Characterization of FFPE-induced bacterial DNA damage and development of a repair method.
DNA damage
base excision repair
formalin-fixed paraffin-embedded
genomics
metagenomics
Journal
Biology methods & protocols
ISSN: 2396-8923
Titre abrégé: Biol Methods Protoc
Pays: England
ID NLM: 101693064
Informations de publication
Date de publication:
2020
2020
Historique:
received:
13
05
2020
revised:
15
07
2020
accepted:
18
07
2020
entrez:
19
10
2020
pubmed:
20
10
2020
medline:
20
10
2020
Statut:
epublish
Résumé
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
Identifiants
pubmed: 33072872
doi: 10.1093/biomethods/bpaa015
pii: bpaa015
pmc: PMC7548031
doi:
Types de publication
Journal Article
Langues
eng
Pagination
bpaa015Informations de copyright
© The Author(s) 2020. Published by Oxford University Press.
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