Ushering in the Next CRISPR Decade

Barrangou, Rodolphe

doi:10.1089/crispr.2020.29085.rba

Cited by 2 publications

(3 citation statements)

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“…• 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 Introduction CRISPR-Cas9 knockout (KO) screens are powerful tools that have ushered a new era for genomic research (Shalem et al 2014;Hartenian and Doench 2015;Barrangou 2020). One of the main successful applications of this technology has been the identification of genes essential for cancer cell survival (i.e.…”

Section: Highlightsmentioning

confidence: 99%

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

Vinceti

Perron

Trastulla

et al. 2022

Preprint

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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

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Section: Highlightsmentioning

confidence: 99%

“…CRISPR-Cas9 knockout (KO) screens are powerful tools that have ushered a new era for genomic research (Barrangou, 2020; Hartenian and Doench, 2015; Shalem et al, 2014). One of the main successful applications of this technology has been the identification of genes essential for cancer cell survival (i.e.…”

Section: Introductionmentioning

confidence: 99%

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

Vinceti

Perron

Trastulla

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…INTRODUCTION CRISPR-Cas9 knockout (KO) screens are powerful tools that have ushered in a new era for genomic research (Shalem et al, 2014;Hartenian and Doench, 2015;Barrangou, 2020). One of the main successful applications of this technology has been the identification of genes that are essential for cancer cell survival (i.e., fitness genes) at a genome scale to support the discovery of new cancer dependencies and therapeutic targets (Tzelepis et al, 2016;Meyers et al, 2017;Tsherniak et al, 2017;Behan et al, 2019), while also widely improving our understanding of human biology (Zhou et al, 2014;Shalem et al, 2015).…”

Section: In Briefmentioning

confidence: 99%