Validation of preimplantation genetic tests for aneuploidy (PGT-A) with DNA from spent culture media (SCM): concordance assessment and implication

A novel non-invasive embryo evaluation method (NICS-Timelapse) with enhanced predictive precision and clinical impact

The selection of the finest possible embryo in in-vitro fertilization (IVF) was crucial and revolutionary, particularly when just one embryo is transplanted to lessen the possibility of multiple pregnancies. However, practical usefulness of currently used methodologies may be constrained. Here, we established a novel non-invasive embryo evaluation method that combines non-invasive chromosomal screening (NICS) and Timelapse system along with artificial intelligence algorithms. With an area under the curve (AUC) of 0.94 and an accuracy of 0.88, the NICS-Timelapse model was able to predict blastocyst euploidy. The performance of the model was further evaluated using 75 patients in various clinical settings. The clinical pregnancy and live birth rates of embryos predicted by the NICS-Timelapse model, showing that embryos with higher euploid probabilities were associated with higher clinical pregnancy and live birth rates. These results demonstrated the NICS-Timelapse model's significantly wider application in clinical IVF due to its excellent accuracy and noninvasiveness.

Culture time to optimize embryo cell-free DNA analysis for frozen-thawed blastocysts undergoing noninvasive preimplantation genetic testing for aneuploidy

OBJECTIVE

To investigate the ideal time in culture to optimize embryo cell-free deoxyribonucleic acid (cfDNA) analysis in frozen-thawed blastocysts undergoing noninvasive preimplantation genetic testing for aneuploidy (PGT-A). Cell-free DNA is released into the spent blastocyst media (spent media) by the embryo. However, the optimal timing to determine maximal cfDNA in the case of frozen-thawed blastocysts undergoing noninvasive PGT-A remains to be elucidated.

DESIGN

In this prospective observational study, 135 spent media and corresponding whole blastocysts were collected from January 2021 through March 2022.

SETTING

Private fertility clinics.

PATIENTS

Day-5 frozen-thawed blastocysts were cultured for 8 hours (Day-5 Short) or 24 hours (Day-5 Long), whereas day-6 frozen-thawed blastocysts were cultured for 8 hours (Day-6 Short). The spent media and whole blastocysts were then collected for further analysis. Spent media and whole blastocysts were amplified using whole genome amplification and sequenced using next-generation sequencing.

MAIN OUTCOME MEASURES

Informativity and concordance rates between cfDNA in spent media and whole blastocyst DNA were compared according to the different times in culture.

RESULTS

When comparing time in culture, informativity rates for spent media were significantly higher for Day-5 Long and Day-6 Short (>91%) compared with the Day-5 Short group (<60%). A similar trend was observed for cases with and without a previous PGT-A. Regarding blastocyst expansion grade, informativity rates were lower on Day-5 Short compared with Day-5 Long and Day-6 Short, regardless of expansion degree. This decrease was significant for Gardner-grade expansion grades 3, 4, and 5-6. In addition, for a similar time in culture, the grade of expansion did not have an impact on the informativity rates. For concordance rates, no significant differences were observed among the 3 groups. In all cases, concordance rates were 90.5% for Day-5 Short, 93.6% for Day-5 Long, and 92.3% for Day-6 Short. No impact of the expansion grade was observed on concordance rates.

CONCLUSION

Noninvasive PGT-A in frozen-thawed blastocysts yields very high concordance rates with whole blastocysts, possibly limiting the need for invasive PGT-A and making it available for a wider range of patients.

Advancements and Applications of Preimplantation Genetic Testing in In Vitro Fertilization: A Comprehensive Review

Preimplantation genetic testing (PGT) has become an integral component of assisted reproductive technology (ART), offering couples the opportunity to screen embryos for genetic abnormalities before implantation during in vitro fertilization (IVF). This comprehensive review explores the advancements and applications of PGT in IVF, covering its various types, technological developments, clinical applications, efficacy, challenges, regulatory aspects, and future directions. The evolution of PGT techniques, including next-generation sequencing (NGS) and comparative genomic hybridization (CGH), has significantly enhanced the accuracy and reliability of genetic testing in embryos. PGT holds profound implications for the future of ART by improving IVF success rates, reducing the incidence of genetic disorders, and mitigating the emotional and financial burdens associated with failed pregnancies and genetic diseases. Recommendations for clinicians, researchers, and policymakers include staying updated on the latest PGT techniques and guidelines, exploring innovative technologies, establishing clear regulatory frameworks, and fostering collaboration to maximize the potential benefits of PGT in assisted reproduction. Overall, this review provides valuable insights into the current state of PGT and its implications for the field of reproductive medicine.

SCM is potential resource for non-invasive preimplantation genetic testing based on human embryos single-cell sequencing

The ongoing development of assisted reproductive technologies has provided hope to individuals struggling with infertility, promising the potential for a healthy pregnancy. One significant innovation in field of pre-implantation genetic screening (PGS) requires the biopsy of embryos or oocytes, which has potential implications for the health and development of the resultant offspring. Therefore, a non-invasive approach to preimplantation genetic screening is highly sought after. The clinical application of non-invasive preimplantation genetic testing (ni-PGT) is currently limited, with its sensitivity and specificity requiring further investigation. In this study, we used 218 human embryos for single-cell whole genome amplification (WGA), along with ni-PGT of blastocoele fluid (BF) and spent culture medium (SCM). Whole blastocyst (WB), trophectoderm biopsy (TB), and inner cell mass (ICM) from embryo biopsies were used as controls to track genomic signal alterations. Our results showed that the overall genome similarity between SCM and ICM was higher than that of BF. Apart from the Y chromosome, both SCM and ICM demonstrated numerous variant sites across other chromosomes.Further categorization of gene variants in these two sample types revealed that missense variants were the most prevalent, single nucleotide polymorphisms were more common than insertions or deletions, and C > T was the dominant single nucleotide variants in both ICM and SCM. Lastly, we found that the mutant genes in SCM and ICM had different biological functions and pathways. This study indicates that SCM provides a more effective source of embryonic DNA for preimplantation genetic screening, offering a novel reference point for genetic screening research.

Noninvasive preimplantation genetic testing using the embryo spent culture medium: an update

PURPOSE OF REVIEW

The presence of cell-free DNA (cf-DNA) in the embryo spent culture medium allows to develop a noninvasive PGT-A (niPGTA). Noninvasive PGT-A may provide a simpler, safer and less costly approach to preimplantation genetic testing of aneuploidy (PGT-A). Furthermore, niPGTA would provide wider access to embryo genetic analysis and circumvent many legal and ethical considerations. However, the concordance rate between the results obtained by PGT-A and niPGTA varies among studies and, their clinical utility has not been already demonstrated. This review evaluates the niPGTA reliability based on SCM and adds new knowledge about the clinical relevance of SCM for noninvasive PGT-A.

RECENT FINDINGS

The most recent concordance studies evaluating the accuracy of niPGTA using SCM showed a high variation in the informativity rate of SCM and the diagnostic concordance. Also, sensitivity and specificity showed similar heterogeneous results. Therefore, these results do not support the clinical utility of niPGTA. Regarding clinical outcome, the data are initial and further research, including randomized and nonselection studies are needed.

SUMMARY

Further research, including randomized and nonselection studies, as well as optimization of embryo culture conditions and medium retrieval, are needed to improve the reliability and clinical utility of niPGTA.

Evaluation of non-invasive gene detection in preimplantation embryos: a systematic review and meta-analysis

BACKGROUND

Genetic abnormalities in embryos are responsible for most miscarriages and repeated embryo implantation failures, so a reliable preimplantation genetic screening method is urgently needed. Non-invasive preimplantation genetic testing (niPGT) is a potential method for embryo genetic diagnosis. However, the value of its application is controversial. This meta-analysis aimed to investigate and validate the diagnostic value of niPGT in patients undergoing in vitro fertilization (IVF).

METHODS

This review used the "Preferred Reporting Items" as a systematic review and meta-analysis of the diagnostic test accuracy (PRISMA-DTA) statement. We searched PubMed, Embase, Web of Science Core Collection, and Cochrane Library up to May 2022 to retrieve non-invasive preimplantation gene detection studies. The eligible research quality was evaluated following the quality assessment study-2 system for diagnostic accuracy. The pooled receiver operator characteristic curve (SROC) and the area under SROC (AUC) were used to evaluate diagnostic performance quantitatively. Threshold effect, subgroup analysis, and meta-regression analysis were used to explore the source of heterogeneity. Deeks' funnel plots and sensitivity analyses were used to test the publication bias and stability of the meta-analysis, respectively.

FINDINGS

Twenty studies met the inclusion criteria. The pooled sensitivity, specificity, and AUC were 0.84 (95% CI 0.72-0.91), 0.85 (95% CI 0.74-0.92), and 0.91 (95% CI 0.88-0.93), respectively. Subgroup analysis showed that the spent culture medium (SCM) subgroup had higher sensitivity and lower specificity than the SCM combined with the blastocoel fluid (BF) subgroup. Subgroup analysis showed that the study sensitivity and specificity of < 100 cases were higher than those of ≥ 100. Heterogeneity (chi-square) analysis revealed that sample size might be a potential source of heterogeneity. Sensitivity analysis and Deeks' funnel plots indicated that our results were relatively robust and free from publication bias.

INTERPRETATION

The present meta-analysis indicated that the pooled sensitivity, specificity, and AUC of niPGT in preimplantation genetic testing were 0.84, 0.85, and 0.91, respectively. niPGT may have high detection accuracy and may serve as an alternative model for embryonic analysis. Additionally, by subgroup analysis, we found that BF did not improve the accuracy of niPGT in embryos. In the future, large-scale studies are needed to determine the detection value of niPGT.

The use of voting ensembles to improve the accuracy of deep neural networks as a non-invasive method to predict embryo ploidy status

PURPOSE

To determine if creating voting ensembles combining convolutional neural networks (CNN), support vector machine (SVM), and multi-layer neural networks (NN) alongside clinical parameters improves the accuracy of artificial intelligence (AI) as a non-invasive method for predicting aneuploidy.

METHODS

A cohort of 699 day 5 PGT-A tested blastocysts was used to train, validate, and test a CNN to classify embryos as euploid/aneuploid. All embryos were analyzed using a modified FAST-SeqS next-generation sequencing method. Patient characteristics such as maternal age, AMH level, paternal sperm quality, and total number of normally fertilized (2PN) embryos were processed using SVM and NN. To improve model performance, we created voting ensembles using CNN, SVM, and NN to combine our imaging data with clinical parameter variations. Statistical significance was evaluated with a one-sample t-test with 2 degrees of freedom.

RESULTS

When assessing blastocyst images alone, the CNN test accuracy was 61.2% (± 1.32% SEM, n = 3 models) in correctly classifying euploid/aneuploid embryos (n = 140 embryos). When the best CNN model was assessed as a voting ensemble, the test accuracy improved to 65.0% (AMH; p = 0.1), 66.4% (maternal age; p = 0.06), 65.7% (maternal age, AMH; p = 0.08), 66.4% (maternal age, AMH, number of 2PNs; p = 0.06), and 71.4% (maternal age, AMH, number of 2PNs, sperm quality; p = 0.02) (n = 140 embryos).

CONCLUSIONS

By combining CNNs with patient characteristics, voting ensembles can be created to improve the accuracy of classifying embryos as euploid/aneuploid from CNN alone, allowing for AI to serve as a potential non-invasive method to aid in karyotype screening and selection of embryos.

Non-invasive evaluation of embryo quality for the selection of transferable embryos in human in vitro fertilization-embryo transfer

The ultimate goal of human assisted reproductive technology is to achieve a healthy pregnancy and birth, ideally from the selection and transfer of a single competent embryo. Recently, techniques for efficiently evaluating the state and quality of preimplantation embryos using time-lapse imaging systems have been applied. Artificial intelligence programs based on deep learning technology and big data analysis of time-lapse monitoring system during in vitro culture of preimplantation embryos have also been rapidly developed. In addition, several molecular markers of the secretome have been successfully analyzed in spent embryo culture media, which could easily be obtained during in vitro embryo culture. It is also possible to analyze small amounts of cell-free nucleic acids, mitochondrial nucleic acids, miRNA, and long non-coding RNA derived from embryos using real-time polymerase chain reaction (PCR) or digital PCR, as well as next-generation sequencing. Various efforts are being made to use non-invasive evaluation of embryo quality (NiEEQ) to select the embryo with the best developmental competence. However, each NiEEQ method has some limitations that should be evaluated case by case. Therefore, an integrated analysis strategy fusing several NiEEQ methods should be urgently developed and confirmed by proper clinical trials.

An Update on Non-invasive Approaches for Genetic Testing of the Preimplantation Embryo

Preimplantation Genetic Testing (PGT) aims to reduce the chance of an affected pregnancy or improve success in an assisted reproduction cycle. Since the first established pregnancies in 1990, methodological approaches have greatly evolved, combined with significant advances in the embryological laboratory. The application of preimplantation testing has expanded, while the accuracy and reliability of monogenic and chromosomal analysis have improved. The procedure traditionally employs an invasive approach to assess the nucleic acid content of embryos. All biopsy procedures require high technical skill, and costly equipment, and may impact both the accuracy of genetic testing and embryo viability. To overcome these limitations, many researchers have focused on the analysis of cell-free DNA (cfDNA) at the preimplantation stage, sampled either from the blastocoel or embryo culture media, to determine the genetic status of the embryo non-invasively. Studies have assessed the origin of cfDNA and its application in non-invasive testing for monogenic disease and chromosomal aneuploidies. Herein, we discuss the state-of-the-art for modern non-invasive embryonic genetic material assessment in the context of PGT. The results are difficult to integrate due to numerous methodological differences between the studies, while further work is required to assess the suitability of cfDNA analysis for clinical application.

Incidence, dynamics and recurrences of reverse cleavage in aneuploid, mosaic and euploid blastocysts, and its relationship with embryo quality

Background

During embryonic development, the normality of cleavage and the ploidy state are closely related to the final clinical outcome. At present, many research teams are focusing on the combined application of timelapse (TL) technology and preimplantation genetic testing (PGT) technology, hoping to find a connection between the two aspects of morphodynamics and genes. In the process of embryonic cleavage, there is a common abnormal cleavage pattern called reverse cleavage (RC). RC refers to blastomere fusion and failed cytokinesis. There are very few reports about it. Whether the occurrence of RC affects blastocyst euploidy is even less clear. Whether the RC phenomenon affects the embryonic developmental potential and whether it is related to the embryo ploidy. This is important for clinicians and embryologists. In this study, we used TL to observe whether there was a phenomenon of RC in each biopsy embryo and then combined it with the ploidy state to give an answer, which provided support for the selection strategy of RC embryos.

Methods

A total of 405 TL-PGT cycles and 1,467 blastocysts were included in the study. All TL data were collected from the Reproductive Medicine Center, Huazhong University of Science and Technology Hospital. Embryos images throughout embryonic development, from post-insemination to day 5 or 6 until biopsy and cryopreservation, were acquired by the Embryoscope Plus TL microscopy system from January 2019 to December 2020. This study investigated the overall incidence of RC during cleavage; the relationship between RC phenomenon and the number of occurrences and ploidy results; the relationship between RC occurrence and blastocyst developmental quality, as well as the dynamics of RC embryos.

Results

Among the 1,453 blastocysts biopsied, 400 blastocysts showed RC phenomenon at the cleavage stage, and the incidence rate was 25.9%. In euploid, mosaic and aneuploid embryos, the incidence of RC was 27.2%, 26.6%, and 25.0%, respectively. The incidence of RC was similar among these three groups with no significant difference (P > 0.05). The number of RC occurrences was not associated with embryo ploidy status (P > 0.05). In general, the blastocyst quality of the RC + group was lower than that of the RC- group. In the ICM score, the proportion of A score in the RC + group was significantly lower than that in RC- group (P < 0.05). In the TE score, there was no significant difference between the two groups of A-grade blastocysts, but the proportion of B-grade blastocysts in the RC + group was significantly lower than that in the RC- group (P < 0.01). In terms of developmental kinetic parameters, the cleavage synchrony parameters s2 and s3 were significantly longer in RC + embryos than in RC- embryos (P < 0.05). However, these changes in kinetic parameters were not significantly different between the euploid, mosaic and aneuploid groups.

Conclusions

The chromosomal euploidy of cleavage-stage embryos with RC phenomenon developed to the blastocyst stage was not significantly different from that of cleavage normal blastocysts. Therefore, RC embryos should not be discarded. It is recommended to select and utilize blastocyst culture, which has similar clinical value to normal cleavage embryos.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13048-022-01026-9.

Embryo selection through non-invasive preimplantation genetic testing with cell-free DNA in spent culture media: a protocol for a multicentre, double-blind, randomised controlled trial

INTRODUCTION

Morphological evaluation is used to select embryos for in vitro fertilisation. However, it does not fully reflect the implantation potential. Preimplantation genetic testing for aneuploidies (PGT-A) can detect embryonic aneuploidy, but biopsy procedure is invasive. Currently, a non-invasive PGT (ni-PGT) approach using spent medium is being evaluated. However, the clinical benefit of ni-PGT has not been clearly demonstrated. A multicentre randomised trial is needed to verify whether ni-PGT can be an new effective tool for evaluating embryos.

METHODS AND ANALYSIS

Overall, 1148 couples aged 35~42 (women) receiving in vitro fertilization-intracytoplasmic sperm injection are planned to be enrolled. Couples will be digitally randomised to (1) ni-PGT and (2) conventional morphology groups at a 1:1 treatment ratio. The primary outcome will be the ongoing pregnancy rate related to the first transfer cycle within 6 months after oocyte retrieval.

ETHICS AND DISSEMINATION

The study protocol is approved by the Ethics Committee of Peking University Third Hospital and the participating hospitals. The results will be disseminated through international conferences and scientific journals.

TRIAL REGISTRATION NUMBER

NCT04339166.

Validation of Non-Invasive Preimplantation Genetic Screening Using a Routine IVF Laboratory Workflow

Embryo selection is needed to optimize the chances of pregnancy in assisted reproduction technology. This study aimed to validate non-invasive preimplantation genetic testing for aneuploidy (niPGT-A) using a routine IVF laboratory workflow. Can niPGT-A combined with time-lapse morphokinetics provide a better embryo-selection strategy? A total of 118 spent culture mediums (SCMs) from 32 couples were collected. A total of 40 SCMs and 40 corresponding trophectoderm (TE) biopsy samples (n = 29) or arrested embryos (n = 11) were assessed for concordance. All embryos were cultured to the blastocyst stage (day 5 or 6) in a single-embryo culture time-lapse incubator. The modified multiple annealing and looping-based amplification cycle (MALBAC) single-cell whole genome amplification method was used to amplify cell-free DNA (cfDNA) from the SCM, which was then sequenced on the Illumina MiSeq system. The majority of insemination methods were conventional IVF. Low cfDNA concentrations were noted in this study. The amplification niPGT-A and conventional PGT-A was 67.7%. Based on this study, performing niPGT-A without altering the daily laboratory procedures cannot provide a precise diagnosis. However, niPGT-A can be applied in clinical IVF, enabling the addition of blastocysts with a better prediction of euploidy for transfer.

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.

Improved Non-Invasive Preimplantation Genetic Testing for Beta-Thalassemia Using Spent Embryo Culture Medium Containing Blastocoelic Fluid

OBJECTIVES

To compare successful beta-thalassemia (β-thalassemia) detection rates obtained using spent culture medium and spent culture medium containing blastocoelic fluid (BF).

METHOD

This study involved data from 10 couples who underwent preimplantation genetic testing (PGT) for β-thalassemia. A total of 26 samples of spent culture medium containing BF (group A) and 33 samples without BF (group B) were collected and analyzed. The DNA concentration and β-thalassemia detection rates were evaluated.

RESULTS

The HBB mutation analysis results of 34 samples were concordant with the biopsy results (34/59, 57.6%). In group A, the HBB mutation analysis results of 19 of 26 samples (73.1%) were concordant with the biopsy results. The concordance rate in group A was higher than that in group B (15/33, 45.5%; P < 0.05). The haplotyping results of 38 samples were concordant with the biopsy results (38/59, 64.4%). The concordance rate in group B was 17/33 (51.5%), which was significantly lower than that in group A (21/26, 80.8%) (P < 0.05). In group A, the mean DNA concentration of samples with <10% fragmentation was 107.3 ± 70.1 ng/μL, which was lower than that of samples with ≥10% fragmentation (194.6 ± 28.0 ng/μL) (P < 0.05). However, the detection rates of <10% and ≥10% fragmentation were not significantly different (P > 0.05).

CONCLUSION

The β-thalassemia detection rate with non-invasive PGT using the spent culture medium containing BF was higher than that using the spent culture medium alone. Fragmentation is associated with DNA concentration in the spent culture medium containing BF.