Methods and applications of in vivo CRISPR screening

A fundamental goal in genetics is to understand the connection between genotype and phenotype in health and disease. Genetic screens in which dozens to thousands of genetic elements are perturbed in a pooled fashion offer the opportunity to generate large-scale, information-rich and unbiased genotype–phenotype maps. Although typically applied in reductionist in vitro settings, methods enabling pooled CRISPR–Cas perturbation screening in vivo are gaining attention as they have the potential to accelerate the discovery and annotation of gene function across cells, tissues, developmental stages, disease states and species. In this Review, we discuss essential criteria for understanding, designing and implementing in vivo screening experiments, with a focus on pooled CRISPR-based screens in mice. We also highlight how the resulting datasets, combined with advances in multi-omics and artificial intelligence, will accelerate progress and enable fundamental discoveries across basic and translational sciences. In vivo CRISPR screens generate high-throughput, unbiased genotype–phenotypes maps for complex biological processes that cannot be studied in vitro. This Review outlines key criteria for understanding, designing and implementing such screens and discusses their potential impact on basic and translational research.