CRISPAltRations: a validated cloud-based approach for interrogation of double-strand break repair mediated by CRISPR genome editing.
CRISPR
Cas12a
Cas9
DNA repair
amplicon sequencing
bioinformatics
genome editing
next-generation sequencing software
non-homologous end joining
off-target analysis
Journal
Molecular therapy. Methods & clinical development
ISSN: 2329-0501
Titre abrégé: Mol Ther Methods Clin Dev
Pays: United States
ID NLM: 101624857
Informations de publication
Date de publication:
11 Jun 2021
11 Jun 2021
Historique:
received:
20
11
2020
accepted:
29
03
2021
entrez:
13
5
2021
pubmed:
14
5
2021
medline:
14
5
2021
Statut:
epublish
Résumé
CRISPR systems enable targeted genome editing in a wide variety of organisms by introducing single- or double-strand DNA breaks, which are repaired using endogenous molecular pathways. Characterization of on- and off-target editing events from CRISPR proteins can be evaluated using targeted genome resequencing. We characterized DNA repair fingerprints that result from non-homologous end joining (NHEJ) after double-stranded breaks (DSBs) were introduced by Cas9 or Cas12a for >500 paired treatment/control experiments. We found that building biological understanding of the repair into a novel analysis tool (CRISPAltRations) improved the quality of the results. We validated our software using simulated, targeted amplicon sequencing data (11 guide RNAs [gRNAs] and 603 on- and off-target locations) and demonstrated that CRISPAltRations outperforms other publicly available software tools in accurately annotating CRISPR-associated indels and homology-directed repair (HDR) events. We enable non-bioinformaticians to use CRISPAltRations by developing a web-accessible, cloud-hosted deployment, which allows rapid batch processing of samples in a graphical user interface (GUI) and complies with HIPAA security standards. By ensuring that our software is thoroughly tested, version controlled, and supported with a user interface (UI), we enable resequencing analysis of CRISPR genome editing experiments to researchers no matter their skill in bioinformatics.
Identifiants
pubmed: 33981780
doi: 10.1016/j.omtm.2021.03.024
pii: S2329-0501(21)00064-4
pmc: PMC8082044
doi:
Types de publication
Journal Article
Langues
eng
Pagination
478-491Informations de copyright
© 2021 Integrated DNA Technologies, Inc.
Déclaration de conflit d'intérêts
G.K., A.M.J., M.S.M., R.T., G.R.R., N.R., H.L., L.T., M.S., Y.W., and M.A.B. are employees or paid contractors/consultants of Integrated DNA Technologies (IDT), which sells reagents used or similar to those used in this manuscript. M.M., K.F., and R.N. are employees of Illumina Inc., which provides a productized cloud-computing platform for doing NGS analysis.
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