NGS-based pipeline for routine non-invasive pre-implantation genetic assessment in IVF

Non-invasive pre-implantation genetic testing for aneuploidy (NIPGT-A) approach facilitates pre-implantation embryo assessment by identifying chromosomal ploidy of the embryo from its culture medium. One of the key limitations of it is the absence of a recommendation for its application to everyday clinical practice. Our objective in this study was to provide a comprehensive workflow for a clinically applicable strategy for NIPGT-A based on next-generation sequencing (NGS) technology and an optimised bioinformatic pipeline. We performed NGS of spent blastocyst culture media of Day 3 embryos fertilised with intracytoplasmic sperm injection (ICSI) with quality score on morphology assessment using the blank culture media as background control. Chromosomal abnormalities were identified by an optimised bioinformatics pipeline based on copy number variation (CNV) detecting algorithm. In this proof of concept, we demonstrate a comprehensive workflow covering both wet- and dry-lab procedures supporting a clinically applicable strategy for NIPGT-A and can be carried out within 48 hours, which is critical for the precious assessment of the same-cycle blastocyst transfer. The described integrated approach of non-invasive evaluation of embryonic DNA content of the culture media can potentially supplement existing pre-implantation genetic screening methods.