Phenomics-Based Quantification of CRISPR-Induced Mosaicism in Zebrafish

Genetic mosaicism can manifest as spatially variable phenotypes that vary from site to site within an organism. Here, we use imaging-based phenomics to quantitate phenotypes at many sites within the axial skeleton of CRISPR-edited G0 zebrafish. Through characterization of loss-of-function cell clusters in the developing skeleton, we identify a distinctive size distribution shown to arise from clonal fragmentation and merger events. We quantitate the phenotypic mosaicism produced by somatic mutations of two genes, plod2 and bmp1a, implicated in human osteogenesis imperfecta. Comparison of somatic, CRISPR-generated G0 mutants to homozygous germline mutants reveals phenotypic convergence, suggesting that CRISPR screens of G0 animals can faithfully recapitulate the biology of inbred disease models. We describe statistical frameworks for phenomic analysis of spatial phenotypic variation present in somatic G0 mutants. In sum, this study defines an approach for decoding spatially variable phenotypes generated during CRISPR-based screens. [Display omitted] •Clonal clusters arising from CRISPR editing follow a universal size distribution•Distinct phenotypic patterns arise from mosaic gene loss•Large-scale phenotyping heightens sensitivity in detecting somatic mutant populations Genetic mosaicism manifests as spatially variable phenotypes, whose detection and interpretation remain challenging. Watson et al. identify biological factors influencing phenotypic patterns in the skeletons of CRISPR-edited mosaic zebrafish and establish methods for their detection using large-scale phenotyping.