{
  "abstract": "Missed genetic deletions can prevent cancer patients from receiving effective targeted therapy. Standard pipelines, such as TSO500, use bin count averaging for copy number variation detection but often overlook focal events. To address this, we developed a machine learning (ML) pipeline for deletion detection and zygosity evaluation within the MASTERsg precision oncology program. We focused on the tumor suppressor gene PTEN, whose loss confers sensitivity to mTOR/Akt inhibition. An Extreme Gradient Boosting model trained on PTEN-deleted and wild-type tumor samples identified focal deletions missed by the TSO500 pipeline and CNVkit that were associated with concordant PTEN protein loss by immunohistochemistry. Importantly, the model detected PTEN deletions in 33/204 profiled samples that were classified as PTEN wild-type by TSO500; 75% (15/20) of stainable cases showed absent or reduced PTEN protein expression. These findings demonstrate the potential of ML to enhance panel sequencing, uncovering therapeutically relevant alterations missed by established diagnostic methods.",
  "abstract_shown": true,
  "affiliations": [
    "Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany. irina.kerle@nct-dresden.de.",
    "Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany. irina.kerle@nct-dresden.de.",
    "German Cancer Consortium (DKTK), partner site Dresden, a partnership between DKFZ and University Hospital Carl Gustav Carus Dresden, Dresden, Germany. irina.kerle@nct-dresden.de.",
    "Department for Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany.",
    "Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany.",
    "Chair of Software Technology, Faculty of Computer Science, Technical University Dresden, Dresden, Germany.",
    "Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases Dresden (NCT/UCC), a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany.",
    "Institute of Pathology, Carl Gustav Carus University Hospital, Dresden, Germany.",
    "German Cancer Consortium (DKTK), partner site Dresden, a partnership between DKFZ and University Hospital Carl Gustav Carus Dresden, Dresden, Germany.",
    "Department of Internal Medicine I, University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany.",
    "Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, USA.",
    "Internal Medicine C, Hematology, Oncology, Stem Cell Transplantation and Palliative Care, University Medicine Greifswald, Greifswald, Germany.",
    "Institute for Clinical Genetics, University Hospital Carl Gustav Carus at TU Dresden, Dresden, Germany.",
    "ERN GEN-TURIS, Hereditary Cancer Syndrome Center Dresden, Dresden, Germany.",
    "National Center for Tumor Diseases (NCT), NCT/UCC Dresden, a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Germany; German Cancer Consortium (DKTK), partner site: Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany.",
    "Institute of Pathology, School of Medicine and Health, Technical University Munich, Munich, Germany."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 19,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Irina A Kerle",
      "orcid": "0000-0002-3650-488X"
    },
    {
      "affs": [
        3,
        4,
        5
      ],
      "name": "Oleksandr Husak"
    },
    {
      "affs": [
        6
      ],
      "name": "Thomas Gross"
    },
    {
      "affs": [
        7
      ],
      "name": "Andreas Hartig"
    },
    {
      "affs": [
        6
      ],
      "name": "Rebecca Prause"
    },
    {
      "affs": [
        3,
        4,
        8
      ],
      "name": "Daniela Richter"
    },
    {
      "affs": [
        7
      ],
      "name": "Sascha Brückmann"
    },
    {
      "affs": [
        3,
        4,
        8,
        9
      ],
      "name": "Maximilian Werner"
    },
    {
      "affs": [
        6
      ],
      "name": "Anja Kögler"
    },
    {
      "affs": [
        3,
        4,
        8,
        9
      ],
      "name": "Dorothea Hanf"
    },
    {
      "affs": [
        3,
        4,
        8,
        10,
        11
      ],
      "name": "Lino Möhrmann"
    },
    {
      "affs": [
        12,
        13,
        14
      ],
      "name": "Doreen William",
      "orcid": "0000-0001-7824-5073"
    },
    {
      "affs": [
        5
      ],
      "name": "Karsten Wendt"
    },
    {
      "affs": [
        15
      ],
      "name": "Nicole Pfarr",
      "orcid": "0000-0002-5977-5375"
    },
    {
      "affs": [
        15
      ],
      "name": "Carolin Mogler",
      "orcid": "0000-0003-3400-7254"
    },
    {
      "affs": [
        7
      ],
      "name": "Daniela E Aust"
    },
    {
      "affs": [
        12,
        13,
        14
      ],
      "name": "Evelin Schröck"
    },
    {
      "affs": [
        3,
        4,
        8
      ],
      "name": "Christoph Heining"
    },
    {
      "affs": [
        3,
        4,
        8
      ],
      "name": "Hanno Glimm"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/1mjr9md1syxzm.bib",
  "cited_by": 0,
  "doi": "10.1038/s41698-026-01756-9",
  "fulltext_url": "https://europepmc.org/articles/PMC13675215",
  "id": "1mjr9md1syxzm",
  "issns": [
    "2397-768X"
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  "landing_url": "https://europepmc.org/article/MED/42888201",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1306|Cancer Genomics and Diagnostics"
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  "pdf_url": "https://europepmc.org/articles/PMC13675215?pdf=render",
  "pmcid": "PMC13675215",
  "pmid": "42888201",
  "published": "2026-10-16",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/1mjr9md1syxzm.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:46Z",
      "native_id": "MED:42888201",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42888201"
    }
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  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:1306|Cancer Genomics and Diagnostics",
      "subfield": "oncology"
    }
  ],
  "title": "Machine learning uncovers previously undetectable genetic deletions in cancer panel sequencing.",
  "title_text": "Machine learning uncovers previously undetectable genetic deletions in cancer panel sequencing.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:46Z",
  "url": "https://research.draconitic.com/paper/1mjr9md1syxzm",
  "venue": "NPJ precision oncology",
  "versions": []
}