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Poly peak parser: method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. A hyperactive piggyBac transposase for mammalian applications. Yusa, K., Zhou, L., Li, M.A., Bradley, A. Agouti C57BL/6N embryonic stem cells for mouse genetic resources. Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression. DNA targeting specificity of RNA-guided Cas9 nucleases. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. A serious adverse event after successful gene therapy for X-linked severe combined immunodeficiency. Mouse embryonic stem cells, but not somatic cells, predominantly use homologous recombination to repair double-strand DNA breaks. Hypermutability of damaged single-strand DNA formed at double-strand breaks and uncapped telomeres in yeast Saccharomyces cerevisiae. Yang, Y., Sterling, J., Storici, F., Resnick, M.A. Microhomology-mediated end joining induces hypermutagenesis at breakpoint junctions. Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions. CRISPR/Cas9-mediated scanning for regulatory elements required for HPRT1 expression via thousands of large, programmed genomic deletions. CRISPR/Cas9 targeting events cause complex deletions and insertions at 17 sites in the mouse genome. Detailed phenotypic and molecular analyses of genetically modified mice generated by CRISPR-Cas9-mediated editing. Parikh, B.A., Beckman, D.L., Patel, S.J., White, J.M. Revealing hidden complexities of genomic rearrangements generated with Cas9. Chromosome engineering in zygotes with CRISPR/Cas9. Deletions, inversions, duplications: engineering of structural variants using CRISPR/Cas in mice. Characterization of genomic deletion efficiency mediated by CRISPR/Cas9 in mammalian cells. A model of oncogenic rearrangements: differences between chromosomal translocation mechanisms and simple double-strand break repair. Chromosomal translocations in human cells are generated by canonical nonhomologous end-joining. Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells. Off-target assessment of CRISPR-Cas9 guiding RNAs in human iPS and mouse ES cells. Tan, E.P., Li, Y., Velasco-Herrera, M.D.C., Yusa, K.
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DNA repair profiling reveals nonrandom outcomes at Cas9-mediated breaks. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Rationally engineered Cas9 nucleases with improved specificity. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Seamless gene correction of β-thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 and piggyBac. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Komor, A.C., Kim, Y.B., Packer, M.S., Zuris, J.A. Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Refining strategies to translate genome editing to the clinic.