ArticleNucleic acids research2021
Marker-free quantification of repair pathway utilization at Cas9-induced double-strand breaks.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Polθ activity modulates sensitivity to standard therapies in DNMT3A-deficient leukemia.Cell reports. Medicine · 2026Article
- Condensins regulate resection-dependent DNA double-strand break repair pathways in replicated chromatin.Nucleic acids research · 2026Article
- Distinctive molecular features of radiation-induced thyroid cancers.Science advances · 2025Article
- PALB2 and 53BP1 govern post-resection homologous recombination DNA repair.Molecular cell · 2025Article
- Refined DNA repair manipulation enables a universal knock-in strategy in mouse embryos.Nature communications · 2025Article
- Article
- DNA repair and the contribution to chemotherapy resistance.Genome medicine · 2025Review
- The interplay of DNA repair context with target sequence predictably biases Cas9-generated mutations.Nature communications · 2024Article
- The interplay of DNA repair context with target sequence predictably biases Cas9-generated mutations.bioRxiv : the preprint server for biology · 2024Article
- ATM inhibition exploits checkpoint defects and ATM-dependent double strand break repair in TP53-mutant glioblastoma.Nature communications · 2024Article
- Sequential requirements for distinct Polθ domains during theta-mediated end joining.Molecular cell · 2024Article
- Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier.Nature communications · 2024Article
- Genetic separation of Brca1 functions reveal mutation-dependent Polθ vulnerabilities.Nature communications · 2023Article
- Article
- Discovery of a 53BP1 Small Molecule Antagonist Using a Focused DNA-Encoded Library Screen.Journal of medicinal chemistry · 2023Article
- Regulation of gene editing using T-DNA concatenation.Nature plants · 2023Article
- BMN673 Is a PARP Inhibitor with Unique Radiosensitizing Properties: Mechanisms and Potential in Radiation Therapy.Cancers · 2022Review
- To indel or not to indel: Factors influencing mutagenesis during chromosomal break end joining.DNA repair · 2022Review
- SIQ: easy quantitative measurement of mutation profiles in sequencing data.NAR genomics and bioinformatics · 2022Article
- Poly(ADP) ribose polymerase promotes DNA polymerase theta-mediated end joining by activation of end resection.Nature communications · 2022Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Genome integrity and genome engineering require efficient repair of DNA double-strand breaks (DSBs) by non-homologous end joining (NHEJ), homologous recombination (HR), or alternative end-joining pathways. Here we describe two complementary methods for marker-free quantification of DSB repair pathway utilization at Cas9-targeted chromosomal DSBs in mammalian cells. The first assay features the analysis of amplicon next-generation sequencing data using ScarMapper, an iterative break-associated alignment algorithm to classify individual repair products based on deletion size, microhomology usage, and insertions. The second assay uses repair pathway-specific droplet digital PCR assays ('PathSig-dPCR') for absolute quantification of signature DSB repair outcomes. We show that ScarMapper and PathSig-dPCR enable comprehensive assessment of repair pathway utilization in different cell models, after a variety of experimental perturbations. We use these assays to measure the differential impact of DNA end resection on NHEJ, HR and polymerase theta-mediated end joining (TMEJ) repair. These approaches are adaptable to any cellular model system and genomic locus where Cas9-mediated targeting is feasible. Thus, ScarMapper and PathSig-dPCR allow for systematic fate mapping of a targeted DSB with facile and accurate quantification of DSB repair pathway choice at endogenous chromosomal loci.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.