Determining the utility of veterinary tissue archives for retrospective DNA analysis

Abstract

Histopathology tissue archives can be an important source of specimens for retrospective studies, as these include samples covering a large number of diseases. In veterinary medicine, archives also contain samples from a large variety of species and may represent naturally-occurring models of human disease. The formalin-fixed, paraffin-embedded (FFPE) tissues comprising these archives are rich resources for retrospective molecular biology studies and pilot studies for biomarkers, as evidenced by a number of recent publications highlighting FFPE tissues as a resource for analysis of specific diseases. However, DNA extracted from FFPE specimens are modified and fragmented, making utilization challenging. The current study examines the utility of FFPE tissue samples from a veterinary diagnostic laboratory archive in five year intervals from 1977 to 2013, with 2015 as a control year, to determine how standard processing and storage conditions has affected their utility for future studies. There was a significant difference in our ability to obtain large amplicons from samples from 2015 than from the remaining years, as well as an inverse correlation between the age of the samples and product size obtainable. However, usable DNA samples were obtained in at least some of the samples from all years tested, despite variable storage, fixation, and processing conditions. This study will help make veterinary diagnostic laboratory archives more useful in future studies of human and veterinary disease.

DNA purification increases PCR-amplifiable DNA extracted from formalin-fixed, paraffin-embedded canine mast cell tumors for routine KIT mutation detection

“…This limits amplification for most FFPE samples to small fragments of <250 base pairs (bp). 1,4 Various techniques have been investigated to optimize extracted DNA integrity and quality for downstream molecular analysis. Type of fixative, length of fixation, extraction method, length of enzymatic tissue digestion, and age of block impact the quality of the DNA end product, and all have been targets for optimization.…”

“…Type of fixative, length of fixation, extraction method, length of enzymatic tissue digestion, and age of block impact the quality of the DNA end product, and all have been targets for optimization. 1,6,8,15,17 Moreover, extraction of high-quality DNA from either FFPE or frozen tissue samples has been reported as peculiarly problematic for MCTs in comparison to other tumor types and normal tissues, most likely as a result of the co-extraction of unknown cell-specific PCR inhibitors. 6,16,17 We investigated poor DNA amplification from 280 FFPE canine MCTs.…”