{
  "abstract": "Large genomic region modification, such as precise haplotype reconstitution, remains challenging due to the low efficiency of homology-directed repair (HDR) and difficulties in generating HDR templates. Here, we present a two-stage protocol for genome engineering in human induced pluripotent stem cells (hiPSCs) using CRISPR-Cas9 to generate homozygous, multi-kilobase isogenic haplotypes. We describe steps for in silico experimental design, large haplotype deletion and reconstruction, followed by edited cell line validation. This optimized protocol improves both editing efficiency and screening throughput while reducing turnaround time.\n\nFor complete details on the use and execution of this protocol, please refer to Xue et al.1",
  "abstract_shown": true,
  "affiliations": [
    "Department of Physiology, University of Arizona College of Medicine-Tucson, Tucson, AZ, USA",
    "Molecular Systems Medicine Initiative, University of Arizona Health Sciences, Tucson, AZ, USA",
    "Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Manoj K. Mishra"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Rajan Pandey"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Bhavika Therani"
    },
    {
      "affs": [
        2
      ],
      "name": "Aron M. Geurts"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Mingyu Liang"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Yong Liu"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/28333mz18t57s.bib",
  "cited_by": 0,
  "doi": "10.1016/j.xpro.2026.104927",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13733452/",
  "id": "28333mz18t57s",
  "issns": [
    "2666-1667"
  ],
  "landing_url": "https://doi.org/10.1016/j.xpro.2026.104927",
  "language": "en",
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Protocol"
    ],
    [
      "openalex",
      "1312|CRISPR and Genetic Engineering"
    ]
  ],
  "openalex": "W7224423098",
  "pdf_url": null,
  "pmcid": "PMC13733452",
  "pmid": "42955943",
  "published": "2026-10-29",
  "publisher": "Elsevier",
  "ris": "https://research.draconitic.com/paper/28333mz18t57s.ris",
  "sources": [
    {
      "first_seen": "2026-11-08T12:23:13Z",
      "native_id": "PMC13733452",
      "source": "pmc",
      "url": "https://doi.org/10.1016/j.xpro.2026.104927"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|CRISPR and Genetic Engineering",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Protocol for precise large-region haplotype modification for isogenic human iPSC generation using CRISPR-Cas9",
  "title_text": "Protocol for precise large-region haplotype modification for isogenic human iPSC generation using CRISPR-Cas9",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T12:23:13Z",
  "url": "https://research.draconitic.com/paper/28333mz18t57s",
  "venue": "STAR Protocols",
  "versions": []
}