Aneuploidy detection in pooled polar bodies using rapid nanopore sequencing

Area of Science:

• Genetics
• Reproductive Medicine
• Bioinformatics

Background:

• Preimplantation genetic testing for aneuploidy (PGT-A) is crucial for reducing implantation failures and miscarriages in in vitro fertilisation (IVF).
• Oxford Nanopore Technology (ONT) has been explored in various tissues, but its application to polar bodies for PGT-A is novel.

Purpose of the Study:

• To evaluate the efficacy of Oxford Nanopore Technology (ONT) for rapid aneuploidy screening using pooled first and second polar bodies.
• To compare ONT-based aneuploidy detection with array-based comparative genomic hybridisation (aCGH).

Main Methods:

• Rapid short nanopore sequencing was performed on pooled polar bodies from 102 oocytes.
• An automated analysis pipeline was developed, accounting for three chromatids per chromosome.
• Results were validated against array-based comparative genomic hybridisation (aCGH).

Main Results:

• ONT demonstrated 96% concordance with aCGH for overall ploidy classification (98/102 samples).
• Chromosome-level ploidy classification concordance was 92.5% (2169/2346 chromosomes), increasing to 97.7% when excluding complex cases.
• Four samples discordant with aCGH were identified as aneuploid by ONT.

Conclusions:

• ONT offers an advantageous method for PGT-A by enabling automated ploidy classification per chromosome.
• The technology can detect shorter duplications or deletions based on sequencing depth.
• ONT surpasses standard aCGH by considering the presence of three chromatids in pooled polar bodies.