Clinical-grade whole genome sequencing-based haplarithmisis enables all forms of preimplantation genetic testing.
Janssen AEJ., Koeck RM., Essers R., Cao P., van Dijk W., Drüsedau M., Meekels J., Yaldiz B., van de Vorst M., de Koning B., Hellebrekers DMEI., Stevens SJC., Sun SM., Heijligers M., de Munnik SA., van Uum CMJ., Achten J., Hamers L., Naghdi M., Vissers LELM., van Golde RJT., de Wert G., Dreesen JCFM., de Die-Smulders C., Coonen E., Brunner HG., van den Wijngaard A., Paulussen ADC., Zamani Esteki M.
High-throughput sequencing technologies have increasingly led to discovery of disease-causing genetic variants, primarily in postnatal multi-cell DNA samples. However, applying these technologies to preimplantation genetic testing (PGT) in nuclear or mitochondrial DNA from single or few-cells biopsied from in vitro fertilised (IVF) embryos is challenging. PGT aims to select IVF embryos without genetic abnormalities. Although genotyping-by-sequencing (GBS)-based haplotyping methods enabled PGT for monogenic disorders (PGT-M), structural rearrangements (PGT-SR), and aneuploidies (PGT-A), they are labour intensive, only partially cover the genome and are troublesome for difficult loci and consanguineous couples. Here, we devise a simple, scalable and universal whole genome sequencing haplarithmisis-based approach enabling all forms of PGT in a single assay. In a comparison to state-of-the-art GBS-based PGT for nuclear DNA, shallow sequencing-based PGT, and PCR-based PGT for mitochondrial DNA, our approach alleviates technical limitations by decreasing whole genome amplification artifacts by 68.4%, increasing breadth of coverage by at least 4-fold, and reducing wet-lab turn-around-time by ~2.5-fold. Importantly, this method enables trio-based PGT-A for aneuploidy origin, an approach we coin PGT-AO, detects translocation breakpoints, and nuclear and mitochondrial single nucleotide variants and indels in base-resolution.