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Bioinformatics. 2014 Oct 15;30(20):2968-70. doi: 10.1093/bioinformatics/btu427. Epub 2014 Jul 1.

Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA).

Author information

1
Department of Genetics and Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115 and Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA.
2
Department of Genetics and Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115 and Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA Department of Genetics and Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115 and Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA.

Abstract

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.

PMID:
24990609
PMCID:
PMC4184265
DOI:
10.1093/bioinformatics/btu427
[Indexed for MEDLINE]
Free PMC Article
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