{
  "abstract": "Copy number alterations are among the most common genomic aberrations in cancer and their accurate identification relies on robust segmentation of sequencing read-depth signals. Existing segmentation methods typically balance computational efficiency against segmentation accuracy and remain sensitive to technical artifacts present in sequencing data. Here, we present QuickSeg, a fast and versatile methodology that uses an exact dynamic programming algorithm to detect copy number segments using median-based error function. Motivated by the observation that sequencing depth distributions contain a small but pervasive population of outlying observations, this approach provides increased robustness to technical noise while simultaneously reducing the computational complexity of the segmentation problem. Across whole-genome sequencing of cancer cohorts, using breakpoint-supported somatic copy number alterations, we demonstrate improved segmentation precision over two widely used baseline methods, Circular Binary Segmentation (CBS) and Piecewise Constant Fitting (PCF), across a broad range of sensitivity thresholds. QuickSeg also consistently outperformed both methods with respect to runtime and memory usage. Collectively, our results show that robust median-based optimization provides both biological and computational advantages for copy number segmentation, enabling accurate analysis of large sequencing cohorts with minimal computational requirements.",
  "abstract_shown": true,
  "affiliations": [
    "University of Copenhagen"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "B. Schlotmann"
    },
    {
      "name": "F. Favero"
    },
    {
      "name": "A. Locallo"
    },
    {
      "name": "J. L. Weischenfeldt"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/4w8t9kjys8ncg.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.08.31.747916",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.08.31.747916v1.full",
  "id": "4w8t9kjys8ncg",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.08.31.747916v1",
  "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",
      "bioinformatics"
    ],
    [
      "openalex",
      "1311|Genomic variations and chromosomal abnormalities"
    ]
  ],
  "openalex": "W7208714714",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.08.31.747916v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-31",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/4w8t9kjys8ncg.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:23Z",
      "native_id": "10.64898/2026.08.31.747916",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.08.31.747916v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "QuickSeg: A fast, versatile and accurate algorithm for genomic copy number segmentation using dynamic programming",
  "title_text": "QuickSeg: A fast, versatile and accurate algorithm for genomic copy number segmentation using dynamic programming",
  "type": "preprint",
  "updated_at": "2026-10-30T12:19:23Z",
  "url": "https://research.draconitic.com/paper/4w8t9kjys8ncg",
  "venue": "bioRxiv",
  "versions": []
}