{
  "abstract": "Somatic SNVs are commonly prioritized by recurrence or sequence annotation, leaving the molecular consequences of private variants unresolved. We developed PrismSNV and Ligo-Seq, a single-cell full-length transcriptome sequencing platform, to quantify transcriptomic displacement associated with within-cell SNV-state toggling. Across 26 samples from three cancer types, more than 60% of candidate SNVs showed significant cell-type-specific displacement with over 30% variation in magnitude. Sequence-based deleteriousness was poorly aligned with cellular displacement, and fewer than 3% of top-displacement SNVs across six tumor types were catalogued in ClinVar. Displacement was strongest in transcriptionally plastic, less differentiated states. Analysis of 655,349 CD4+ T-cell transcriptomes further showed that SNV-gene associations changed in magnitude and sometimes direction during activation. Lack of recurrence or clinical annotation does not imply transcriptomic inertness; variant impact is shaped by cellular context rather than sequence alone, establishing the variant-cell pair as a critical unit for interpreting somatic variation.",
  "abstract_shown": true,
  "affiliations": [
    "MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China; School of"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 29,
  "authors": [
    {
      "name": "P. Sun"
    },
    {
      "name": "P. Jia"
    },
    {
      "name": "C. Lou"
    },
    {
      "name": "X. Li"
    },
    {
      "name": "M. Li"
    },
    {
      "name": "R. Zhang"
    },
    {
      "name": "H. Lin"
    },
    {
      "name": "X. Li"
    },
    {
      "name": "Y. Zhou"
    },
    {
      "name": "S. Cai"
    },
    {
      "name": "Z. Zhang"
    },
    {
      "name": "P. Zhang"
    },
    {
      "name": "T. Xu"
    },
    {
      "name": "S. Wang"
    },
    {
      "name": "Y. Wang"
    },
    {
      "name": "M. Li"
    },
    {
      "name": "Y. Gong"
    },
    {
      "name": "G. Sang"
    },
    {
      "name": "J. Yin"
    },
    {
      "name": "J. Li"
    },
    {
      "name": "Q. Xie"
    },
    {
      "name": "Z. Yue"
    },
    {
      "name": "D. Xu"
    },
    {
      "name": "X. Yang"
    },
    {
      "name": "S. J. Bush"
    },
    {
      "name": "S. Geng"
    },
    {
      "name": "D. Meng"
    },
    {
      "name": "X. Li"
    },
    {
      "affs": [
        0
      ],
      "name": "K. Ye"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/77r75bjs1gwtp.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.28.760887",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.28.760887v1.full",
  "id": "77r75bjs1gwtp",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.28.760887v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "genetics"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.28.760887v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-28",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/77r75bjs1gwtp.ris",
  "sources": [
    {
      "first_seen": "2026-11-03T00:20:40Z",
      "native_id": "10.64898/2026.10.28.760887",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.28.760887v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:genetics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Cellular context shapes the transcriptomic impact of somatic variants",
  "title_text": "Cellular context shapes the transcriptomic impact of somatic variants",
  "type": "preprint",
  "updated_at": "2026-11-04T00:21:04Z",
  "url": "https://research.draconitic.com/paper/77r75bjs1gwtp",
  "venue": "bioRxiv",
  "versions": []
}