{
  "abstract": "DNA ploidy is an important predictor of tumor behavior and prognosis, and its accurate estimation is essential for robust genomic analysis in translational cancer research and diagnostics. However, the most common in silico methods for ploidy estimation using next-generation-sequencing-based copy-number aberration (CNA)-calling algorithms are often inaccurate due to inherent ambiguity in fitting ploidy solutions. This study evaluates the accuracy of state-of-the-art CNA callers using whole-genome sequencing by comparing their ploidy estimates with gold-standard ploidy measurements derived by flow cytometry (FC). We demonstrate that CNA callers are up to 38% inaccurate in cancers with complex genomes, which impacts the accurate estimation of copy number of cancer genes and could have clinical implications and impacts on inferences of tumor evolution. Critically, flow-cytometry-based calibration of CNA callers yields highly accurate ploidy estimates (ρPearson = 0.92, p < 0.001), providing a robust solution to the substantial inaccuracies that compromise clinical decision-making and evolutionary inference in complex cancers.",
  "abstract_shown": true,
  "affiliations": [
    "Research Department of Pathology, Cancer Institute, University College London, London, UK",
    "University College London Medical School, London, UK",
    "European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK",
    "Department of Pathology, Royal National Orthopaedic Hospital, Stanmore, UK",
    "IRIBHM Jacques E. Dumont, Université Libre de Bruxelles, Brussels, Belgium",
    "University of California, San Diego, San Diego, CA, USA",
    "Research Department of Oncology, University College London, London, UK",
    "Flow Cytometry TTP, Cancer Institute, University College London, London, UK",
    "Wellcome Sanger Institute, Cambridge, UK",
    "Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA",
    "Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 21,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Thomas Butters"
    },
    {
      "affs": [
        0
      ],
      "name": "Dahmane Oukrif"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Punn Tannirandorn"
    },
    {
      "affs": [
        2
      ],
      "name": "Ianthe AEM van Belzen"
    },
    {
      "affs": [
        0
      ],
      "name": "Jianan Chen"
    },
    {
      "affs": [
        0
      ],
      "name": "Christopher Davies"
    },
    {
      "affs": [
        0
      ],
      "name": "Runtian Lin"
    },
    {
      "affs": [
        0,
        3
      ],
      "name": "Solange De Noon"
    },
    {
      "affs": [
        4
      ],
      "name": "Dalil Taher"
    },
    {
      "affs": [
        1
      ],
      "name": "Chloe Cutler"
    },
    {
      "affs": [
        1
      ],
      "name": "Mark Markov"
    },
    {
      "affs": [
        3
      ],
      "name": "Anna Tollit"
    },
    {
      "affs": [
        3
      ],
      "name": "Fatine Oumlil"
    },
    {
      "affs": [
        5
      ],
      "name": "Christopher D. Steele"
    },
    {
      "affs": [
        6
      ],
      "name": "Matthew Fittall"
    },
    {
      "affs": [
        7
      ],
      "name": "Yanping Guo"
    },
    {
      "affs": [
        2,
        8
      ],
      "name": "Isidro Cortés-Ciriano"
    },
    {
      "affs": [
        9,
        10
      ],
      "name": "Peter Van Loo"
    },
    {
      "affs": [
        0,
        3
      ],
      "name": "Adrienne M. Flanagan"
    },
    {
      "affs": [
        0,
        3
      ],
      "name": "Nischalan Pillay"
    },
    {
      "affs": [
        1,
        4
      ],
      "name": "Maxime Tarabichi"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/730hhrhbhcf0e.bib",
  "cited_by": 0,
  "doi": "10.1016/j.crmeth.2026.101570",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13721756/",
  "id": "730hhrhbhcf0e",
  "issns": [
    "2667-2375"
  ],
  "landing_url": "https://doi.org/10.1016/j.crmeth.2026.101570",
  "language": "en",
  "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": [
    [
      "heading",
      "Article"
    ],
    [
      "openalex",
      "1306|Cancer Genomics and Diagnostics"
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  "openalex": "W7204818616",
  "pdf_url": null,
  "pmcid": "PMC13721756",
  "pmid": "42673959",
  "published": "2026-08-31",
  "publisher": "Elsevier",
  "ris": "https://research.draconitic.com/paper/730hhrhbhcf0e.ris",
  "sources": [
    {
      "first_seen": "2026-11-03T12:22:23Z",
      "native_id": "PMC13721756",
      "source": "pmc",
      "url": "https://doi.org/10.1016/j.crmeth.2026.101570"
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  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:1306|Cancer Genomics and Diagnostics",
      "subfield": "oncology"
    }
  ],
  "title": "Improving computational tumor ploidy estimation in complex cancer genomes through flow-cytometry-guided calibration",
  "title_text": "Improving computational tumor ploidy estimation in complex cancer genomes through flow-cytometry-guided calibration",
  "type": "peer-reviewed",
  "updated_at": "2026-11-03T12:22:23Z",
  "url": "https://research.draconitic.com/paper/730hhrhbhcf0e",
  "venue": "Cell Reports Methods",
  "versions": []
}