Precision Embryo Genotyping and CRISPR Chromosome Deletions (Genomic Prediction)

This recent Cell paper received a lot of attention as it suggests that CRISPR editing can result in chromosome loss. It was cited in the recent National Academies report Heritable Human Genome Editing (2020) as an example of unexpected consequences / side-effects from CRISPR.

Allele-Specific Chromosome Removal after Cas9 Cleavage in Human Embryos 

https://doi.org/10.1016/j.cell.2020.10.025  

Correction of disease-causing mutations in human embryos holds the potential to reduce the burden of inherited genetic disorders and improve fertility treatments for couples with disease-causing mutations in lieu of embryo selection. Here, we evaluate repair outcomes of a Cas9-induced double-strand break (DSB) introduced on the paternal chromosome at the EYS locus, which carries a frameshift mutation causing blindness. We show that the most common repair outcome is microhomology-mediated end joining, which occurs during the first cell cycle in the zygote, leading to embryos with non-mosaic restoration of the reading frame. Notably, about half of the breaks remain unrepaired, resulting in an undetectable paternal allele and, after mitosis, loss of one or both chromosomal arms. Correspondingly, Cas9 off-target cleavage results in chromosomal losses and hemizygous indels because of cleavage of both alleles. These results demonstrate the ability to manipulate chromosome content and reveal significant challenges for mutation correction in human embryos. 

BioRxiv preprint 

My Genomic Prediction colleagues Jia Xu, Diego Marin, and Nathan Treff are co-authors of the paper. GP's precision embryo genotyping capabilities were necessary to determine that a paternal chromosome is sometimes deleted in the embryo due to CRISPR. In GP's standard embryo testing process both parents are genotyped as well as the embryo. The parental genotypes are used to error correct the embryo genotype: DNA amplification starting from just a few biopsied cells introduces noise, but it can be removed. GP can determine whether specific alleles from a parent are present in the embryo. Detection of the deletion of an entire chunk of chromosome would be fairly straightforward.

WIRED: In Embryos, Crispr Can Cut Out Whole Chromosomes—That's Bad