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

Affiliations
  • 1Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands.
  • 2Department of Genetics and Cell Biology, GROW Research Institute Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands.
  • 3Faculty of Psychology and Neuroscience, Section Applied Social Psychology, Maastricht University, Maastricht, The Netherlands.
  • 4Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands.
  • 5Department of Obstetrics and Gynaecology, GROW Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands.
  • 6Department of Health, Ethics and Society, GROW Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands.
  • 7CAPHRI Research Institute for Public Health and Primary Care, Maastricht University, Maastricht, The Netherlands.
  • 8Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands. masoud.zamaniesteki@mumc.nl.
  • 9Department of Genetics and Cell Biology, GROW Research Institute Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands. masoud.zamaniesteki@mumc.nl.
  • 10Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention & Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden. masoud.zamaniesteki@mumc.nl.

|

Abstract

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.