A critical spotlight on the paradigms of FFPE-DNA sequencing Article Swipe
Tim Alexander Steiert
,
Genı́s Parra
,
Marta Gut
,
Norbert Arnold
,
Jean-Rémi Trotta
,
Raúl Tonda
,
Alice Moussy
,
Zuzana Gerber
,
Peter M. Abuja
,
Kurt Zatloukal
,
Christoph Röcken
,
Trine Folseraas
,
Marit M. Grimsrud
,
Arndt Vogel
,
Benjamin Goeppert
,
Stéphanie Roessler
,
Sebastian Hinz
,
Clemens Schafmayer
,
Philip Rosenstiel
,
Jean‐François Deleuze
,
Marta Gut
,
André Franke
,
Michael Förster
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkad519
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkad519
In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was developed as a fixation and conservation method and is still used to this day in routine clinical and pathological practice. The implementation of state-of-the-art nucleic acid sequencing technologies has sparked much interest for using historical FFPE samples stored in biobanks as they hold promise in extracting new information from these valuable samples. However, formalin fixation chemically modifies DNA, which potentially leads to incorrect sequences or misinterpretations in downstream processing and data analysis. Many publications have concentrated on one type of DNA damage, but few have addressed the complete spectrum of FFPE-DNA damage. Here, we review mitigation strategies in (I) pre-analytical sample quality control, (II) DNA repair treatments, (III) analytical sample preparation and (IV) bioinformatic analysis of FFPE-DNA. We then provide recommendations that are tested and illustrated with DNA from 13-year-old liver specimens, one FFPE preserved and one fresh frozen, applying target-enriched sequencing. Thus, we show how DNA damage can be compensated, even when using low quantities (50 ng) of fragmented FFPE-DNA (DNA integrity number 2.0) that cannot be amplified well (Q129 bp/Q41 bp = 5%). Finally, we provide a checklist called ‘ERROR-FFPE-DNA’ that summarises recommendations for the minimal information in publications required for assessing fitness-for-purpose and inter-study comparison when using FFPE samples.
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Metadata
- Type
- review
- Language
- en
- Landing Page
- https://doi.org/10.1093/nar/gkad519
- https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad519/50685648/gkad519.pdf
- OA Status
- gold
- Cited By
- 56
- References
- 112
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4381715159
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4381715159Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/nar/gkad519Digital Object Identifier
- Title
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A critical spotlight on the paradigms of FFPE-DNA sequencingWork title
- Type
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reviewOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2023Year of publication
- Publication date
-
2023-06-23Full publication date if available
- Authors
-
Tim Alexander Steiert, Genı́s Parra, Marta Gut, Norbert Arnold, Jean-Rémi Trotta, Raúl Tonda, Alice Moussy, Zuzana Gerber, Peter M. Abuja, Kurt Zatloukal, Christoph Röcken, Trine Folseraas, Marit M. Grimsrud, Arndt Vogel, Benjamin Goeppert, Stéphanie Roessler, Sebastian Hinz, Clemens Schafmayer, Philip Rosenstiel, Jean‐François Deleuze, Marta Gut, André Franke, Michael FörsterList of authors in order
- Landing page
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https://doi.org/10.1093/nar/gkad519Publisher landing page
- PDF URL
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https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad519/50685648/gkad519.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
- OA URL
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https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkad519/50685648/gkad519.pdfDirect OA link when available
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Biology, DNA sequencing, Computational biology, DNA, Genetics, Evolutionary biologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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56Total citation count in OpenAlex
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2025: 33, 2024: 22, 2023: 1Per-year citation counts (last 5 years)
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112Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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