{
  "abstract": "Genomic, transcriptomic and epigenomic characterization has accelerated the discovery of clinically-relevant alterations in cancer, predominantly using fresh frozen (FF) specimens. However, clinical molecular pathology laboratories prefer formalin-fixed paraffin-embedded (FFPE) methods, known to introduce artifacts at the nucleic acid level, over fresh frozen methods. Extending the multi-platform analysis to FFPE specimens for comprehensive clinical molecular diagnosis requires a thorough understanding of the consequence of formalin-fixation. We present a detailed multi-platform characterization of FFPE preservation using paired FF specimens as the 'gold standard'. DNA and RNA were obtained from 38 patients across 6 cancer types using a FFPE optimized co-isolation. The impact of FFPE on exome sequencing was dependent on filtering, where a minimum coverage or supporting read filter can mitigate FFPE-specific false positives. Copy number alterations, MSI assessment, mutational signatures, and DNA methylation were comparable between FFPE and FF. FFPE biases in RNA expression can be overcome when using biology-relevant genes and we describe a novel consequence of FFPE on miRNA species diversity. Collectively, this data provides a broad view of FFPE artifact and offers best practices for overcome these biases.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 44,
  "authors": [
    {
      "name": "E. J. Zmuda"
    },
    {
      "name": "K. R. Covington"
    },
    {
      "name": "C. Kandoth"
    },
    {
      "name": "C. K. Y. Ng"
    },
    {
      "name": "D. J. Weisenberger"
    },
    {
      "name": "R. Bowlby"
    },
    {
      "name": "A. Chu"
    },
    {
      "name": "R. Corbett"
    },
    {
      "name": "D. Brooks"
    },
    {
      "name": "A. D. Cherniack"
    },
    {
      "name": "B. Murray"
    },
    {
      "name": "S. Ling"
    },
    {
      "name": "W. Zhao"
    },
    {
      "name": "E. Shinbrot"
    },
    {
      "name": "R. S. Lim"
    },
    {
      "name": "M. S. Bootwalla"
    },
    {
      "name": "T. Hinoue"
    },
    {
      "name": "J. Hu"
    },
    {
      "name": "N. Kakkar"
    },
    {
      "name": "M. Lawrence"
    },
    {
      "name": "M. McLellan"
    },
    {
      "name": "C. Miller"
    },
    {
      "name": "D. Morton"
    },
    {
      "name": "A. J. Mungall"
    },
    {
      "name": "D. Muzny"
    },
    {
      "name": "C. Sougnez"
    },
    {
      "name": "P. Stojanov"
    },
    {
      "name": "L. Xi"
    },
    {
      "name": "N. Schultz"
    },
    {
      "name": "R. Akbani"
    },
    {
      "name": "C. Curtis"
    },
    {
      "name": "B. Fulton"
    },
    {
      "name": "R. A. Gibbs"
    },
    {
      "name": "G. Getz"
    },
    {
      "name": "P. Spellman"
    },
    {
      "name": "M. Marra"
    },
    {
      "name": "M. Ladanyi"
    },
    {
      "name": "R. Tarnuzzer"
    },
    {
      "name": "H. Sofia"
    },
    {
      "name": "The Cancer Genome Atlas Research Network"
    },
    {
      "name": "C. Hutter"
    },
    {
      "name": "D. A. Wheeler"
    },
    {
      "name": "J. Gastier-Foster"
    },
    {
      "name": "Lair"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/b6h6xptr6hjbb.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.08.31.748145",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.08.31.748145v1.full",
  "id": "b6h6xptr6hjbb",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.08.31.748145v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.08.31.748145v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-31",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/b6h6xptr6hjbb.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:05Z",
      "native_id": "10.64898/2026.08.31.748145",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.08.31.748145v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Comprehensive characterization of genomic, transcriptomic and epigenomic artifacts introduced in formalin-fixed, paraffin-embedded tissues.",
  "title_text": "Comprehensive characterization of genomic, transcriptomic and epigenomic artifacts introduced in formalin-fixed, paraffin-embedded tissues.",
  "type": "preprint",
  "updated_at": "2026-10-30T12:19:05Z",
  "url": "https://research.draconitic.com/paper/b6h6xptr6hjbb",
  "venue": "bioRxiv",
  "versions": []
}