Efficient strategies to detect genome editing and integrity in CRISPR-Cas9 engineered ESCs

CRISPR-mediated genome engineering provides a powerful tool to study the function of genes and proteins. In the past decades, the advances in genome and transcriptome sequencing techniques have shed light on the genetic causes underlying many human diseases, such as neurodevelopmental disabilities or cancer. Sometimes, a single point-mutation in a protein coding gene has been identified as the primary cause of the disease. CRISPR-Cas offers the possibility to introduce or remove such a mutation of interest to understand disease mechanisms and even bears therapeutic potential. We describe the adaptation of an experimental strategy that allows the mutation of protein residues in mouse embryonic stem cells (ESCs) and propose a new screening method, Mismatch-qPCR, to reliably detect editing events in clonal cell lines as an alternative to restriction digest or Sanger sequencing. Finally, we show that RNA-Sequencing (RNA-Seq) data or low-coverage genomic sequencing data can be used to detect large chromosomal deletions and rearrangements that frequently occur at the CRISPR-targeting site.