Application of cell free DNA in ART

Development of a rapid and sensitive RPA-CRISPR/Cas12a assay for non-invasive pre-implantation genetic testing

BACKGROUND

Pre-implantation genetic testing (PGT) is served as the primary technology for diagnosing genetic disorders. However, invasive operation may affect embryonic development, which indicates non-invasive methods might have important clinical value. Free DNA in blastocoele fluid provides the possibility for non-invasive diagnosis. The combination of RPA and CRISPR/Cas12a technology is expected to achieve analysis of free DNA in blastocoele fluid and develop an instant diagnostic platform for non-invasive PGT.

RESULTS

In this study, we collected 65 samples of day 6/7 blastocysts formed through intracytoplasmic sperm injection, and blastocysts hatched from the zona pellucida, with the corresponding blastocoele fluid, from the Center of Reproductive Medicine at the Second Affiliated Hospital of Zhengzhou University. The TSPY1 and TBC1D3 genes were analyzed using the RPA-CRISPR/Cas12a system to investigate the diagnostic potential of free DNA in the blastocoele fluid. A single-tube dual-gene assay for blastocoele fluid was successfully constructed using the RPA-CRISPR/Cas12a technology achieving specific detection of the Y chromosome and fluorescence visualization. Interpretatable results could be completed within 1h. By detecting the TSPY1 and TBC1D3 genes in 65 pairs of blastocysts, the accuracy of the Y chromosome in the interpretable results reached 95.4 %.

SIGNIFICANCE

Free DNA in the blastocoele fluid could serve as a genetic information source for non-invasive PGT. We first established a single-tube dual-gene RPA-CRISPR/Cas12a assay to detect free DNA in blastocoele fluid and achieved rapid amplification and detection with the advantages of easy operation and fluorescence visualization, providing a rapid detection platform for the diagnosis of sex-linked disorders.

A study on methods for preimplantation genetic testing (PGT) on in vivo- and in vitro-produced equine embryos, with emphasis on embryonic sex determination

Two methods for preimplantation genetic testing (PGT) have been described for equine embryos: trophoblast cell biopsy (TCB) or blastocoele fluid aspiration (BFA). While TCB is widely applied for both in vivo- and in vitro-produced embryos, BFA has been mostly utilized for in vivo-produced embryos. Alternative methods for PGT, including analysis of cell-free DNA (CFD) in the medium where in vitro-produced embryos are cultured, have been reported in humans but not for equine embryos. In Experiment 1, in vivo- (n = 10) and in vitro-produced (n = 13) equine embryos were subjected to BFA, cultured for 24 h, then subjected to TCB, and cultured for additional 24 h. No detrimental effect on embryonic diameter or re-expansion rates was observed for either embryo group (P > 0.05). In Experiment 2, the concordance (i.e., agreement on detecting the same embryonic sex using two techniques) among BFA, TCB, and the whole embryo (Whole) was studied by detecting the sex-determining region Y (SRY) or testis-specific y-encoded protein 1 (TSPY) (Y-chromosome), and androgen receptor (AR; X-chromosome) genes using PCR. Overall, a higher concordance for detecting embryonic sex was observed among techniques for in vivo-produced embryos (67-100 %; n = 14 embryos) than for in vitro-produced embryos (31-92 %; n = 13 embryos). The concordance between sample types increased when utilizing TSPY (77-100 %) instead of SRY (31-100 %) as target gene. In Experiment 3, CFD analysis was performed on in vitro-produced embryos to determine embryonic sex via PCR (SRY [Y-chromosome] and amelogenin - AMEL [X- and Y-chromosomes]). Overall, CFD was detected in all medium samples, and the concordance between CFD sample and the whole embryo was 60 % when utilizing SRY and AMEL genes. In conclusion, equine embryos can be subjected to two biopsy procedures (24 h apart) without apparent detrimental effects on embryonic size. For in vivo-, but not for in vitro-produced equine embryos, BFA can be considered a potential alternative to TCB for PGT. Finally, CFD can be further explored as a non-invasive method for PGT in in vitro produced equine embryos.

Preimplantation genetic testing: A remarkable history of pioneering, technical challenges, innovations, and ethical considerations

Preimplantation genetic testing (PGT) has emerged as a powerful companion to assisted reproduction technologies. The origins and history of PGT are reviewed here, along with descriptions of advances in molecular assays and sampling methods, their capabilities, and their applications in preventing genetic diseases and enhancing pregnancy outcomes. Additionally, the potential for increasing accuracy and genome coverage is considered, as well as some of the emerging ethical and legislative considerations related to the expanding capabilities of PGT.

The Ratio of cf-mtDNA vs. cf-nDNA in the Follicular Fluid of Women Undergoing IVF Is Positively Correlated with Age

Age-related mitochondrial markers may facilitate the prognosis of artificial reproductive technology outcomes. In this report, we present our study concerning the ratio of cf-mtDNA/cf-nDNA, namely the amount of cell-free mitochondrial DNA relative to cell-free nuclear DNA, in the follicular fluid (FF) of women undergoing IVF, aiming to generate a molecular fingerprint of oocyte quality. The values of this ratio were measured and compared among three groups of women (101 in total): (A) 31 women with polycystic ovary syndrome (PCOS), (B) 34 women younger than 36 years, and (C) 36 women older than 35 years of age. Real-time quantitative PCR (qPCR) was performed to quantify the ratio by using nuclear- and mitochondrial-specific primers and analyzed for potential correlation with age and pregnancy rate. Our analysis showed that the level of FF-cf-mtDNA was lower in the group of advanced-age women than in the groups of PCOS and non-PCOS women. Moreover, a significant positive correlation between FF-cf-mtDNA and the number of mature (MII) oocytes was observed. Collectively, the data show that the relative ratio of cf- mtDNA to cf-nDNA content in human FF can be an effective predictor for assessing the corresponding oocyte's age-related performance in IVF.

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.