Effect of formalin fixation on pcr amplification of DNA isolated from healthy autopsy tissues

Vitošević, Katarina; Todorović, Miloš; Varljen, Tatjana; Slović, Živana; Matić, Sanja; Todorović, D. M.

doi:10.1016/j.acthis.2018.09.005

Cited by 27 publications

(23 citation statements)

References 34 publications

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“…Actually, Vitošević et al reported that DNA fragmentation in autopsy FFPE tissues proceeded according to the period of formalin fixation. [ 11 ] Bonin et al mentioned that the average fragment length of DNA is 300 to 400 bases in biopsy FFPE tissues, but much shorter in postmortem FFPE tissues, most often less than 100 bases. [ 12 ] This was also the case with our study, as our PCR analyses using primer pairs for a >200-bp product showed negative results, whereas for ≤110-bp producing primer pairs, the results were positive and stable.…”

Section: Discussionmentioning

confidence: 99%

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A case report on death from acute bacterial cholangitis accompanied by von Meyenburg complexes

Watanabe¹,

Ohno²,

Sakuma³

et al. 2021

Medicine

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Rationale: In some cases, autopsy is the first opportunity to find a previously unrecognized critical infection. Pathogens are identified by various methods, such as microscopic examination, special stains, culture tests, and immunohistochemistry. Here, we report a case of 16S ribosomal RNA (rRNA) gene sequencing using a postmortem formalin-fixed, paraffin-embedded (FFPE) tissue, which was useful for identifying pathogenic microbes. Patient concerns: Autopsy was performed on an 87-year-old man who had chronic renal failure and had developed sepsis from a central venous catheter infection 10 days before his death. Prior to these events, von Meyenburg complexes (VMCs) were also found during regular checkups. Diagnosis: Postmortem microscopic examination revealed acute purulent cholangitis with numerous microabscesses, accompanied by VMCs. Gram-negative rods were observed in some microabscesses, which were considered causative pathogens. Interventions: 16S rRNA gene sequencing using postmortem FFPE tissue Outcomes: Pseudomonas aeruginosa was identified, different from the one detected in the central venous catheter culture while alive. Lessons: 16S rRNA gene sequencing is a useful tool for identifying pathogenic microbes in postmortem FFPE tissues. This technique may be useful for amplicon sizes of approximately 100 bp or less.

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Section: Discussionmentioning

confidence: 99%

“…In autopsy cases, elongated formalin fixation is known to result in DNA degradation. [ 11 , 12 ] In addition, there is a risk of bacterial contamination, possibly from the postmortem proliferation of resident flora in patients or through its introduction during the autopsy and FFPE processing.…”

Section: Introductionmentioning

confidence: 99%

A case report on death from acute bacterial cholangitis accompanied by von Meyenburg complexes

Watanabe¹,

Ohno²,

Sakuma³

et al. 2021

Medicine

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“…This may be due to the fact that the specimen was exposed to formalin. Formalin degrades DNA by causing cross-linking between nucleic acids and proteins, which can affect the success of PCR amplification (Vitosˇevic´et al, 2018). However, the 3 samples in this investigation that were exposed to formalin amplified in the ITS1þ2 PCR well.…”

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confidence: 82%

Molecular Confirmation of a Fasciola Gigantica × Fasciola Hepatica Hybrid in a Chadian Bovine

Evack

Schmidt

Boltryk

et al. 2020

Journal of Parasitology

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“…This reduce antigenicity and causes degradation of nucleic acid, compromising immunohistochemistry and molecular analysis. 15–17 Although specimens should be fixed in at least ten times their volume of fixative, 1 in reality, containers for fixation are often small and the brain is often only fixed in two- or three times its volume of formalin. Refreshing the formalin after one week or fixing in 20% rather than 10% neutral buffered formalin are alternatives.…”

Section: Methodsmentioning

confidence: 99%

Fetal and Perinatal Brain Autopsy: Useful Macroscopic Techniques Including Agar In-situ and Pre-Embedding Methods

et al. 2021

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Fragile perinatal and fetal brains are the rule rather than the exception for developmental neuropathologists. Retrieving the fresh brain from the skull and examining early fetal, macerated or severely hydrocephalic brains after fixation can be a challenge. Textbooks on neurodevelopmental pathology mention these challenges to macroscopic examination of the developing central nervous system only in passing, but many perinatal pathologists recognize this diagnostic problem. We reviewed protocols and publications on the removal, fixation, slicing and sampling of these fetal- and perinatal brains. In addition, we describe a technique to facilitate the removal of severely hydrocephalic brains with very thin cerebral walls from the skull by replacing the intraventricular fluid with agar in-situ. Furthermore, we present a method for post-fixation pre-embedding in agar to facilitate slicing, macroscopic examination and sampling of fragile and macerated brains.

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Effect of formalin fixation on pcr amplification of DNA isolated from healthy autopsy tissues

Cited by 27 publications

References 34 publications

A case report on death from acute bacterial cholangitis accompanied by von Meyenburg complexes

A case report on death from acute bacterial cholangitis accompanied by von Meyenburg complexes

Molecular Confirmation of a Fasciola Gigantica × Fasciola Hepatica Hybrid in a Chadian Bovine

Fetal and Perinatal Brain Autopsy: Useful Macroscopic Techniques Including Agar In-situ and Pre-Embedding Methods

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