PT  - JOURNAL ARTICLE
AU  - Julie A. Dias
AU  - Shibing Deng
AU  - Vinicius Bonato
TI  - Computational correction of cell-specific gene-independent effects in CRISPR-Cas9 essentiality screens: REStricted CUbic SplinEs with Mixed Models (RESCUE-MM)
AID  - 10.1101/2021.10.22.465496
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.10.22.465496
4099  - http://biorxiv.org/content/early/2021/10/24/2021.10.22.465496.short
4100  - http://biorxiv.org/content/early/2021/10/24/2021.10.22.465496.full
AB  - Increased gene copy number has been associated with a greater antiproliferative response upon genome editing, regardless of the true essentiality profile of the targeted gene. Many methods have been developed to adjust for genomic copy number technical artifacts. Existing methods use a two-step correction by pre-processing the data prior to the final analysis. It has been shown that two-step corrections can produce unreliable results, due to the creation of a correlation structure in the corrected data. If this structure is unaccounted for, gene-essentiality levels can be inflated or underestimated, affecting the False Discovery Rate (FDR). We propose a one-step correction using restricted cubic splines (RCS) to be a simpler alternative which reduces the bias in downstream analyses. Moreover, most existing methods combine guide-level results to yield gene-level estimates which can misrepresent the true gene essentiality profile depending on the guide-averaging method. Our model-based approach (RESCUE-MM) for copy number correction provides a more flexible framework that allows for guide-level essentiality estimation while accommodating more complex designs with grouped data. We provide comparisons to existing copy number correction methods and suggest how to include copy number adjustment in a one-step correction fashion in multiple experimental designs.Competing Interest StatementVinicius Bonato and Shibing Deng are currently full time employees at Pfizer Inc. Julie-Alexia Dias received payment as working for Pfizer as a summer intern student from May until August of 2021.