Reduced gene templates for supervised analysis of scale-limited CRISPR-Cas9 fitness screens

Summary Pooled genome-wide CRISPR-Cas9 screens are furthering our mechanistic understanding of human biology and have allowed us to identify new oncology therapeutic targets. Scale-limited CRISPR-Cas9 screens – typically employing guide RNA libraries targeting subsets of functionally related genes, individual biological pathways, or portions of the druggable genome – constitute an optimal setting for investigating narrow hypotheses and they are easier to execute on complex models, such as organoids and in vivo models. Different supervised methods are used for the computational analysis of genome-wide CRISPR-Cas9 screens; most are not well suited for scale-limited screens as they require large sets of positive/negative control genes (gene templates) to be included among the screened ones. We have developed a computational framework identifying optimal subsets of known essential and nonessential genes (at different subsampling percentages) that can be used as templates for supervised analyses of scale-limited CRISPR-Cas9 screens, while having a reduced impact on the size of the employed library. Highlights Scale-limited CRISPR-Cas9 screens are experimentally easier than genome-wide screens Reference gene templates are used for supervised analyses of genome-wide screens Reduced templates allow supervised analyses of scale-limited CRISPR-Cas9 screens We present optimal reduced templates and a computational method to assemble them Graphical abstract