Successful restoration of archived ovine formalin fixed paraffin-embedded tissue DNA and single nucleotide polymorphism analysis.
FFPE DNA restoration
FFPE tissues
Illumina Ovine SNP50 BeadChip
SNP analysis
Sheep
Journal
Veterinary research communications
ISSN: 1573-7446
Titre abrégé: Vet Res Commun
Pays: Switzerland
ID NLM: 8100520
Informations de publication
Date de publication:
Jan 2023
Jan 2023
Historique:
received:
23
03
2022
accepted:
09
05
2022
pubmed:
27
5
2022
medline:
27
1
2023
entrez:
26
5
2022
Statut:
ppublish
Résumé
Archived formalin fixed paraffin-embedded (FFPE) tissues are powerful tools in medicine, capable of harboring diagnostic and genetic answers to challenging clinical questions. Successful utilization of DNA derived from FFPE samples is dependent upon repairing DNA damage generated from the fixation process. Methods to repair FFPE DNA have been successful in human medicine for a variety of research and clinical applications, yet remain underutilized in veterinary medicine. Despite the available technology, our study is the first to evaluate the repair of FFPE derived DNA from veterinary species for single-nucleotide polymorphism (SNP) analysis using the Illumina OvineSNP50 BeadChip and Illumina FFPE QC and DNA Restore kit. To accomplish this, 48 ovine FFPE samples were run using the Illumina OvineSNP50 BeadChip with and without restoration. Compared to pre-restore data, we found increased sample call rates, SNP call frequency, and assay metrics for all samples post-restoration. Further, we utilized four sheep with available parallel fresh DNA and FFPE DNA to compare assay metrics and genotype calls between the two starting sample types. Although fresh samples generated increased call rates, we found 99% concordance in allele calls between restored FFPE and fresh DNA for all four samples. Our results indicate successful restoration and genotyping of ovine FFPE samples using this technology, with potential for utilization in other veterinary species.
Identifiants
pubmed: 35618986
doi: 10.1007/s11259-022-09937-0
pii: 10.1007/s11259-022-09937-0
pmc: PMC9873697
doi:
Substances chimiques
Formaldehyde
1HG84L3525
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
131-139Informations de copyright
© 2022. The Author(s).
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