{
  "abstract": "Accurate quantification of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-induced insertions and deletions (indels) is essential in chicken genome-editing studies, where low editing efficiencies and mosaicism can complicate the assessment of target-site modifications. Existing assays often involve a trade-off between affordability and the sensitivity orsequence information needed for detailed analysis. Here, we introduce IndelQuant, a cost-efficient workflow integrating sample-specific barcode PCR, pooled amplicon library construction, AdapterRemoval3-based read processing, and CRISPResso2-based indel quantification. The workflow provides graphical and tabularsummaries of editing efficiency, indel positions, indel-size distributions, and sample-level mutation profiles. We evaluated the workflow in TYR-edited DF-1 cells and genome-edited chickens. In edited chickens, IndelQuant detected tissue-specific indel signals, most below 5%, while negative controls showed background frequencies from 0 to 0.03%. These findings indicate that IndelQuant retains the sequence-level information provided by amplicon sequencing while simplifying sample processing and analysis, offering a practical approach to routine screening for low-frequency and mosaic indels in poultry genome-editing studies.",
  "abstract_shown": true,
  "affiliations": [
    "School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China",
    "School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China",
    "Carilion Clinic, Roanoke, VA 24016, USA"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Yujuan Duan"
    },
    {
      "affs": [
        0
      ],
      "name": "Ke Xu"
    },
    {
      "affs": [
        0
      ],
      "name": "Hao Zhou"
    },
    {
      "affs": [
        0
      ],
      "name": "Chuan He"
    },
    {
      "affs": [
        0
      ],
      "name": "Jinmei Ding"
    },
    {
      "affs": [
        0
      ],
      "name": "Chao Qin",
      "orcid": "0009-0003-2566-7119"
    },
    {
      "affs": [
        2
      ],
      "name": "Yan Zhang",
      "orcid": "0000-0003-0906-9410"
    },
    {
      "affs": [
        1
      ],
      "name": "Chengxiao Han",
      "orcid": "0000-0003-0767-7818"
    },
    {
      "affs": [
        0
      ],
      "name": "He Meng",
      "orcid": "0000-0002-3374-2241"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/2yakemxn7awaz.bib",
  "cited_by": 0,
  "doi": "10.3390/ijms27209054",
  "fulltext_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13705014/?tool=EBI",
  "id": "2yakemxn7awaz",
  "issns": [
    "1422-0067"
  ],
  "landing_url": "https://www.mdpi.com/1422-0067/27/20/9054",
  "language": "eng",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|CRISPR and Genetic Engineering"
    ]
  ],
  "openalex": "W7221674756",
  "pdf_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13705014/pdf/?tool=EBI",
  "pmcid": "PMC13705014",
  "pmid": null,
  "published": "2026-10-01",
  "publisher": "MDPI AG",
  "ris": "https://research.draconitic.com/paper/2yakemxn7awaz.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:55Z",
      "native_id": "10.3390/ijms27209054",
      "source": "crossref",
      "url": "https://www.mdpi.com/1422-0067/27/20/9054"
    },
    {
      "first_seen": "2026-10-30T12:21:34Z",
      "native_id": "PMC:PMC13705014",
      "source": "europepmc",
      "url": "https://europepmc.org/article/PMC/PMC13705014"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|CRISPR and Genetic Engineering",
      "subfield": "molecular-biology"
    }
  ],
  "title": "IndelQuant: A Workflow for Cost-Efficient Amplicon Sequencing Analysis of Genome-Edited Chickens",
  "title_text": "IndelQuant: A Workflow for Cost-Efficient Amplicon Sequencing Analysis of Genome-Edited Chickens",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:21:34Z",
  "url": "https://research.draconitic.com/paper/2yakemxn7awaz",
  "venue": "International Journal of Molecular Sciences",
  "versions": []
}