Login / Signup

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

Anouk E J JanssenRebekka M KoeckRick EssersPing CaoWanwisa van DijkMarion DrüsedauJeroen MeekelsBurcu YaldizMaartje van de VorstBart de KoningDebby M E I HellebrekersServi J C StevensSu Ming SunMalou HeijligersSonja A de MunnikChris M J van UumJelle AchtenLars HamersMarjan NaghdiLisenka E L M VissersRon J T van GoldeGuido M W R De WertJos C F M DreesenChristine de Die-SmuldersEdith CoonenHan G BrunnerArthur van den WijngaardAimée D C PaulussenMasoud Zamani Esteki
Published in: Nature communications (2024)
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.
Keyphrases
  • mitochondrial dna
  • copy number
  • genome wide
  • single cell
  • high throughput
  • stem cells
  • healthcare
  • pregnant women
  • small molecule
  • cell death
  • mesenchymal stem cells
  • sensitive detection
  • affordable care act