Pores for thought: preimplantation genetic testing using a nanopore-based DNA sequencer - Fertility and Sterility

The genetic factor having the most potent influence on embryonic potential is chromosomal status (aneuploid or euploid). Numerous studies have conclusively shown that aneuploidy can be observed in most in vitro fertilization (IVF) embryos that fail to implant and that it is the underlying cause of most miscarriages. It therefore seems reasonable to speculate that screening embryos for such abnormalities should enable the identification of those having the greatest implantation potential. This idea forms the basis of preimplantation genetic testing for aneuploidy (PGT-A). Aneuploidy detection has evolved considerably over the last 20 years, beginning with the use of fluorescent in situ hybridization (FISH), a method with significant technical limitations. Multiple randomized controlled trials were unable to demonstrate an improvement in IVF outcomes following FISH analysis applied at the cleavage stage. More recently, the development of comprehensive chromosome screening methods (CCS), combined with blastocyst stage culture and trophectoderm (TE) biopsy, has radically improved the technical performance of PGT-A. The use of CCS for embryo analysis has led to significant improvements in clinical outcomes in several randomized controlled trials (RCTs), although some controversy concerning its clinical application remains. Currently, the clear majority of PGT-A strategies utilize next generation sequencing (NGS) techniques to detect embryonic aneuploidy. NGS-based approaches are both more cost-effective and sensitive compared to other methods such as array comparative genomic hybridization. The increased sensitivity allows the identification of abnormalities that are challenging to detect with alternative techniques, especially mosaicism. Most NGS-based protocols are incapable of generating results within a a fresh embryo transfer (ET) compatible time frame. Moreover, the lower costs of current NGS methods, with respect to other aneuploidy detection methodologies, can only be achieved when running sequencing instruments at full capacity. This requires multiple samples to be tested in parallel and, for this reason, samples from several patients are usually batched together. Since NGS protocols are long and laborious, and given the financial need to batch samples that were often collected on different days, it is typical for blastocysts undergoing PGT-A to be vitrified after biopsy, with those found to be euploid transferred in subsequent cycles. It is critically important that any new CCS methodology is thoroughly validated prior to any clinical application,