A systematic review on concurrent aneuploidy screening and preimplantation genetic testing for hereditary disorders: What is the prevalence of aneuploidy and is there a clinical effect from aneuploidy screening?

A Novel and Comprehensive Whole-Genome Sequencing-Based Preimplantation Genetic Testing Approach for Different Genetic Conditions

Preimplantation genetic testing (PGT) is an essential tool for selecting embryos free of genetic abnormalities. However, current PGT methods often require separate platforms for aneuploidy (PGT-A), monogenic disorders (PGT-M), and structural rearrangements (PGT-SR), leading to increased costs and operational complexity when multiple PGT tests are needed for a single embryo. Here, we present KaryoSeq, a low-pass whole-genome sequencing-based comprehensive PGT approach that integrates PGT-A, PGT-M, and PGT-SR into a single platform. An assistant decision-making system was constructed to pre-evaluate the required sequencing depth for specific genes or regions. Clinical validation of KaryoSeq was performed on 166 blastocyst samples from 31 families previously diagnosed by using conventional PGT methods. KaryoSeq achieved 100% concordance with traditional platforms using the Infinium Asian Screening Array in combination with low-coverage whole-genome sequencing (approximately 0.1×); it also offered improved whole-genome coverage, reduced variability, and efficient simultaneous analysis of PGT-A, PGT-M, and PGT-SR at a whole-genome sequencing depth of approximately 2× for most genes. In addition, KaryoSeq identified triploidy, uniparental disomy, parental origin of copy number variations, and maternal cell contamination, further enhancing its clinical utility and efficiency in PGT applications.

Biopsy vs comprehensive embryo/blastocyst analysis: a closer look at embryonic chromosome evaluation

STUDY QUESTION

Compared with embryonic cytogenetic constitution of biopsied samples in human pre-implantation embryos, are there any differences in whole embryos?

SUMMARY ANSWER

Whole embryos exhibit a significantly higher euploidy rate and reduction in mosaic aneuploidy rate compared to biopsied samples.

WHAT IS KNOWN ALREADY

Much of the existing evidence of cytogenetic constitution of human pre-implantation embryos is based on biopsied cells obtained from blastomeres or trophectoderm biopsies. The mosaic rate of biopsies taken from blastocyst trophectoderm ranges widely, from 2% to 25%.

STUDY DESIGN SIZE DURATION

We investigated the embryonic cytogenetic constitution of 221 whole human embryos/blastocysts from 2019 to 2022, including 41 high-quality blastocysts, 57 low-quality blastocysts, and 123 arrested embryos/blastocysts.

PARTICIPANTS/MATERIALS SETTING METHODS

The cytogenetic constitution of whole embryos/blastocysts was assessed using next-generation sequencing. Mosaicism was diagnosed using a cut-off threshold of 30-70%, with embryos displaying 30-70% aneuploid cells classified as mosaic.

MAIN RESULTS AND THE ROLE OF CHANCE

Among high-quality blastocysts, the euploidy rate was 82.9%, with a remarkably low mosaic aneuploidy of only 2.5%. The euploidy rates of viable low-quality blastocysts and arrested embryos/blastocysts were 38.6% and 13.0%, respectively. The mosaic aneuploidy rate decreased progressively with embryonic development, from 93.2% at the cleavage stage to 40% at the blastocyst stage. Chaotic aneuploidy was the primary factor (66.1%, 39/59) contributing to embryonic arrest at the cleavage stage. Additionally, 26.1% of embryos/blastocysts exhibited segmental aneuploidy, with segmental duplications (30.6%, 22/72) and deletions (54.2%, 39/72) being the most common types of segmental aneuploidy.

LIMITATIONS REASONS FOR CAUTION

The sample size in this study is relatively small, especially in the subgroup analysis. Furthermore, whole-embryo analysis is not a foolproof diagnostic method, since it may underestimate the presence of mosaicism.

WIDER IMPLICATIONS OF THE FINDINGS

The cytogenetic constitution of whole embryos provides a more accurate reflection of their physiological state compared to biopsied samples. The low mosaic aneuploidy rate in high-quality blastocysts supports the practice of transferring mosaic embryos in patients without euploid embryos. If blastocysts reach stage III by Day 6 post-fertilization, nearly half are euploid, suggesting that extending embryo culture to Day 7 may be beneficial in cases where high-quality embryos are lacking.

STUDY FUNDING/COMPETING INTERESTS

This study was supported by the Natural Science Foundation of Guangdong Province (No. 2023A1515010250) and Pilot Program-China Reproductive Health Public Welfare Fund Project (No. SZ202413). The authors report no conflicts of interest.

TRIAL REGISTRATION NUMBER

N/A.

Clinical outcomes following preimplantation genetic testing for monogenic conditions: a systematic review of observational studies

OBJECTIVE

We aimed to report a summary of clinical outcomes following preimplantation genetic testing for monogenic conditions, by performing a systematic review of published literature on clinical pregnancy and live birth rates following preimplantation genetic testing due to a monogenic indication. Additionally, we aimed to undertake a subgroup analysis of clinical outcomes of concurrent monogenic and aneuploidy screening.

DATA SOURCES

Three electronic databases (MEDLINE, EMBASE, and PubMed) were searched from inception to May 2024.

STUDY ELIGIBILITY CRITERIA

Quantitative data audits, observational studies, and case series reporting clinical outcomes for individuals undergoing preimplantation genetic testing for a monogenic indication were included. Only studies using blastocyst biopsies with polymerase chain reaction-based or genome-wide haplotyping methods for molecular analysis were eligible to reflect current laboratory practice.

METHODS

Quality assessment was performed following data extraction using an adaptation of the Joanna Briggs critical appraisal tool for case series. Results were extracted, and pooled mean clinical pregnancy rates and birth rates were calculated with 95% confidence intervals (95% CI). We compared outcomes between those with and without concurrent preimplantation genetic testing for aneuploidy.

RESULTS

Our search identified 1372 publications; 51 were eligible for inclusion. Pooled data on 5305 cycles and 5229 embryo transfers yielded 1806 clinical pregnancies and 1577 births. This translated to clinical pregnancy and birth rates of 34.0% [95% CI: 32.8%-35.3%] and 29.7% [95% CI: 28.5%-31.0%] per cycle and 24.8% [95% CI: 23.6%-26.0%] and 21.7% [95% CI: 20.8%-23.1%] per embryo transfer. In studies with concurrent aneuploidy screening, clinical pregnancy and birth rates were 43.3% [95% CI: 40.2%-46.5%] and 37.6% [95% CI: 34.6%-40.8%] per cycle and 37.0% [95% CI: 33.9%-40.3%] and 31.8% [95% CI: 28.8%-35.0%] per embryo transfer. Studies without aneuploidy screening reported clinical pregnancy and birth rates of 32.5% [95% CI: 31.0%-34.1%] and 28.1% [95% CI: 26.6%-29.7%] per cycle and 21.2% [95% CI: 19.8%-22.6%] and 18.6% [95% CI: 17.3%-20.0%] per embryo transfer.

CONCLUSION

This systematic review reveals promising clinical outcome figures for this indication group. Additionally, synthesizing the published scientific literature on clinical outcomes from preimplantation genetic testing for monogenic conditions provides a rigorous, noncommercial evidence base for counseling.

Aneuploidy rates and likelihood of obtaining a usable embryo for transfer among in vitro fertilization cycles using preimplantation genetic testing for monogenic disorders and aneuploidy compared with in vitro fertilization cycles using preimplantation genetic testing for aneuploidy alone

OBJECTIVE

To compare aneuploidy rates among in vitro fertilization (IVF) cycles using preimplantation genetic testing for monogenic disorders (PGT-M) and aneuploidy (PGT-A) compared with IVF cycles using PGT-A alone, and to determine the likelihood of obtaining at least one usable embryo in cycles using PGT-M+PGT-A compared with cycles using PGT-A alone.

DESIGN

Retrospective cohort study.

SETTING

Single genetics laboratory.

PATIENT(S)

All IVF cycles for patients aged 18-45 undergoing PGT-A with or without concurrent PGT-M at a single genetics laboratory from November 2019 to March 2023.

INTERVENTION(S)

Use of PGT-M+PGT-A vs. use of PGT-A alone.

MAIN OUTCOME MEASURE(S)

Per cycle aneuploidy rate stratified by age, and per cycle likelihood of obtaining at least one usable embryo stratified by age and inheritance pattern of monogenic disease.

RESULT(S)

A total of 72,522 IVF cycles were included; 4,255 cycles (5.9%) using PGT-M+PGT-A and 68,267 cycles (94.1%) using PGT-A alone. The PGT-M+PGT-A group was younger than the PGT-A alone group (<35 years old: 56.1% vs. 30.5%). The majority of PGT-M cycles were performed for autosomal dominant pathogenic variants (42.4%), followed by autosomal recessive (36.5%), X-linked dominant (13.3%), and X-linked recessive (7.5%). The median number of embryos biopsied was higher in PGT-A alone compared with PGT-M+PGT-A cycles for patients aged <35, but it was equivalent in all other age groups. Age stratified aneuploidy rates did not significantly differ between PGT-M+PGT-A compared with PGT-A alone cycles. The probability of having a usable embryo declined with increasing age across all inheritance patterns. Compared with PGT-A alone, PGT-M+PGT-A cycles for patients aged ≤40 across all inheritance patterns were significantly less likely to yield a usable embryo, except in cycles for autosomal recessive diseases in the 38-40 age group and X-linked recessive diseases in the 35-37 age group. There were no consistent differences seen between groups in patients over 40. Cycles for patients with autosomal dominant diseases had the lowest likelihood of yielding a usable embryo for patients aged <43.

CONCLUSION(S)

In vitro fertilization cycles using PGT-M+PGT-A have similar age-specific aneuploidy rates to those using PGT-A alone. Cycles for patients ≤40 using PGT-M+PGT-A are significantly less likely to yield a usable embryo compared with those using PGT-A alone.

Frequency of embryos appropriate for transfer following preimplantation genetic testing for monogenic disease

PURPOSE

To identify specific likelihoods that an embryo will be classified as appropriate for transfer after preimplantation genetic testing for detection of a monogenic disorder (PGT-M), with or without preimplantation genetic testing for aneuploidy (PGT-A), separated by inheritance pattern.

METHODS

Retrospective chart review of 181 selected PGT-M cycles performed at CooperGenomics in 2018 or 2019. For each cycle, the following main outcome data was collected: the number of embryos classified as affected with monogenic disease, the number detected to be chromosomally abnormal, the number that were recombinant, the number that had no result, and if applicable, the number which were aneuploid.

RESULTS

There were significantly fewer embryos appropriate to consider for transfer when PGT-A was included for autosomal recessive and X-linked disorders. There were also fewer for autosomal dominant disorders, though this was not statistically significant. When PGT-A was not included, 45.8% of autosomal dominant, 69% of autosomal recessive, and 47.8% of X-linked embryos were appropriate to consider for transfer. When PGT-A analysis was included, 29% of autosomal dominant, 41% of autosomal recessive, and 22% of X-linked embryos were appropriate to consider for transfer. 96.8% of women elect to include PGT-A when pursuing PGT-M.

CONCLUSION

This study resulted in specific likelihoods that an embryo would be found appropriate for clinicians and patients to consider for transfer based on the inheritance pattern of the monogenic disease being tested for and whether aneuploidy analysis was included.

Whole Genome Amplification in Preimplantation Genetic Testing in the Era of Massively Parallel Sequencing

Successful whole genome amplification (WGA) is a cornerstone of contemporary preimplantation genetic testing (PGT). Choosing the most suitable WGA technique for PGT can be particularly challenging because each WGA technique performs differently in combination with different downstream processing and detection methods. The aim of this review is to provide insight into the performance and drawbacks of DOP-PCR, MDA and MALBAC, as well as the hybrid WGA techniques most widely used in PGT. As the field of PGT is moving towards a wide adaptation of comprehensive massively parallel sequencing (MPS)-based approaches, we especially focus our review on MPS parameters and detection opportunities of WGA-amplified material, i.e., mappability of reads, uniformity of coverage and its influence on copy number variation analysis, and genomic coverage and its influence on single nucleotide variation calling. The ability of MDA-based WGA solutions to better cover the targeted genome and the ability of PCR-based solutions to provide better uniformity of coverage are highlighted. While numerous comprehensive PGT solutions exploiting different WGA types and adjusted bioinformatic pipelines to detect copy number and single nucleotide changes are available, the ones exploiting MDA appear more advantageous. The opportunity to fully analyse the targeted genome is influenced by the MPS parameters themselves rather than the solely chosen WGA.

Disrupting the biological clock: Fertility benefits, egg freezing and proactive fertility management

In the last decade, the in-vitro fertilization (IVF) sector has witnessed a shift from so-called 'reactive IVF' to a new model of proactive fertility care. Whereas IVF was traditionally developed to treat people who found they were unable to conceive, the indication for IVF has broadened significantly to include a much wider group of potential patients through a new focus on proactive treatment of future (in)fertilities. This shift combines a number of new trends pertaining to preservation, prediction, private equity and platformization, all of which have gained influence in contemporary assisted reproduction. This article focuses on the emergence of company-sponsored fertility benefits, which combines each of these trends. Whereas fertility benefits - especially egg freezing insurance - have primarily been discussed in terms of women's empowerment or disenfranchisement, this article instead calls attention to the discursive, clinical and infrastructural shifts in contemporary assisted reproduction that have emerged with the rising popularity of these benefits. The analysis addresses these underdiscussed aspects of fertility benefits by focusing on the dynamics of demand; the shifts in the rationalization of intensified treatment pathways in the face of new reimbursement practices; and the online, platform-based infrastructures that are built to provide these treatments. In doing so, it analyses how this remaking of fertility towards an ethos of proactive fertility management reflects broader capitalist tailwinds.

Analysis of bovine blastocysts indicates ovarian stimulation does not induce chromosome errors, nor discordance between inner-cell mass and trophectoderm lineages

Contemporary systems for oocyte retrieval and culture of both cattle and human embryos are suboptimal with respect to pregnancy outcomes following transfer. In humans, chromosome abnormalities are the leading cause of early pregnancy loss in assisted reproduction. Consequently, pre-implantation genetic testing for aneuploidy (PGT-A) is widespread and there is considerable interest in its application to identify suitable cattle IVP embryos for transfer. Here we report on the nature and extent of chromosomal abnormalities following transvaginal follicular aspiration (OPU) and IVP in cattle. Nine sexually mature Holstein heifers underwent nine sequential cycles of OPU-IVP (six non-stimulated and three stimulated cycles), generating 459 blastocysts from 783 oocytes. We adopted a SNP-array approach normally employed in genomic evaluations but reanalysed (Turner et al., 2019; Theriogenology125: 249) to detect levels of meiotic aneuploidy. Specifically, we asked whether ovarian stimulation increased the level of aneuploidy in either trophectoderm (TE) or inner-cell mass (ICM) lineages of blastocysts generated from OPU-IVP cycles. The proportion of Day 8 blastocysts of inseminated was greater (P < 0.001) for stimulated than non-stimulated cycles (0.712 ± 0.0288 vs. 0.466 ± 0.0360), but the overall proportion aneuploidy was similar for both groups (0.241 ± 0.0231). Most abnormalities consisted of meiotic trisomies. Twenty in vivo derived blastocysts recovered from the same donors were all euploid, thus indicating that 24 h of maturation is primarily responsible for aneuploidy induction. Chromosomal errors in OPU-IVP blastocysts decreased (P < 0.001) proportionately as stage/grade improved (from 0.373 for expanded Grade 2 to 0.128 for hatching Grade 1 blastocysts). Importantly, there was a high degree of concordance in the incidence of aneuploidy between TE and ICM lineages. Proportionately, 0.94 were "perfectly concordant" (i.e. identical result in both); 0.01 were imperfectly concordant (differing abnormalities detected); 0.05 were discordant; of which 0.03 detected a potentially lethal TE abnormality (false positives), leaving only 0.02 false negatives. These data support the use of TE biopsies for PGT-A in embryos undergoing genomic evaluation in cattle breeding. Finally, we report chromosome-specific errors and a high degree of variability in the incidence of aneuploidy between donors, suggesting a genetic contribution that merits further investigation.