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Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA)
Open accessAbstract
Summary: Clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies have revolutionized human genome engineering and opened countless possibilities to basic science, synthetic biology and gene therapy. Albeit the enormous potential of these tools, their performance is far from perfect. It is essential to perform a posterior careful analysis of the gene editing experiment. However, there are no computational tools for genome editing assessment yet, and current experimental tools lack sensitivity and flexibility. We present a platform to assess the quality of a genome editing experiment only with three mouse clicks. The method evaluates next-generation data to quantify and characterize insertions, deletions and homologous recombination. CRISPR Genome Analyzer provides a report for the locus selected, which includes a quantification of the edited site and the analysis of the different alterations detected. The platform maps the reads, estimates and locates insertions and deletions, computes the allele replacement efficiency and provides a report integrating all the information. Availability and implementation: CRISPR-GA Web is available at http://crispr-ga.net . Documentation on CRISPR-GA instructions can be found at http://crispr-ga.net/documentation.html Contact: mguell@genetics.med.harvard.edu
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“The limit of detection in these experiments is based on the inherent error rate of the Illumina platform (up to 0.4%), which has previously been described for genome editing experiment analyzed by NGS71–73.”
From A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells (2018) · cites this paper as [73]
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Metadata
- Authors
- Güell, M., Yang, L., & Church, G. M.
- Affiliations
- Harvard University (US)
- Corresponding author
- Church, George M.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-07-01
- Volume
- 30
- Issue
- 20
- Pages
- 2968-2970
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC4184265
- OpenAlex
- W2161871693
- Semantic Scholar
- 513d19c6d364f6a5d5c30c3a2edd41581cc2f9b0
- Cited by
- 142
- References
- 19
- Citations by year
- 2026: 1 · 2025: 8 · 2024: 9 · 2023: 11 · 2022: 11 · 2021: 16 · 2020: 18 · 2019: 13 · 2018: 16 · 2017: 11 · 2016: 13 · 2015: 8 · 2014: 7
- FWCI
- 5.33
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (P50HG005550, HG005550)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- CRISPR gene editing, indels, homologous recombination, next-generation sequencing data analysis, web-based analysis tool
- MeSH terms
- Alleles, Genetic Engineering, Humans, User-Computer Interface, Genome, Human, Genomics, High-Throughput Nucleotide Sequencing, Clustered Regularly Interspaced Short Palindromic Repeats
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