NANOPORE SEQUENCING TECHNOLOGY IN REPRODUCTIVE GENETICS – CURRENT APPLICATIONS AND FUTURE PERSPECTIVES

Problem statement

Genetic diagnostic in fertility treatment can be very time-consuming and costly. With the introduction of next-generation sequencing (NGS), genetic diagnostics became more accessible for IVF clinics. However, specialized genetic diagnostics, including preimplantation genetic testing for monogenetic diseases (PGT-M) or breakpoint-identification require extended genetic workup of parental DNA and personalized analysis. Additionally, NGS requires large investment costs, high running expenses and highly trained staff for laboratory workup and data analysis. Long-read nanopore sequencing can overcome some of these challenges by providing comprehensive, fast and cost-effective solutions for a number of different genetic analyses.

Methods

Here, we present possible applications of nanopore sequencing and its prospective transition into the clinical routine. Therefore, latest literature is reviewed for the application in reproductive genetics. Additionally, we highlight our own nanopore sequencing research including endometrial microbiome analysis, PGT-A from polar bodies and non-invasive PGT-A using embryo culture medium.

Results

Several studies have successfully demonstrated the application of nanopore sequencing in the context of structural variants for breakpoint-mapping and the identification of translocation carrier embryos. Here the long reads are particularly advantageous and allow cost-effective, efficient, direct breakpoint identification and haplotype phasing of parental DNA utilized for PGT-SR, PGT-M, or mutation analysis in male infertility.

Short-read nanopore sequencing has been successfully applied for PGT-A analysis of trophectoderm samples. In our laboratory, we applied nanopore PGT-A of polar bodies and found concordant results in 96/99 samples (97% concordance). Additionally, we analyzed culture medium for non-invasive PGT-A and found around 80% concordance with PGT-A from trophectoderm samples. Recently, the feasibility of prenatal NIPT-test using nanopore technology has been demonstrated. Additionally, nanopore sequencing has been demonstrated feasible for vaginal, endometrial and semen microbiome analysis, utilizing full-length 16S rRNA gene sequencing.

Conclusion

Nanopore sequencing technology is rapidly advancing in the field of reproductive genetics and has the potential to enable comprehensive, cost-efficient, and rapid genetic analysis across various reproductive scenarios. Low investment and running cost make nanopore sequencing an attractive tool for smaller genetic laboratories and IVF clinics. However, large-scale comparative studies are required before this new technology can be introduced into clinical routine diagnostics.