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. 2023 Jan;47(1):131-139.
doi: 10.1007/s11259-022-09937-0. Epub 2022 May 26.

Successful restoration of archived ovine formalin fixed paraffin-embedded tissue DNA and single nucleotide polymorphism analysis

Amanda Kravitz  1 , Ron Tyler  1 , B Murali Manohar  2 , B Samuel Masilamoni Ronald  2 , Michael T Collins  3 , Nammalwar Sriranganathan  4
Affiliations

Successful restoration of archived ovine formalin fixed paraffin-embedded tissue DNA and single nucleotide polymorphism analysis

Amanda Kravitz et al. Vet Res Commun. 2023 Jan.

Abstract

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.

Keywords: FFPE DNA restoration; FFPE tissues; Illumina Ovine SNP50 BeadChip; SNP analysis; Sheep.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Fig. 1
Fig. 1
FFPE QC vs. Call Rate
Fig. 2
Fig. 2
p10GC vs. Call Rate
Fig. 3
Fig. 3
Legend: SNP and Sample Inclusion Criteria
See this image and copyright information in PMC

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