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Open AccessArticle

A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay

1
Small Animal Clinic, University of Veterinary Medicine Hannover, Hannover D-30559, Germany
2
Hematology Oncology and Palliative Medicine, Clinic III, University of Rostock, Rostock D-18057, Germany
3
Department of Pathology, University of Veterinary Medicine Hannover, Hannover D-30559, Germany
4
Institute of Veterinary Medicine, Georg-August-University Göttingen, Göttingen D-37077, Germany
*
Author to whom correspondence should be addressed.
Academic Editor: Dario Marchetti
Int. J. Mol. Sci. 2016, 17(5), 724; https://doi.org/10.3390/ijms17050724
Received: 24 March 2016 / Revised: 2 May 2016 / Accepted: 4 May 2016 / Published: 13 May 2016
(This article belongs to the Section Biochemistry)
Mammary neoplasms are the tumors most affecting female dogs and women. Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable source of archived biological material. Fresh frozen (FF) tissue is considered ideal for gene expression analysis. However, strategies based on FFPE material offer several advantages. Branched-DNA assays permit a reliable and fast workflow when analyzing gene expression. The aim of this study was to assess the comparability of the branched-DNA assay when analyzing certain gene expression patterns between FF and FFPE samples in canine mammary tumors. RNA was isolated from 109 FFPE samples and from 93 FF samples of different canine mammary tissues. Sixteen (16) target genes (Tp53; Myc; HMGA1; Pik3ca; Mcl1; MAPK3; FOXO3; PTEN; GATA4; PFDN5; HMGB1; MAPK1; BRCA2; BRCA1; HMGA2; and Her2) were analyzed via branched-DNA assay (b-DNA). ACTB, GAPDH, and HPRT1 were used as data normalizers. Overall, the relative gene expression of the two different origins of samples showed an agreement of 63%. Still, care should be taken, as FFPE specimens showed lower expression of the analyzed targets when compared to FF samples. The fact that the gene expression in FFPE proved to be lower than in FF specimens is likely to have been caused by the effect of storage time. ACTB had the best performance as a data normalizer. View Full-Text
Keywords: branched-DNA assay; formalin-fixed, paraffin-embedded specimens; fresh frozen tissue; canine mammary tumor; gene expression; RNA branched-DNA assay; formalin-fixed, paraffin-embedded specimens; fresh frozen tissue; canine mammary tumor; gene expression; RNA
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Lüder Ripoli, F.; Mohr, A.; Conradine Hammer, S.; Willenbrock, S.; Hewicker-Trautwein, M.; Hennecke, S.; Murua Escobar, H.; Nolte, I. A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay. Int. J. Mol. Sci. 2016, 17, 724.

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