PT  - JOURNAL ARTICLE
AU  - Anders Rasmussen
AU  - Tarmo Äijö
AU  - Mariano Ignacio Gabitto
AU  - Nicholas Carriero
AU  - Neville Sanjana
AU  - Jane Skok
AU  - Richard Bonneau
TI  - CRISPR-Decryptr reveals cis-regulatory elements from noncoding perturbation screens
AID  - 10.1101/2020.08.13.247007
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.08.13.247007
4099  - http://biorxiv.org/content/early/2020/08/19/2020.08.13.247007.short
4100  - http://biorxiv.org/content/early/2020/08/19/2020.08.13.247007.full
AB  - Clustered Regularly Interspace Short Palindromic Repeats (CRISPR)-Cas9 genome editing methods provide the tools necessary to examine phenotypic impacts of targeted perturbations in high-throughput screens. While these technologies have the potential to reveal functional elements with direct therapeutic applications, statistical techniques to analyze noncoding screen data remain limited. We present CRISPR-Decryptr, a computational tool for the analysis of CRISPR noncoding screens. Our method leverages experimental design: accounting for multiple conditions, controls, and replicates to infer the regulatory landscape of noncoding genomic regions. We validate our method on a variety of mutagenesis, CRISPR activation, and CRISPR interference screens, extracting new insights from previously published data.Competing Interest StatementA.R. owns stock in Editas medicine and 10x Genomics. T.A. owns stock in 10x Genomics. R.B. has ongoing or recent consulting or advisory relationships with Eli Lily, Merus, Merck and Epistemic AI.