First clinical validation of whole genome screening on standard trophectoderm biopsies of preimplantation embryos

Abstract

Whole genome screening is currently not available in preimplantation genetic testing (PGT) due to poor performance of whole genome amplification methods. Here, we present the first validation study using our latest whole genome amplification (WGA) protocol, which yields amplified DNA with comparable quality to genomic DNA when perfoming whole genome sequencing assays. We started by validating PGT for aneuploidy (PGT-A) using our WGA protocol on cell lines and donated human embryos, where amplification success rates were >99.9% and 96.2% respectively. Accuracy on both was >99.9% on aneuploidy status. We next validated whole genome sequencing using amplified and genomic DNA from the Genome in the Bottle reference sample NA12878 to demonstrate accuracy, specificity, sensitivity, and precision of our WGA methods. Amplified DNA and genomic DNA are comparable in this case, with 99.99% accuracy, 99.99% specificity, 98.0% sensitivity and 98.1% precision with our WGA protocol. We additionally examined variant calls between biopsies and the remaining embryos from which they were derived. Again, 99.99% accuracy, 99.99% specificity, 98.1% sensitivity and 98.0% precision were observed. Mitochondrial heteroplasmy between biopsies and embryos was validated, and 99.9% accuracy, 100% specificity, 99.1% sensitivity and 100% precision were observed. Finally, we demonstrated the ability to improve the accuracy of certain types of mendelian variants in our data to close to 100% by leveraging parental and a born child’s genome to perform linkage analysis.

Clinical-grade whole genome sequencing-based haplarithmisis enables all forms of preimplantation genetic testing

“…We demonstrate that all mtDNA positions in the samples sequenced at 10X coverage have a mtDNA coverage of more than 100X except for one site. While prior studies have demonstrated the ability to identify mtDNA variants and heteroplasmy levels from WGS data 45,46 , integrating these into an all-in-one PGT method is an important step forward that makes PGT scalable and accessible.…”

Concordance of whole-genome amplified embryonic DNA with the subsequently born child

“…Previous research has attempted to evaluate the efficacy of whole-genome preimplantation genetic screening by comparing against born siblings and parents, attempting to statistically reconstruct the true genome of the child by identifying shared chromosomal segments [6] [7] . This screening has until recently only been available on a research but not clinical basis [8] . Imputing an embryo genome has many limitations, including that it cannot detect de-novo variants in an embryo.…”

“…Since de novo variants have a substantial impact on disease pathogenicity, employing a technology to identify and characterize these variants before an affected pregnancy begins and before childbirth is highly meaningful. Orchid Health recently released the first clinically available whole-genome preimplantation screening (PGT-WGS) utilizing custom whole-genome amplification protocols [8] . While the precision and sensitivity of whole-genome sequencing on amplified DNA have been evaluated against known inherited variants, the ability to validate and quantify the detection of inherited variants without probe development as well as de novo variants has been limited until a child screened via PGT-WGS was born [7] .…”