ArticleBiology methods & protocols2020
Characterization of FFPE-induced bacterial DNA damage and development of a repair method.
Article in Biology methods & protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Highly Sensitive DNA Testing of Fusobacterium nucleatum in Colorectal Tumors.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2025Article
- Application of Amplicon Metagenomics to Identify Fungal Pathogens in Formalin-Fixed Paraffin-Embedded Samples: Proof of Concept in Animals with Fungal Pathologies.Microorganisms · 2025Article
- Microbiome and bladder cancer: the role of probiotics in treatment.Future microbiology · 2025Review
- The oncobiome; what, so what, now what?Microbiome research reports · 2025Review
- A critical spotlight on the paradigms of FFPE-DNA sequencing.Nucleic acids research · 2023Review
- Review
- Understanding and harnessing triple-negative breast cancer-related microbiota in oncology.Frontiers in oncology · 2022Review
- An efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections.Biology methods & protocols · 2022Article
- Article
- Fusobacterium nucleatum: caution with interpreting historical patient sample cohort.Journal of pathology and translational medicine · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Formalin-fixed, paraffin-embedded (FFPE) specimens have huge potential as source material in the field of human microbiome research. However, the effects of FFPE processing on bacterial DNA remain uncharacterized. Any effects are relevant for microbiome studies, where DNA template is often minimal and sequences studied are not limited to one genome. As such, we aimed to both characterize this FFPE-induced bacterial DNA damage and develop strategies to reduce and repair this damage. Our analyses indicate that bacterial FFPE DNA is highly fragmented, a poor template for PCR, crosslinked and bears sequence artefacts derived predominantly from oxidative DNA damage. Two strategies to reduce this damage were devised - an optimized decrosslinking procedure reducing sequence artefacts generated by high-temperature incubation, and secondly, an
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