OnePGT: A single workflow for concurrent PGT-M, PGT-SR and PGT-A on blastomere and trophectoderm biopsies
Aimee Paulussen1, Cindy Melotte2, Edith Coonen3, Jos Dreesen4, John Dumoulin5, Chris Van Uum6, Marion Drüsedau6, John Engelen1, Kasper Derks7, Ron Van Golde5, Eftychia Dimitriadou2, Heleen Masset2, Katrien François8, Joke Allemeersch9, Rebecca Richards8, Sara Moeys8, Jessie Theuns10, Masoud Zamani Esteki11, Christine de Die-Smulders1, Joris Vermeesch12
1Maastricht University Medical Center, Maastricht, Netherlands
2Center for Human Genetics, University hospital of Leuven, KU Leuven, Leuven, Belgium
31Department of Clinical Genetics and 2Center for Reproductive Medicine, GROW School for Oncology and Developmental Biology Maastricht University Medical Center+, Maastricht, Netherlands
4dept of Clinical Genetics, Maastricht, Netherlands
5Center for Reproductive Medicine, GROW School for Oncology and Developmental Biology, Maastricht, Netherlands
6Department of Clinical Genetics, GROW School for Oncology and Developmental Biology Maastricht University Medical Center+, Maastricht, Netherlands
7Department of Clinical Genetics, GROW School for Oncology and Developmental Biology Maastricht University Medical Center+, Maastricht, Oman
8Agilent Technologies, Diagnostics and Genomics Group, Leuven, Belgium
9Agilent Technologies, Leuven, Belgium
10Agilent Technologies, Niel, Belgium
111Department of Clinical Genetics, GROW School for Oncology and Developmental Biology Maastricht University Medical Center+; 3Center for Human Genetics, University hospital of Leuven, KU Leuven, Maastricht, Netherlands
12Center for Medical genetics, Katholieke Universiteit Leuven, Leuven, Belgium
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 (Pre-implantation genetic testing of monogenic disorders), PGT-SR (Pre implantation genetic testing of structural rearrangements) and PGT-A (Pre implantation genetic testing of aneuploidies) hence enables enhanced genetic profiling.
In collaboration with MUMC and KULeuven, 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, 179 blastomere and 48 trophectoderm biopsies, were included in the study; 118 embryos were obtained from KULeuven, and 109 from MUMC. For the KULeuven-arm of the study, left-over whole genome amplified DNA from the embryo biopsies was processed, while in the MUMC-arm, a second biopsy was taken and amplified. NGS libraries were generated using proprietary OnePGT reagents for all WGA embryo samples and for gDNA 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 tools.
Results
A OnePGT call was made in 90.5 % of the embryos analyzed for PGT-M. Of these, 92% were included in concordance analysis, resulting in 100% concordance. The samples excluded from concordance analysis, are under further investigation.
For PGT-SR, 36 embryos from MUMC were included in the study and fully analyzed. Due to mitotic errors, 3 embryos had to be excluded from concordance analysis. Of the remaining 33, all embryos (100%) were concordant with the Gold Standard.
On the embryos obtained via UZLeuven, a PGT-A analysis was performed and 100% concordance was obtained for chromosomal aberrations > 50 Mb (limit reference method).
Conclusions
The proprietary OnePGT solution, consisting of all-in-one library preparation reagents and dedicated software for concurrent analysis of PGT-M, PGT-SR and PGT-A on a single embryo biopsy, successfully identified the presence of 26 different SGDs, translocations and chromosomal aneuploidies in over 200 embryo biopsies, with a concordance of 100% for PGT-M, PGT-SR and PGT-A. Hence this innovative genome-wide solution is expected to be of added value to improve ranking of IVF embryos based on enhanced genetic profiling.
