{"doi":"10.1016/j.omtm.2021.03.024","title":"CRISPAltRations: A validated cloud-based approach for interrogation of double-strand break repair mediated by CRISPR genome editing","abstract":"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.","journal":"Molecular Therapy - Methods & Clinical Development","year":2021,"id":5946,"datarank":1.258406699267431,"base_score":3.6375861597263857,"endowment":3.6375861597263857,"self_citation_contribution":0.5456379239589579,"citation_network_contribution":0.7127687753084732,"self_endowment_contribution":0.5456379239589579,"citer_contribution":0.7127687753084732,"corpus_percentile":null,"corpus_rank":null,"citation_count":37,"citer_count":23,"citers_with_citation_signal":20,"citers_with_endowment":20,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0481,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-06-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":18366,"name":"Rolf Turk","orcid":"0000-0003-1283-9594","position":1,"is_corresponding":false},{"id":30887,"name":"Alexandra P. Lewis","orcid":"0000-0002-6195-4786","position":2,"is_corresponding":false},{"id":56599,"name":"Nathan Roberts","orcid":"0000-0002-8955-1823","position":3,"is_corresponding":false},{"id":18368,"name":"Garrett R. Rettig","orcid":"0000-0003-4634-5787","position":4,"is_corresponding":false},{"id":56600,"name":"Ashley M. Jacobi","orcid":"0000-0002-9364-6518","position":5,"is_corresponding":false},{"id":56601,"name":"Lauren Tso","orcid":null,"position":6,"is_corresponding":false},{"id":56602,"name":"Morgan Sturgeon","orcid":"0000-0003-4814-1446","position":7,"is_corresponding":false},{"id":56603,"name":"Massimo Mertens","orcid":null,"position":8,"is_corresponding":false},{"id":56604,"name":"Roel Noten","orcid":null,"position":9,"is_corresponding":false},{"id":56605,"name":"Kurt Florus","orcid":null,"position":10,"is_corresponding":false},{"id":18371,"name":"Mark A. Behlke","orcid":"0000-0002-4218-857X","position":11,"is_corresponding":false},{"id":22277,"name":"Yu Wang","orcid":"0000-0003-4635-7059","position":12,"is_corresponding":false},{"id":18369,"name":"Matthew S. McNeill","orcid":"0000-0002-8737-785X","position":13,"is_corresponding":false},{"id":18370,"name":"Gavin Kurgan","orcid":"0000-0002-4047-1427","position":0,"is_corresponding":true}],"reference_count":68,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}