relatively common in at least some populations, and highly likely to cause disease when both copies of the gene are affected. Women are also screened for X-linked conditions, since a mother who carries a variant on the X chromosome can pass the disorder to sons even if the father is unaffected.¹ When carrier screening flags an at-risk pairing, the couple can pursue PGT-M on their embryos to avoid transferring an affected one.

PGT-A and Chromosome Counting

PGT-A is the most widely used form of embryo genetic testing. Its purpose is to count chromosomes. A normal human embryo has 46 chromosomes. When an embryo has too many or too few, that is called aneuploidy, and it is the leading cause of failed implantation, early miscarriage, and conditions like Down syndrome. PGT-A screens for these whole-chromosome errors, but modern platforms can also detect smaller-scale problems like segmental deletions and duplications, as well as chromosomal mosaicism, where some cells in the embryo are normal and others are not.²

The clinical value of PGT-A depends heavily on who is using it. In patients with recurrent miscarriage, one study found that screening embryos before transfer cut early pregnancy loss from about 75% down to roughly 18% and increased the live birth rate per transfer from about 13% to 50%. Patients with repeated implantation failure also saw gains, with implantation rates roughly doubling in the screened group.³ For older patients, PGT-A reduced biochemical pregnancy losses but did not significantly improve the live birth rate, which makes sense: older patients produce fewer embryos, so discarding aneuploid ones leaves fewer to transfer.

This trade-off came into sharper focus in a large analysis of over 133,000 autologous IVF cycles reported to the U.S. national registry. For patients aged 40 and under, those who used PGT-A actually had a lower cumulative live birth rate than those who skipped it. Rates of multiple gestations, preterm birth, early pregnancy loss, and low birth weight were all higher in the group that did not use PGT-A, meaning those patients had more complications per pregnancy but more babies overall. Only among patients over 40 was there no decrease in cumulative live birth rate with PGT-A.⁴

The takeaway is nuanced. PGT-A reliably improves the success of each individual transfer by weeding out embryos unlikely to result in a healthy pregnancy, which can reduce heartbreak and time. But because it also reduces the total number of embryos available for transfer, younger patients who would have had several good embryos anyway may end up with fewer overall chances. For someone with a specific history of recurrent loss or failed implantation, the math looks different than for a younger patient in a first cycle.

PGT-M for Single-Gene Conditions

Where PGT-A is a broad screen, PGT-M is a targeted search. It looks for a specific gene variant that is already known to run in one or both parents’ families. In principle, PGT-M can be designed for any condition caused by a single identifiable gene change.⁵ The list of conditions that have been tested is long and continues to grow, ranging from cystic fibrosis, Huntington disease, and BRCA-related cancer predisposition to blood disorders like sickle cell disease and thalassemia. For families affected by hemoglobinopathies, for instance, PGT-M offers a way to ensure only unaffected embryos are transferred.⁶

Because PGT-M requires knowing exactly which variant to look for, it almost always follows carrier screening or a known family diagnosis. The lab develops a custom test protocol, often using flanking genetic markers around the gene in question, which adds preparation time and cost compared to PGT-A. If both parents are carriers discovered through ECS, PGT-M is the downstream step that lets them use that information during their IVF cycle.

PGT-SR for Structural Rearrangements

Some people carry chromosomes that are structurally rearranged, typically translocations or inversions, where pieces of chromosomes have swapped positions or flipped. Carriers of these rearrangements are usually healthy because they still have all the necessary genetic material, just reorganized. But when their cells divide to make eggs or sperm, the shuffle can produce embryos with missing or extra segments. PGT-SR identifies which embryos inherited a balanced set and which ended up with unbalanced chromosomes likely to cause miscarriage or birth defects.⁷ This testing is specifically for couples where one partner is a known carrier of a translocation or inversion, and it uses many of the same laboratory platforms as PGT-A.

How the Biopsy Is Done

All forms of PGT require removing cells from the embryo for analysis. In the early days of the technology, biopsies were performed on day three, when the embryo is only about eight cells. Removing one or two cells at that stage takes away a significant fraction of the whole embryo. A landmark randomized trial showed that day-three biopsy cut sustained implantation by about 39% compared with unbiopsied controls: only 30% of biopsied embryos led to live births versus 50% of controls.⁸

Because of findings like these, the field shifted to blastocyst biopsy, performed on day five or six when the embryo has expanded to over a hundred cells. A few cells are taken from the trophectoderm, the outer layer destined to become the placenta, leaving the inner cell mass, which will become the fetus, untouched. Implantation rates after blastocyst biopsy are roughly equivalent to those of unbiopsied embryos. Blastocyst biopsy also delivers better diagnostic quality: one study comparing biopsy stages for PGT-M found complete diagnoses in about 84% of blastocyst biopsies versus 69% of cleavage-stage biopsies.⁹ Blastocyst biopsy is now the standard of care at most clinics.

What Happens When an Embryo Is Mosaic

Mosaicism is one of the more confusing results a patient can get back. It means the trophectoderm biopsy found a mix of chromosomally normal and abnormal cells, so the embryo is neither clearly normal nor clearly abnormal. Mosaicism is common: most clinics now report it in a substantial fraction of biopsied blastocysts.

Should a mosaic embryo be transferred? The data suggest caution but not hopelessness. Live birth rates after mosaic embryo transfer are lower than after transfer of fully normal embryos, roughly 47% versus 59% in one matched comparison.¹⁰ However, babies born from low-level mosaic embryo transfers appear healthy. A study of pregnancies following transfer of mosaic blastocysts found normal prenatal karyotyping results and no significant differences in birth weight or health outcomes compared with babies from fully normal embryos.¹¹ The going approach at most clinics is to prioritize fully normal embryos, but to consider mosaic embryos, particularly those with low levels of abnormal cells, when no normal embryos are available. Genetic counseling plays an important role in these decisions.

Mitochondrial DNA Quantification

A more experimental layer of embryo analysis involves counting mitochondrial DNA copies. The idea is straightforward: embryos under metabolic stress might ramp up mitochondrial DNA production, and measuring it could provide an additional signal about which embryos are most likely to implant. Research has confirmed that aneuploid embryos tend to have higher mitochondrial DNA content than normal ones.¹² Among normal embryos specifically, higher mitochondrial DNA levels have been linked to higher miscarriage rates and lower live birth rates, suggesting it could help rank embryos that all passed PGT-A.¹³

That said, the technology is not yet reliable enough for routine clinical use. In cleavage-stage embryos, mitochondrial DNA content did not predict implantation, morphology grade, embryo sex, or maternal age in a meaningful way.¹² Some researchers have proposed that normalizing the measurement could improve its predictive power,¹⁴ but this remains a research tool rather than something most clinics use to guide decisions. It is worth knowing about, especially if you see it offered as a premium add-on.

Polygenic Risk Scores for Embryos

PGT-P, where the P stands for polygenic, represents the newest and most controversial frontier. Unlike PGT-M, which looks for a single gene causing a single condition, PGT-P uses statistical models to estimate an embryo’s risk for common, complex diseases like heart disease, diabetes, or schizophrenia. These conditions are influenced by thousands of small genetic variations rather than one clear-cut mutation. Polygenic risk scores aggregate all those small effects into a single number for each embryo, and the couple can then use those scores to inform which embryo to transfer.¹⁵

The controversy is significant. Polygenic risk scores are population-level statistics, not individual prophecies. They work best in the populations in which they were developed, predominantly people of European ancestry, and perform poorly across different ethnic backgrounds. Choosing between five embryos based on a polygenic score offers only a modest reduction in absolute risk for any given disease. The technology also opens the door to selection for non-medical traits like height or educational attainment, which raises ethical questions the field is still grappling with. A small number of companies offer PGT-P commercially, but most reproductive medicine societies have stopped short of endorsing it for routine use.

Non-Invasive PGT and Its Limitations

One of the more appealing ideas in the pipeline is non-invasive PGT, or niPGT. Instead of physically removing cells from the embryo, it analyzes tiny fragments of DNA that embryos naturally shed into their surrounding culture medium. If it worked reliably, it could eliminate the biopsy step entirely.

So far, the accuracy is not there. A recent evaluation comparing non-invasive PGT-A results with standard trophectoderm biopsy results found only about 64% overall agreement between the two methods. The sensitivity for detecting aneuploidy was around 57%, meaning the non-invasive approach missed nearly half of chromosomally abnormal embryos. Its specificity was about 67%, so it also incorrectly flagged a third of normal embryos as abnormal.¹⁶ These numbers make it unreliable as a replacement for biopsy-based testing. Researchers see potential in the approach, but it remains investigational.

Technical Errors in PGT-M

No genetic test is perfect, and PGT-M has a specific vulnerability called allele dropout, where one of the two copies of a gene fails to amplify during the testing process. If the dropped allele happens to be the disease-causing one, the embryo could be incorrectly labeled as unaffected. A systematic assessment of allele dropout in PGT-M found it at about 11% of tested gene locations, spread across 70 different genes, and affecting roughly a quarter of all patients tested.¹⁷ Labs use multiple detection methods and linked genetic markers to catch and compensate for dropout, and misdiagnosis rates in practice are quite low. Still, the risk is not zero, which is why professional guidelines recommend confirming PGT-M results with prenatal diagnostic testing during pregnancy.¹⁸

Sex Selection and Ethical Boundaries

Because PGT-A reveals the sex chromosomes of every embryo, it can be used for sex selection. When sex selection is medically indicated, the ethics are relatively settled: if a family carries an X-linked condition like hemophilia, choosing to transfer female embryos avoids passing the disease to sons. The more contested question is whether clinics should offer sex selection for non-medical reasons, typically family balancing.

The American Society for Reproductive Medicine’s Ethics Committee has described preimplantation sex selection as ethically controversial and encourages clinics to develop transparent policies on it. The committee also states that practitioners are under no ethical obligation to either provide or refuse non-medically indicated sex selection.¹⁹ In practice, clinic policies vary widely: some will accommodate requests for family balancing, while others decline. Outside the United States, many countries ban non-medical sex selection outright. The broader research landscape on PGT ethics has grown tenfold over two decades, though most of it concentrates in a handful of countries and focuses on theoretical concerns about selecting “optimal” offspring rather than on what is actually happening in clinics.²⁰

Costs and Insurance Gaps

Cost is one of the biggest practical barriers to genetic testing in IVF. PGT-A typically adds several thousand dollars to an already expensive IVF cycle, and PGT-M with its custom probe development can cost more. Carrier screening for both partners adds another layer of expense. For many Americans, insurance covers little or none of this. Even in states with IVF mandates, coverage for PGT specifically is inconsistent, and out-of-pocket costs put the technology out of reach for a large segment of the population.²¹ This creates an equity problem: the families most likely to benefit, those carrying known genetic conditions, are not always the families who can afford the testing.

The Emotional Side of Embryo Decisions

Genetic testing generates information, and information generates decisions. Deciding whether to pursue PGT in the first place, what to do with mosaic results, whether to discard affected embryos, how to weigh imperfect probabilities: these are not straightforward calls. Research on patient experience has found that the PGT decision-making process is highly stressful, with adverse emotional consequences including sustained distress and uncertainty.²² Patients sometimes describe feeling caught between wanting every piece of information and dreading what it might reveal.

Genetic counseling before and after testing can help, and most reputable clinics build it into the process. Counselors walk patients through the specific risks being tested, the meaning of possible results, and the residual uncertainty that remains even after a “normal” result. For anyone entering an IVF cycle with genetic testing, understanding that these emotions are common and expected can itself be a useful piece of preparation.

Epigenetic Questions About IVF and Embryo Culture

Beyond the tests themselves, a background concern in reproductive genetics involves epigenetics, the chemical modifications to DNA that affect how genes are turned on or off without changing the underlying code. Early research in animal models suggested that the IVF process and the culture media embryos grow in could introduce abnormal patterns of these modifications, particularly at genes that are “imprinted,” meaning only one parent’s copy is supposed to be active.²³ In humans, large epidemiological studies have found that children conceived through IVF are overwhelmingly healthy, but there has been a small observed increase in imprinting disorders like Beckwith-Wiedemann syndrome. Whether the biopsy step in PGT adds any additional epigenetic risk on top of the IVF process itself remains an open question. Current evidence does not suggest it does, but the field is young enough that long-term follow-up studies on PGT-conceived children are still accumulating.