ClockWork: Genotyping of frameshift mutations induced by CRISPR-Cas9
Summary
Here we present Clockwork, a high-throughput bioinformatics pipeline for genotyping
CRISPR-Cas9 induced frameshift mutations in single neurons. Clockwork is part of a project that
aims to elucidate the molecular mechanisms of replication-independent mutations associated with the
mutational signature SBS5. In this project key components involved in DNA repair and mutagenesis
are mutated by CRISPR-Cas9, introducing frameshift mutations and subsequently studying its effect on
the mutational rate, pattern and load. However, the success rate of CRISPR-Cas9 is highly dependent
on the local sequence context and guide sequences, with samples frequently having no mutations.
Therefore Clockwork addresses a need for genotyping successful frameshifts, saving valuable resources
by avoiding whole genome sequencing of unedited samples. Clockwork’s efficacy is interrogated with a
proof-of-concept dataset consisting of hybrid Mus musculus and Mus spretus embryonic stem cells as
well as human retinal pigment epithelium cells.