Agilent Technologies OnePGT solution: External verification on both blastomere and trophectoderm biopsies

Abstract

Objectives OnePGT is a genome-wide next-generation sequencing haplarithmisis-based solution designed to reinforce ranking of IVF embryos. The single workflow solution, consisting of wet-lab reagents and dedicated data analysis software, allows concurrent PGT-M (preimplantation genetic testing of monogenic disorders), PGT-SR (preimplantation genetic testing of structural rearrangements) and PGT-A (preimplantation genetic testing of aneuploidies) hence enabling enhanced genetic profiling. In collaboration with MUMC and KU Leuven, a study was set up to assess the level of concordance between OnePGT and Gold Standard analysis of both single and few cell embryo biopsies for PGT-M, PGT-SR and PGT-A. Methods A total of 227 embryo samples (191 PGT-M; 36 PGT-SR) were included in the study, consisting of 179 blastomere and 48 trophectoderm biopsies, of which 118 embryos were obtained from KU Leuven, and 109 from MUMC. For the KU Leuven site of the study, left-over whole genome amplified (WGAed) DNA from the embryo biopsies was processed, while in the MUMC site, a second biopsy was taken and WGAed. Libraries for NGS were generated using proprietary OnePGT reagents for all WGAed embryo biopsies and for bulk DNA samples from parents and reference family member(s) in case of PGT-M. Libraries were sequenced on NextSeq500 (Illumina) and resulting data were analyzed with the dedicated proprietary OnePGT software suite. Results For PGT-M analysis, a OnePGT conclusion was made for 91 % of embryos determined to be of sufficient quality (n=161). Of these, four were shown to have mitotic aberrations resulting from chromosome instability phenomenon and three did not receive a conclusion from the Gold Standard. The remaining 154 embryos showed 100% concordance with the standard PGT techniques. For PGT-SR analysis (n=36), three embryos were shown to have mitotic aberrations resulted from chromosome instability phenomenon, the remaining 33 embryos 100% concordance with the standard PGT methods. For PGT-A analysis, 100% concordance (> 50 Mb) was shown between OnePGT and standard PGT methods for which a PGT-A result was available (n=118). Conclusion The proprietary OnePGT solution, consisting of all-in-one library preparation reagents and dedicated software suite for concurrent PGT-M, PGT-SR and PGT-A in a single assay, successfully identified the presence of 26 different monogenic disorders, translocations and chromosomal aneuploidies in over 200 embryo biopsies, with a concordance rate of 100%. This indicates that this innovative genome-wide solution is expected to boost the current PGT practice and to facilitate effective ranking of IVF embryos based on enhanced genetic profiling.