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Journal article
The comparative performance of a custom Canine NanoString® panel on FFPE and snap frozen liver biopsies
Research in veterinary science, Vol.159, pp.225-231
2023
Abstract
Formalin-Fixed Paraffin Embedded (FFPE) biopsies would provide a critical mass of cases to allow investigation of canine liver disease, however their use is often limited by challenges typically associated with transcriptomic analysis. This study evaluates the capability of NanoString® to measure the expression of a broad panel of genes in FFPE liver samples. RNA was isolated from matched histopathologically normal liver samples using FFPE (n = 6) and snap frozen in liquid nitrogen (n = 6) and measured using a custom NanoString® panel. Out of the 40 targets on the panel, 27 and 23 targets were above threshold for non-diseased snap frozen and FFPE tissue respectively. The binding density and total counts were significantly reduced in the FFPE samples relative to the snap frozen samples (p = 0.005, p = 0.01, respectively), confirming a reduction in sensitivity. The concordance between the snap frozen and FFPE samples was high, with correlations (R) ranging between 0.88 and 0.99 between the paired samples. An additional 14 immune-related targets, undetectable the non-diseased FFPE liver, were above threshold when the technique was applied to a series of diseased samples, further supporting their inclusion on this panel. This use of NanoString® based analysis opens up huge opportunity for retrospective evaluation of gene signatures in larger caseloads through harnessing the capacity of archived FFPE samples This information used alongside clinical and histological data will not only afford a way to explore disease etiopathogenesis, it may also offer insight into sub-types of liver disease in dogs, which cannot be discerned using more traditional diagnostic methods.
Details
- Title
- The comparative performance of a custom Canine NanoString® panel on FFPE and snap frozen liver biopsies
- Authors/Creators
- Marion T. Ryan - School of Veterinary Medicine, University College Dublin, Belfield, Co. Dublin, IrelandCarlos Martinez - Department of Internal Medicine, AÚNA Especialidades Veterinarias - IVC Evidensia, Valencia, SpainHanne Jahns - School of Veterinary Medicine, University College Dublin, Belfield, Co. Dublin, IrelandCarmel T. Mooney - School of Veterinary Medicine, University College Dublin, Belfield, Co. Dublin, IrelandJohn A. Browne - School of Agriculture and Food Science, University College Dublin, Belfield, Co. Dublin, IrelandEmma J. O'Neill - School of Veterinary Medicine, University College Dublin, Belfield, Co. Dublin, IrelandRobert E Shiel
- Publication Details
- Research in veterinary science, Vol.159, pp.225-231
- Publisher
- Elsevier Ltd
- Identifiers
- 991005572070107891
- Copyright
- © 2023 The Authors.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- 1 Clinical & Life Sciences
- 1.54 Molecular & Cell Biology - Genetics
- 1.54.1454 PCR Techniques
- Web Of Science research areas
- Veterinary Sciences
- ESI research areas
- Plant & Animal Science