{
  "abstract": "Sensitive detection of minimal residual disease (MRD) remains a major unmet need in high-risk neuroblastoma. MYCN amplification, a hallmark of high-risk disease, typically occurs on extrachromosomal DNA (ecDNA), but the potential of ecDNA-associated genomic rearrangements for individualized MRD monitoring has not been fully exploited. Here, we applied neuroblastoma-specific hybrid capture-based panel sequencing to identify patient-unique breakpoints within MYCN amplicons, and used Circle-seq and Nanopore sequencing to resolve the extrachromosomal amplicon structure in representative samples. Analysis of 8 neuroblastoma cell lines and 22 primary tumors identified 69 tumor-specific breakpoints. Those selected for assay development were validated by breakpoint-specific PCR and Sanger sequencing. Breakpoints detected in primary tumors remained detectable at relapse, supporting their stability as MRD markers. Breakpoint-specific real-time quantitative PCR and droplet digital PCR detected these junctions in bone marrow aspirates with high specificity and reached sensitivities down to a tumor DNA fraction of 10^-6. We applied this approach to 53 serial bone marrow aspirates from 14 patients with high-risk neuroblastoma to monitor MRD dynamics, resolving treatment response and molecular persistence. In six samples, breakpoint-positive DNA was detected in bone marrow that was negative by conventional cytology and immunocytology, highlighting the added value of molecular monitoring. Together, these findings establish ecDNA breakpoint-based detection as a strategy for MRD assessment in neuroblastoma, that is, in principle, applicable to any ecDNA-amplified oncogene.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Pediatric Oncology and Hematology, Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin and Humboldt-Universitaet zu"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 28,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "A. Szymansky"
    },
    {
      "name": "F. Hertwig"
    },
    {
      "name": "A. Winkler"
    },
    {
      "name": "R. Chamorro Gonzalez"
    },
    {
      "name": "K. Helmsauer"
    },
    {
      "name": "A.-M. Schroeer"
    },
    {
      "name": "M. J. Witthauer"
    },
    {
      "name": "E. Karaman"
    },
    {
      "name": "M. Lodrini"
    },
    {
      "name": "J. Wuenschel"
    },
    {
      "name": "N. Wittstruck"
    },
    {
      "name": "S. Fuchs"
    },
    {
      "name": "J. Theissen"
    },
    {
      "name": "B. Hero"
    },
    {
      "name": "R. P. Koche"
    },
    {
      "name": "M. J. Barz"
    },
    {
      "name": "L. Heukamp"
    },
    {
      "name": "K. Astrahantseff"
    },
    {
      "name": "K. Schmelz"
    },
    {
      "name": "P. Hundsdoerfer"
    },
    {
      "name": "J. Toedling"
    },
    {
      "name": "A. Eggert"
    },
    {
      "name": "C. Eckert"
    },
    {
      "name": "B. Spanjaard"
    },
    {
      "name": "H. E. Deubzer"
    },
    {
      "name": "M. Fischer"
    },
    {
      "name": "A. G. Henssen"
    },
    {
      "name": "J. H. Schulte"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/7rb09kcbd05n2.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.06.749680",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.06.749680v1.full",
  "id": "7rb09kcbd05n2",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.06.749680v1",
  "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",
      "cancer biology"
    ],
    [
      "openalex",
      "2728|Neuroblastoma Research and Treatments"
    ]
  ],
  "openalex": "W7212175653",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.06.749680v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-06",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/7rb09kcbd05n2.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:20:52Z",
      "native_id": "10.64898/2026.09.06.749680",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.06.749680v2"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "biorxiv:cancer biology",
      "subfield": "oncology"
    }
  ],
  "title": "Quantitative and sensitive neuroblastoma minimal residual disease detection using extrachromosomal DNA (ecDNA) breakpoints",
  "title_text": "Quantitative and sensitive neuroblastoma minimal residual disease detection using extrachromosomal DNA (ecDNA) breakpoints",
  "type": "preprint",
  "updated_at": "2026-10-30T12:21:43Z",
  "url": "https://research.draconitic.com/paper/7rb09kcbd05n2",
  "venue": "bioRxiv",
  "versions": []
}