A benchmark of algorithms for the analysis of pooled CRISPR screens

Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, we provide a review of the c...

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Detalles Bibliográficos
Autores principales: Bodapati, Sunil, Daley, Timothy P., Lin, Xueqiu, Zou, James, Qi, Lei S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Review
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7063732/
https://www.ncbi.nlm.nih.gov/pubmed/32151271
http://dx.doi.org/10.1186/s13059-020-01972-x
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author Bodapati, Sunil
Daley, Timothy P.
Lin, Xueqiu
Zou, James
Qi, Lei S.
author_facet Bodapati, Sunil
Daley, Timothy P.
Lin, Xueqiu
Zou, James
Qi, Lei S.
author_sort Bodapati, Sunil
collection PubMed
description Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, we provide a review of the commonly used algorithms in the computational analysis of pooled CRISPR screens. We develop a comprehensive simulation framework to benchmark and compare the performance of these algorithms using both synthetic and real datasets. Our findings inform parameter choices of CRISPR screens and provide guidance to researchers on the design and analysis of pooled CRISPR screens.
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spelling pubmed-70637322020-03-13 A benchmark of algorithms for the analysis of pooled CRISPR screens Bodapati, Sunil Daley, Timothy P. Lin, Xueqiu Zou, James Qi, Lei S. Genome Biol Review Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-pooled screens. Here, we provide a review of the commonly used algorithms in the computational analysis of pooled CRISPR screens. We develop a comprehensive simulation framework to benchmark and compare the performance of these algorithms using both synthetic and real datasets. Our findings inform parameter choices of CRISPR screens and provide guidance to researchers on the design and analysis of pooled CRISPR screens. BioMed Central 2020-03-09 /pmc/articles/PMC7063732/ /pubmed/32151271 http://dx.doi.org/10.1186/s13059-020-01972-x Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Review
Bodapati, Sunil
Daley, Timothy P.
Lin, Xueqiu
Zou, James
Qi, Lei S.
A benchmark of algorithms for the analysis of pooled CRISPR screens
title A benchmark of algorithms for the analysis of pooled CRISPR screens
title_full A benchmark of algorithms for the analysis of pooled CRISPR screens
title_fullStr A benchmark of algorithms for the analysis of pooled CRISPR screens
title_full_unstemmed A benchmark of algorithms for the analysis of pooled CRISPR screens
title_short A benchmark of algorithms for the analysis of pooled CRISPR screens
title_sort benchmark of algorithms for the analysis of pooled crispr screens
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7063732/
https://www.ncbi.nlm.nih.gov/pubmed/32151271
http://dx.doi.org/10.1186/s13059-020-01972-x
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