Searching journal content for articles similar to Gupta et al. 23 (6): 1008.

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  1. Methods: Targeted chromosomal deletions in human cells using zinc finger nucleases
    • Hyung Joo Lee,
    • Eunji Kim,
    • and Jin-Soo Kim
    Genome Res. January 2010 20: 81-89; Published in Advance December 1, 2009, doi:10.1101/gr.099747.109
    ...Targeted chromosomal deletions in human cells using zinc finger nucleases Hyung Joo Lee 1 , 3 , Eunji Kim 1 , 3 and Jin-Soo Kim 1 , 2 , 4 1 Department of Chemistry, Seoul National University, Gwanak-gu, Seoul 151-742, South Korea...
  2. Method: High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9
    • Gaurav K. Varshney,
    • Wuhong Pei,
    • Matthew C. LaFave,
    • Jennifer Idol,
    • Lisha Xu,
    • Viviana Gallardo,
    • Blake Carrington,
    • Kevin Bishop,
    • MaryPat Jones,
    • Mingyu Li,
    • Ursula Harper,
    • Sunny C. Huang,
    • Anupam Prakash,
    • Wenbiao Chen,
    • Raman Sood,
    • Johan Ledin,
    • and Shawn M. Burgess
    Genome Res. July 2015 25: 1030-1042; Published in Advance June 5, 2015, doi:10.1101/gr.186379.114
    .../ Cas9 is by far the most efficient gene targeting method in zebrafish. At the sequence level, indel mutations generated by these gene-editing nucleases can be classified as simple insertions, simple deletions, and complex changes that include both deletion and random insertion (Fig. 3B). Our data...
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  3. Method: Highly efficient gene knockout in mice and zebrafish with RNA-guided endonucleases
    • Young Hoon Sung,
    • Jong Min Kim,
    • Hyun-Taek Kim,
    • Jaehoon Lee,
    • Jisun Jeon,
    • Young Jin,
    • Jung-Hwa Choi,
    • Young Ho Ban,
    • Sang-Jun Ha,
    • Cheol-Hee Kim,
    • Han-Woong Lee,
    • and Jin-Soo Kim
    Genome Res. January 2014 24: 125-131; Published in Advance November 19, 2013, doi:10.1101/gr.163394.113
    ...sequences to the human . Genome Biol 10: R25. Lee HJ, Kim E, Kim JS. 2009. Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome Res 20: 81–89. Lee HJ, Kweon J, Kim E, Kim S, Kim JS. 2011. Targeted chromosomal duplications and inversions in the human using zinc finger nucleases...
  4. Method: Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair
    • Thomas O. Auer,
    • Karine Duroure,
    • Anne De Cian,
    • Jean-Paul Concordet,
    • and Filippo Del Bene
    Genome Res. January 2014 24: 142-153; Published in Advance October 31, 2013, doi:10.1101/gr.161638.113
    ...demonstrated in mouse and zebrafish (Bedell et al. 2012; Chang et al. 2013; Hwang et al. 2013a; Wang et al. 2013; Wefers et al. 2013). Inducing DSBs with TALENs or RGNs at two sites on a chromosome can be used to trigger chromosomal deletions and inversions in cultured cells and zebrafish (Carlson et al. 2012...
  5. Methods: An Efficient Method to Generate Chromosomal Rearrangements by Targeted DNA Double-Strand Breaks in Drosophila melanogaster
    • Dieter Egli,
    • Ernst Hafen,
    • and Walter Schaffner
    Genome Res. July 2004 14: 1382-1393; Published in Advance June 14, 2004, doi:10.1101/gr.2279804
    ...recombinogenic ends. Recombination with DE20 inactivates y + by inserting the 3xP3 - EGFP marker and deleting the first exon. Gene targeting to a DSB is essentially identical to the chromosomal inversion or translocation, except that in this case recombination takes place between a chromosomal and an episomal...
  6. Method: Obligate Ligation-Gated Recombination (ObLiGaRe): Custom-designed nuclease-mediated targeted integration through nonhomologous end joining
    • Marcello Maresca,
    • Victor Guosheng Lin,
    • Ning Guo,
    • and Yi Yang
    Genome Res. March 2013 23: 539-546; Published in Advance November 14, 2012, doi:10.1101/gr.145441.112
    ...targeted integration of the vector at the Nras locus without additional genomic insertion events (Fig. 3B). Clone 1 had a smaller band hybridizing to the Nras-specific probe (NR), which might represent a deleted allele present in their largely tetraploid (CasasDelucchi et al. 2011).We sequenced...
  7. LETTER: A Comparative Map of the Zebrafish Genome
    • Ian G. Woods,
    • Peter D. Kelly,
    • Felicia Chu,
    • Phuong Ngo-Hazelett,
    • Yi-Lin Yan,
    • Hui Huang,
    • John H. Postlethwait,
    • and William S. Talbot
    Genome Res. December 1, 2000 10: 1903-1914; doi:10.1101/gr.164600
    ..., apparently reflecting the relatively frequent occurrence of inversions and other intrachromosomal rearrangements since the divergence of teleost and tetrapod ancestors. Comparative mapping also shows that there is not a one-to-one correspondence between zebrafish and human chromosomes. Mapping of duplicate...
  8. ARTICLE: Zebrafish Comparative Genomics and the Origins of Vertebrate Chromosomes
    • John H. Postlethwait,
    • Ian G. Woods,
    • Phuong Ngo-Hazelett,
    • Yi-Lin Yan,
    • Peter D. Kelly,
    • Felicia Chu,
    • Hui Huang,
    • Alicia Hill-Force,
    • and William S. Talbot
    Genome Res. December 1, 2000 10: 1890-1902; doi:10.1101/gr.164800
    ...that translocations should be much more common than inversions in vertebrate evolution ( Ehrlich et al. 1997 ). If inversions are infrequent with respect to translocations, then the orthologous zebrafish and human chromosomes should be colinear. Figure 1 A compares gene orders along the corresponding chromosome...
  9. Research: Long-read sequencing for non-small-cell lung cancer genomes
    • Yoshitaka Sakamoto,
    • Liu Xu,
    • Masahide Seki,
    • Toshiyuki T. Yokoyama,
    • Masahiro Kasahara,
    • Yukie Kashima,
    • Akihiro Ohashi,
    • Yoko Shimada,
    • Noriko Motoi,
    • Katsuya Tsuchihara,
    • Susumu S. Kobayashi,
    • Takashi Kohno,
    • Yuichi Shiraishi,
    • Ayako Suzuki,
    • and Yutaka Suzuki
    Genome Res. September 2020 30: 1243-1257; Published in Advance September 4, 2020, doi:10.1101/gr.261941.120
    ...chromosomal rearrangements. In addition, we identified several medium-sized structural aberrations consisting of complex combinations of local duplications, inversions, and microdeletions. These complex mutations occurred even in key cancer-related genes, such as STK11, NF1, SMARCA4, and PTEN. The biological...
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  10. Research: Optical genome mapping identifies rare structural variants in neural tube defects
    • Nikhil S. Sahajpal,
    • Jane Dean,
    • Benjamin Hilton,
    • Timothy Fee,
    • Cindy Skinner,
    • Alex Hastie,
    • Barbara R. DuPont,
    • Alka Chaubey,
    • Michael J. Friez,
    • and Roger E. Stevenson
    Genome Res. April 2025 35: 798-809; Published in Advance March 19, 2025, doi:10.1101/gr.279318.124
    ..., copy number changes (deletions and duplications), balanced and unbalanced events (insertions, inversions, and translocations), and repeat expansions and contractions, with a higher sensitivity and resolution compared to conventional methods (Broeckel et al. 2024). The strengths and limitations of OGM...
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