Rapid and minimally invasive preimplantation genetic testing for aneuploidies (PGT-A) based on polar body and nanopore sequencing: a viable alternative to conventional trophectoderm-based PGT-A?

TL;DR

This study explores using polar body and nanopore sequencing as a less invasive alternative to traditional methods for preimplantation genetic testing of aneuploidies, showing promising results for clinical use.

Contribution

The study introduces a novel TGS-based polar body analysis method as a viable alternative to conventional trophectoderm biopsy for PGT-A.

Findings

PB-based PGT-A showed a higher euploidy rate (55.4%) compared to blastocyst-stage PGT-A (43.1%).

TGS improved the cost-effectiveness and reduced the turnaround time for PB-based PGT-A.

PB analysis is minimally invasive and reduces the number of cryopreserved aneuploid embryos.

Abstract

Can third-generation sequencing (TGS)-based polar body (PB) analysis serve as a viable alternative to conventional trophectoderm (TE) biopsy for preimplantation genetic testing for aneuploidy (PGT-A)?

This study demonstrates the feasibility of using TGS and PB biopsy for clinical PGT-A, particularly in advanced maternal age (AMA) patients.

TE biopsy, the current standard approach for PGT-A, is limited by embryonic mosaicism. Mosaicism potentially leads to false-positive aneuploidy diagnoses, resulting in the discard of genetically normal embryos and compromising the cumulative live birth rates (CLBRs).

A total of 125 oocytes were collected from 30 couples. First (PB1) and second (PB2) polar bodies from 89 oocytes were individually amplified and sequenced, while those from the remaining 36 oocytes were processed jointly (PB1 + PB2). Then, 74 oocytes were successfully fertilized and developed into blastocysts (59.2% blastulation rate), and from these, corresponding TE biopsies were obtained.

Both PB and TE samples underwent whole-genome amplification (WGA) using multiple annealing and looping-based amplification cycles (MALBAC), followed by next-generation sequencing (NGS; all samples) and TGS (PB samples only). Copy number variation (CNV) analysis was performed for aneuploidy screening. Single-nucleotide polymorphisms (SNPs) from TE samples and parental peripheral blood were analyzed to determine the origin of CNVs and investigate discrepancies between TE- and PB-based PGT-A results. Clinical information from patients was collected for inter-group statistical comparisons.

The amplification success rate was 97.75% (87/89) for PB1 and 92.13% (82/89) for PB2, while the amplification success rate for PB1 + PB2 was 97.22% (35/36), comparable to that of TE-biopsied cells. The concordance rate of CNV results between NGS and TGS was 96.81%, with observed discrepancies primarily attributed to differences in the sizes of segmental imbalances and varying levels of intermediate copy numbers. However, when inferring oocyte ploidy status from PB analysis, the concordance rate with TE-biopsied CNV results (blastocyst formation rate 59.2%) was 75.68% (56/74). Among the 56 embryos with consistent results, the CNV profiles of 40 embryos were identical, while the remaining 16 were embryos with paternal meiotic or mitotic abnormalities. Our results demonstrated a higher euploidy rate with PB-based PGT-A (55.4%) compared to blastocyst-stage PGT-A (43.1%). Additionally, the euploidy rate in oocytes from AMA patients (>38 years) was 40%, which was lower than that in younger patients (≤38 years; 64%).

PGT-A via PB biopsy is subject to specific technical limitations and clinical risks that warrant attention. PB biopsy for PGT-A can only detect maternal meiotic abnormalities; it cannot detect mitotic errors or paternal meiotic abnormalities. Moreover, PBs are single cells with limited DNA quantity and are prone to degradation over time. The timing and technical execution of the biopsy are critical for the success of WGA. Amplification failure can occur due to sample loss, experimental error, or the absence of genetic material in PBs resulting from meiotic errors.

PB analysis represents a minimally invasive strategy that reduces the number of cryopreserved aneuploid embryos, decreases the number of embryo transfers required per live birth, and lowers miscarriage rates. Furthermore, TGS improves the cost-effectiveness and shortens the turnaround time of PB-based PGT-A, making it particularly suitable for fresh cleavage-stage (D3) transfers. This TGS-enhanced PB approach offers a clinically viable alternative to conventional TE biopsy by effectively combining the historical benefits of PB analysis with recent technological advances. The method shows significant promise for optimizing both clinical outcomes and laboratory efficiency in ART practice. Beyond PGT-A, the future may see the development of comprehensive, integrated PGT platforms (including PGT-M for monogenic disorders and PGT-SR for structural rearrangements) based on PB biopsy.

This work was supported by the National Natural Science Foundation of China (Grant No. 82273465) and the Pioneer and Leading Goose R&D Program of Zhejiang (Grant No. 2023C03034). All authors declare no competing interests.

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