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

Abstract

SummaryPooled 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.HighlightsScale-limited CRISPR-Cas9 screens are experimentally easier than genome-wide screensReference gene templates (RTs) are used for supervised analyses of genome-wide screensReduced RTs allow supervised analyses of scale-limited CRISPR-Cas9 screensWe present optimal reduced RTs and a computational method to assemble themGraphical abstract