Overstated false benefits of IVF genetic testing - PGT-A / PGS

[Angelica Cheng]

Hidden in plain sight: the overstated benefits and underestimated losses of potential implantations associated with advertised PGT-A success rates

Abstract. The utilization of preimplantation genetic testing for aneuploidy (PGT-A) has understandable intuitive appeal in reassuring the clinician that ‘e

academic.oup.com

Hidden in plain sight: the overstated benefits and underestimated losses of potential implantations associated with advertised PGT-A success rates

Abstract

The utilization of preimplantation genetic testing for aneuploidy (PGT-A) has understandable intuitive appeal in reassuring the clinician that ‘everything possible’ has been done to assure the birth of a healthy baby. Whereas the development of the PGT-A technology is still in a relatively early stage, great strides have nevertheless been made in the understanding of the genetics of the preimplantation human embryo. The problem lies not in the progress that has been achieved, but rather, in the reality that PGT-A is being actively marketed as a mature technology. Those that market the technology overstate its benefits and underestimate the losses of potential implantations that are the consequence of the practice of PGT-A. The implication is that the PGT-A technology is accurate, has minimal errors and is ready to be applied to every case of IVF. This approach is not evidence-based. Substantial losses of potential implantations are even evident in the analysis of the numbers presented by marketing materials themselves. In order to provide accurate, evidence-based counseling for patients undergoing IVF, we need to apply an appropriate level of scientific scrutiny to the data that are available and apply PGT-A selectively to those cases in which the benefits clearly outweigh the costs.

Introduction

It is easy to appreciate the intuitive appeal of preimplantation genetic testing for aneuploidy (PGT-A) in helping all of us achieve our common goal of a healthy baby after IVF. Patients as well as clinicians want to maximize the probability of a successful pregnancy following embryo transfer (ET), while minimizing the risk of multiple gestations. There is also the satisfaction of feeling that one has done ‘everything possible’ to minimize the disappointment of a failed ET, miscarriage or even a pregnancy termination triggered by a chromosomally abnormal pregnancy. Genetics and genomics play an increasingly important role in our field, and genetic analysis of the preimplantation human embryo, especially if it can be achieved without the trauma of an embryo biopsy (Ho et al., 2018), may provide important information about the biology of human preimplantation development.

Marketing PGT-A

The problem with the current clinical application of PGT-A is that its use has become highly marketed. Commercial ventures are selling this technology, which is still quite early in its development, as a mature, established diagnostic technique. As a consequence, clinicians are presented by marketing rather than carefully scrutinized scientific data. Those that market PGT-A want to see it applied to every case of IVF and are understandably motivated to overstate the magnitude of the anticipated benefits. For example, advertised numbers (Igenomix, n.d.) suggest that ongoing embryo implantation rates (implantations leading to a live birth or successful pregnancy) in women younger than 35 years increase from 49.4% to 65% when blastocysts are transferred without and with, respectively, the prior use of PGT-A. These numbers contrast with the published results of Kang et al. (2016), who reported unchanged ongoing embryo implantation rates (of ~50%) in women younger than 35 years whose blastocysts did or did not undergo testing with PGT-A. The advertised numbers also contrast with those reported in the STAR trial (Illumina, 2019), a multi-center randomized clinical trial, which sought to demonstrate superior implantation rates in the PGT-A group, but which actually demonstrated similar ongoing implantation rates of ~50% in both study and control groups among women younger than 35 years. Both of the latter studies confirmed that the ongoing implantation rates of ~50% observed with PGT-A in women older than 35 years were higher than the declining ongoing implantation rates observed in the controls. However, implantation rates of higher than 60% were not observed.

Implantation rates in untested embryos, PGT-A tested embryos and the aneuploidy rates as presented in the patient brochure available at genomix.com*


Table I
Implantation rates in untested embryos, PGT-A tested embryos and the aneuploidy rates as presented in the patient brochure available at genomix.com*.

Age (years)	Untested implantation rate	PGT-A tested implantation rate	Aneuploidy rate
<35	49.4%	65.0%	51.8%
35–37	42.3%	64.5%	54.4%
38–40	32.9%	61.1%	67.9%
41–42	20.7%	60.2%	77.9%
>42	7.8%	53.7%	79.8%

PGT-A: preimplantation genetic testing for aneuploidy.
*Available at: https://www.igenomix.us/hubfs/USA/PGS/PDF/PGS patient trifold US.pdf. Accessed 10 June 2019.

At the same time, those that seek to market the PGT-A technology substantially underestimate the magnitude of losses associated with PGT-A. For example, a recent publication proposing the cost-effectiveness of PGT-A estimated that ‘PGT-A is associated with a 5% relative reduction in live birth rate due to the theoretical biopsy-related damage to the embryo and to the false-positive results that may derive from the inherent technical error of chromosomal diagnostics’ (Somigliana et al., 2019). This very low estimate of 5% is in direct conflict not only with scientific publications, but also with actual advertised numbers. However, the advertised numbers must be analyzed to reveal this discrepancy, and that is the purpose of the following analysis.

PGT-A as a purification procedure

The method by which PGT-A seeks to increase implantation rates of transferred embryos is not by improving the quality of the embryos but rather by eliminating from the cohort of embryos those that are less likely to implant. This can be thought of as a purification procedure, such as one that might be applied to the purification of a specific chemical from a mixture of chemicals or to gold being extracted from gold ore. In all these cases, in order to increase the purity of a desired substance from an impure mixture of substances, some part of the original sample is discarded with the intent that the remaining sample will have a higher concentration of the desired substance. Since purification procedures are not perfect, each purification method is necessarily associated with unintended losses of some of the desired substance. The amount of the desired substance that remains in the sample is reflective of the efficiency of the purification. In the case of PGT-A, the desired substance is ‘embryos capable of implantation’ and the ‘purity’ of the substance is the ‘implantation rate of the embryos in the cohort.’ Embryos that are judged by PGT-A to be ‘aneuploid’ are discarded from the cohort, with the intent of increasing the implantation rate of the remaining embryos. The fact that some ‘aneuploid’ embryos have been found to implant (Patrizio et al., 2019) provides evidence that the selection is not perfect. This is analogous to discarding some gold from the purification of gold ore. In the case of PGT-A, there is a second possible mechanism for the loss of potential implantations, because biopsied embryos that are classified as ‘euploid’ may have decreased implantation rates due to the trauma of the embryo biopsy. Thus, discarding normal embryos and decreasing the implantation rate of the remaining embryos are two separate effects, which combine to produce losses of potential implantations. Their individual contributions cannot be calculated with the available data, but it is possible to calculate the total losses.

 

[Angelica Cheng]

The calculated efficiency of PGT-A

Since PGT-A is a purification method, its efficacy and efficiency can be expressed mathematically. In a chemical separation, for example, it is intuitive that if we remove 50% of the original unpurified sample and none of the desired substance is lost, the concentration of the desired substance in the remaining sample should increase to twice the original concentration:
Concentration=x1−0.5=x0.5=2x.

The generalized form of this equation is
Expected concentration=Original concentration1−(amount discarded).

To translate this into the language of PGT-A:
Expected implatation rate=Untested implantation rate1−(Aneuploidy rate).

The efficiency of the process can then be calculated (Patkar, n.d.) by examining the actual implantation rate achieved after PGT-A and comparing it to the expected implantation rate:
Efficiency=Actual PGT A implantation rateExpected implantation rate.

The loss of potential implantations is then
Percentage implantations lost=1−(efficiency).

The entities ‘untested implantation rate,’ ‘actual PGT-A implantation rate’ and ‘aneuploidy rate’ are available in multiple marketing materials. For this analysis, data from a patient brochure in a commercial website (Igenomix, n.d.) have been summarized in Table I. The individual values can be entered into the appropriate equations and the ‘expected implantation rate,’ ‘efficiency’ and ‘percentage implantations lost’ can be calculated. These results are presented in Table II. Note that these numbers are directly calculated from the rates that are being advertised and marketed by providers of PGT-A in an effort to present the technology in as positive a light as possible. For most of the age groups, they demonstrate a rate of loss of potential implantations between 30% and 40%.

Table II
Calculated expected implantation rates, efficiency and percentage of embryos los.

Age (years)	Expected implantation rate =Untested implant.rate1−Aneuploidy rate

	Efficiency =Actual PGTA implant.rateExpected implant.rate

	Implantations lost =1−Efficiency
<35	49.4/48.2 = 102.5%	65.0/102.5 = 63.4%	36.6%
35–37	42.3/45.6 = 92.7%	64.5/92.7 = 69.6%	30.4%
38–40	32.9/32.1 = 102.5%	61.1/102.5 = 59.6%	40.4%
41–42	20.7/22.1 = 93.7%	60.2/93.7 = 64.2	35.8%
>42	7.8/20.2 = 38.6%	53.7/38.6 = 139.1%	−39.1% (additional implantations)

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Some of the calculations produce results that seem like nonsense, but they are calculated directly from the numbers that are presented in the advertisement. For example, the expected implantation rate is over 100% in the <35 years age group. It is intuitive that if the untested ongoing implantation rate is 49.4%, we should not be discarding (for aneuploidy) 51.8% of the embryos, since those numbers add up to more than 100%. (For example, if we start with a 50% implantation rate, then discard 60% of embryos and end up with a 100% implantation rate, the formula still works. The ‘expected implantation rate’ is calculated as 0.5/0.4 = 125%, and the efficiency is 1.0/1.25 = 80%, meaning that 20% of potential implantations were discarded. This is a correct mathematical conclusion, even though the expected implantation rate doesn’t seem reasonable.) In the >42 years age group, the implantation rate is stated to increase from 7.8% to 53.7% as a result of PGT-A, a nearly 7-fold increase. Given the 79.8% aneuploidy rate, this would represent a net increase of 39% implantations, which is not plausible. The only possible conclusion is that the advertised numbers are, in this case, not correct.

Implications of the calculated loss rate

What does a loss of 30% of implantations mean? A young patient with 20 blastocysts representing 10 potential live births may choose PGT-A testing, which will produce a reduction in the total number of implantations to 7. A patient older than 40 years with three cleavage-stage embryos and a 20% cumulative potential for a live birth who chooses PGT-A testing will reduce that potential to 14%. Assuming that she continues treatment with additional egg retrievals, in order to achieve the same cumulative probability of a live birth with PGT-A as she would in an untested cycle, she would need to undergo 43% more egg retrievals (1/0.7 = 1.43). Therefore, the additional cost of PGT-A is not just the cost of the genetic analysis, but an additional 43% of retrievals. This is a clear demonstration of a decrease in cumulative live birth rates in the face of increased ongoing implantation rates (Griesinger, 2016). It also represents an estimate of the magnitude of this decrease, based on the advertised numbers.

The science of PGT-A

It would be helpful if these findings could be used to improve the process of PGT-A. However, the details of the materials and methods of PGT-A studies are often glossed over. What kind of trophectoderm biopsy was taken? What kind of platform was used for the genetic testing? What kind of bioinformatic tools and cut-off values were used to identify aneuploidy? False-positive and false-negative values as well as positive and negative predictive values can only be calculated from non-selection trials. A control group should undergo ET without embryo biopsy. The study group should undergo embryo biopsy prior to ET, with PGT-A results available only after the implantation outcome is known. Only one non-selection study has been performed to date, in spite of many cycles of PGT-A performed worldwide (Scott et al., 2012). We need to be able to analyze new information as scientists and independent thinkers rather than accepting information from marketing materials.

Conclusion: when is the use of PGT-A justified?

If PGT-A is not appropriate in all cycles, is there any setting in which this technology could be applied clinically? It can be argued that in a specific clinical situation, it may be reasonable to offer PGT-A testing. If a patient has a specific chromosomal defect, PGT-A offers a solution to avoiding an unbalanced karyotype, as well as permitting sex selection. If a patient older than 35 years has many blastocysts available (Illumina 2019, Kang et al. 2016), it may be reasonable to trade the losses of potential ongoing implantations against the information offered by PGT-A. On the other hand, it is very hard to justify the use of PGT-A in a fertility preservation patient with a small number of cryopreserved oocytes. Most patients older than 40 years also produce few oocytes and even fewer blastocysts. Losing 30% of potential implantations through the use of PGT-A may make the difference between pregnancy and failure (Paulson, 2016). In order to counsel patients appropriately, it is crucial that we have accurate, evidence-based estimates of both the benefits (increased implantation rates) as well as the costs (potential implantations lost) associated with PGT-A (Paulson, 2017). The information promised by the genetic analysis of preimplantation human embryos is too important to be treated with only a superficial analysis of outcomes. It is only through careful scrutiny of studies and their replication by other investigators that we can advance this very important aspect of our field.

 

[Colourfulgiraffe]

Angelin


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[Angelica Cheng]

Angelin


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Experts Say Genetic Embryo Screening Prior To IVF May Be Costly And Useless

Experts Say Genetic Embryo Screening Prior To IVF May Be Costly And Useless

Despite its hefty price tag, a study has found that genetic screening of embryos prior to IVF does not increase women's chances of motherhood.

www.babygaga.com

Despite its hefty price tag, genetic screening of embryos prior to implantation using in-vitro fertilization (IVF) does not increase women's chances of successfully carrying a baby.

In a recent study published by the European Society of Human Reproduction and Embryology, researchers found that pre-implantation genetic testing (PGT) found no difference in women's chances of giving birth within a year after having PGT or IVF on its own.

Many fertility clinics in the UK offer PGT to women of advanced maternal age, claiming that it is able to screen out embryos with genetic abnormalities, therefore giving them the best chance of carrying a baby to term. Many women over 40 encounter genetic issues with their eggs, which often contain fewer or more than 23 chromosomes - ultimately resulting in abnormalities. In fact, this affects over 50 percent of eggs in women over 40.

PGT comes at a cost, however, with some prominent UK clinics charging women up to £2,000 per cycle, or approximately $2,500 US. But a major study published in the Oxford Academic journal, Human Reproduction, confirmed that there is no difference in live birth rates between women who receive PGT, and those who pursue IVF without it. The randomized controlled trial - the largest of its kind to date - followed 396 women from around the world between the ages of 36 and 40 and allocated them into two groups. One group received PGT-A (pre-implantation testing for chromosomal abnormality), and the other did not.

Within 12 months of the study, the percentage of women who had a live birth in both groups was identical: 24 percent - indicating that there is no benefit to PGT's ability to increase live birth rates, or even that it works. In fact, some experts believe that it's all just a cash grab, and takes advantage of couples who may be struggling to start a family. Jan Brosens, professor of Obstetrics & Gynaecology at the University of Warwick strongly disagrees with the way clinics handle these controversial treatments.

“All too often couples requiring IVF treatment are taken for a ride when it comes to a bewildering array of unproven tests and adjuvant treatments,” he said.

While the study did not confirm benefits relating to an increased live birth rate, it did, however, show that women who received PGT screening were less likely to experience a miscarriage (7% versus 14%), however experts warn that this is a secondary end-point, and should be interpreted "with caution," according to Ying Cheong, professor of reproductive medicine at the University of Southampton.

 

[Angelica Cheng]

Angelin


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Why Assessing Genetic Normality Of IVF Embryos By AI Is A Better Option – Dr Alexis Heng Boon Chin - CodeBlue

It might be preferable for older women undergoing IVF to screen their embryos for genetic abnormalities, before transferring them into their wombs.

codeblue.galencentre.org

Why Assessing Genetic Normality Of IVF Embryos By AI Is A Better Option

With rapid economic growth and urbanisation in Malaysia over the past few decades, there is an increasing trend for women to delay marriage and childbearing, as they now enjoy improved educational and employment opportunities.


However, with older maternal age, there is an increasing likelihood of a woman’s eggs having an extra chromosome copy, which in turn increases the risks of spontaneous birth defects in their offspring.


Besides Down syndrome caused by an extra copy of chromosome 21, older women are also at increased risk of Edwards syndrome (extra copy of chromosome 18), Patau syndrome (extra copy of chromosome 13), and Klinefelter syndrome (extra X chromosome).

Graphic courtesy of Dr Alexis Heng Boon Chin.




Although such genetic defects in foetuses can be accurately diagnosed in pregnant women by non-invasive prenatal testing (NIPT), they have to face the agonising dilemma of whether or not to abort their unborn child, upon getting a positive diagnosis.


To avoid the moral dilemma and emotional trauma of abortion, it might be preferable for older women undergoing IVF (in vitro fertilisation) to screen their embryos for genetic abnormalities, before transferring them into their wombs.


This may be achieved by a highly expensive and invasive procedure known as Preimplantation Genetic Screening (PGS) or Preimplantation Genetic Testing – Aneuploidy (PGT-A).


Typically, PGS (PGT-A) increases the total IVF medical fees by around 40 to 50 per cent, so it would a lucrative business model for fertility clinics to encourage more patients to add-on this expensive procedure to their IVF treatment.


Nevertheless, patients must be wary of the aggressive sales pitch and marketing gimmicks that could be used on them.


One example is how the concept of relative risk can be misrepresented to patients to play on their fears of birth defects.


For example, if the risk of Down syndrome is 0.1 per cent at age 20, and increases to 1 per cent at age 40, and subsequently to 4 per cent at age 45, then another way of presenting the data would be to say that the risk of Down syndrome increases tenfold from age 20 to 40, and forty-fold from age 20 to 45.


Hence, through a sly manipulation of words and figures, the risks of genetic defects can be ‘exaggerated’ to patients who are unfamiliar with medical statistics.


PGS (PGT-A) is also highly invasive, as it involve drilling a hole through the embryo shell (Zona Pellucida) and extracting cells from the embryo for genetic testing (biopsy), which is potentially harmful, and can impair it’s development.


Many experts have pointed out that studies claiming no ill effects on embryos are often based on PGS (PGT-A) of excellent quality, healthy, robust embryos rather than more ‘delicate’ embryos that might suffer more.


Hence, if an IVF patient has just one or two embryos, it might not be worth taking the risk. No matter how well-trained is the lab staff (embryologist) performing this procedure, there is still a risk of human error.


The more busy the IVF lab is, the greater the risk of human error, as lab staff are under pressure to complete procedures as fast as possible.

 

[Angelica Cheng]

Graphic courtesy of Dr Alexis Heng Boon Chin.




Another deficiency of PGS (PGT-A) is that it involves extracting and sampling cells from the outer embryo layer (Trophectoderm, TE) that gives rise to the placenta and umbilical cord.


This is not representative of the inner embryo layer (Inner Cell Mass, ICM) that goes on to form the actual embryo proper, which gives rise to the baby.

Graphic courtesy of Dr Alexis Heng Boon Chin.




Mosaic embryos, which are embryos with a mixture of genetically normal and abnormal cells occur quite frequently and commonly among women undergoing IVF.


Genetic testing often leads to the misdiagnosis and discarding of mosaic embryos, which have been shown to be capable of giving rise to a normal and healthy baby.

Graphic courtesy of Dr Alexis Heng Boon Chin.




There is scientific evidence that mosaic embryos are able to “self-correct”, which increases the chances of normal birth. This “self-correction” mechanism involve pushing out the genetically abnormal cells into the outer embryo layer, which gives rise to the placenta and umbilical cord.


Older women with low ovarian reserves have much fewer embryos during IVF. Therefore, excluding or discarding of mosaic embryos that can potentially give rise to a normal baby, would in fact substantially reduce their chances of IVF success. Some older women may have no embryos left to transfer after genetic testing.


Indeed, in neighbouring Singapore, PGS (PGT-A) is still not approved as mainstream clinical treatment, due to ambiguous results and a high attrition rate of 72 per cent in local clinical trials, as reported by the Singapore Ministry of Health in 2021.


Recently, a much cheaper and less invasive alternative to PGS (PGT-A) was announced, with groundbreaking results from an international study published in the reputable Human Reproduction journal.


A novel artificial intelligence (AI) algorithm called “Life Whisperer Genetics” was successfully developed by American health care company Presegen to accurately assess the genetic normality of embryos, based only on microscopy images.


Interestingly, Alpha IVF in Malaysia was a major collaborative partner in the development of this new reproductive technology platform, which is non-invasive, low-cost, and provides results instantly, and therefore very much preferable to the expensive, time-consuming and invasive PGS (PGT-A) technique.

 

[Angelica Cheng]

According to Presagen Chief Medical Science Officer Dr Sonya Diakiw, this AI screening technique based on microscopy images alone, may not be as accurate as PGS (PGT-A) itself, which involves actual DNA sequencing.


Nevertheless, a relatively high accuracy rate of 77.4 per cent was reported in Human Reproduction.


This does not compare too badly with results from the PGS (PGT-A) technique, which themselves can be variable, due to their small sampling size.


Typically, PGS (PGT-A) only tests around five cells from a total of around 200 cells in a blastocyst-stage embryo, so it is not always representative of the entire embryo.


Hence, there is a risk of misdiagnosis of false positive and false negatives, particularly with mosaic embryos.


By contrast, the Life Whisperer Genetics AI algorithm is a whole-embryo assessment of genetic integrity that does not require any invasive procedures, which can be used to prioritise embryos for use in IVF procedures.

Graphic courtesy of Dr Alexis Heng Boon Chin.




Because instantaneous results can be obtained through AI screening, unlike time-consuming PGS (PGT-A) that take at least a few weeks, there is no obligatory requirement to freeze the entire batch of tested IVF embryos, while waiting for the test results.


This could be advantageous for some patients with a few weak embryos that maybe harmed by the freeze-thaw process.

However, a current deficiency of this new technology platform is its inability to reveal the sex of the embryo, unlike conventional genetic testing with PGS (PGT-A).


It is possible that this might be remedied in the near future, with the development of new AI algorithms that could identify the sex of IVF embryos with some degree of accuracy with microscopy imaging.


Given the much lower costs and reduced risks of harming the embryo, albeit slightly less accuracy and inability to carry out sex selection, it maybe more worthwhile and cost-efficient for patients to do AI-based screening of IVF embryos, rather than actual genetic testing with PGS (PGT-A).


At the end of the day, it is up to patients to decide on the technique that will give them better value for their hard-earned money, based on their individual risk-cost-benefit analysis.