Demonstration of accurate whole genome sequencing and haplotyping of blastocyst biopsies as the ultimate pre-implantation genetic test. Homo sapiens

Currently, the methods available for pre-implantation genetic diagnosis (PGD) of in vitro fertilized embryos can be blind to a large number of potential genomic defects, especially de novo mutations which have been shown to cause a large fraction of genetic diseases. Here we describe the analysis of the embryonic genome by advanced, highly accurate whole genome sequencing (WGS) technologies. 9 biopsies of up to 10 cells from 7 blastocyst-stage embryos and blood samples from both parents and paternal grandparents were analysed by WGS; 87%-97% of the genome was confidently called in each sample. In a subset of embryos, high quality WGS with haplotype data were also generated using Long Fragment Read (LFR) technology. In these LFR-analysed embryos we demonstrate a detection rate of up to 82% of de novo single nucleotide variants (SNVs) with a false positive rate of as few as 1.3 errors per Gb resulting in fewer than 10 false heterozygous SNVs per embryo. This is the first demonstration that cost-effective advanced WGS can be used as the ultimate PGD to avoid implanting a substantial proportion of the embryos with inherited or de novo disease-causing genetic defects, from point mutations to large structural variants, with a tolerable misdiagnosis rate of healthy embryos due to sequencing errors.