A review of the optimisation of the use of formalin fixed paraffin embedded tissue for molecular analysis in a forensic post-mortem setting

Reid, Kate Megan; Maistry, Sairita; Ramesar, Raj; Heathfield, Laura Jane

doi:10.1016/j.forsciint.2017.09.020

Cited by 19 publications

(19 citation statements)

References 52 publications

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“…The negative impacts of formalin fixation (or other aldehyde fixatives) on DNA are many and include DNA-protein cross linking, DNA degradation and methylation and lower recovered DNA yields especially when conventional DNA extractions kits are used (Campos & Gilbert, 2012;Chakraborty et al, 2006;Chambers & Hebert, 2016;Dietrich et al, 2013;Duval et al, 2010;Gilbert et al, 2007;Hykin et al, 2015;Reid et al, 2017;Schander & Halanych, 2003). The quality of DNA from a formalin-fixed specimen is also difficult to predict, with the success of DNA extraction (and subsequent sequencing) from fish specimens shown to be limited and patchy (Chakraborty et al, 2006;De Bruyn et al, 2011;Garrigos et al, 2013;Hykin et al, 2015;Raja et al, 2011;Shedlock et al, 1997).…”

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confidence: 99%

Assessing DNA for fish identifications from reference collections: the good, bad and ugly shed light on formalin fixation and sequencing approaches

Appleyard

Maher

Pogonoski

et al. 2021

Journal of Fish Biology

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Natural history collections are repositories of biodiversity and are potentially used by molecular ecologists for comparative taxonomic, phylogenetic, biogeographic and forensic purposes. Specimens in fish collections are preserved using a combination of methods with many fixed in formalin and then preserved in ethanol for long-term storage. Formalin fixation damages DNA, thereby limiting genetic analyses. In this study, the authors compared the DNA barcoding and identification success for frozen and formalin-fixed tissues obtained from specimens in the CSIRO Australian National Fish Collection. They studied 230 samples from fishes (consisting of >160 fish species). An optimized formalin-fixed, paraffin-embedded DNA extraction method resulted in usable DNA from degraded tissues. Four mini barcoding assays of the mitochondrial DNA (mtDNA) were characterized with Sanger and Illumina amplicon sequencing. In the good quality DNA (without exposure to formalin), up to 88% of the specimens were correctly matched at the species level using the cytochrome oxidase subunit 1 (COI) mini barcodes, whereas up to 58% of the specimens exposed to formalin for less than 8 weeks were correctly identified to species. In contrast, 16S primers provided higher amplification success with formalin-exposed tissues, although the COI gene was more successful for identification. Importantly, the authors found that DNA of a certain size and quality can be amplified and sequenced despite exposure to formalin, and Illumina sequencing provided them with greater power of resolution for taxa identification even when there was little DNA present.Overall, within parameter constraints, this study highlights the possibilities of recovering DNA barcodes for identification from formalin-fixed fish specimens, and the authors provide guidelines for when successful identification could be expected.

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mentioning

confidence: 99%

Assessing DNA for fish identifications from reference collections: the good, bad and ugly shed light on formalin fixation and sequencing approaches

Appleyard

Maher

Pogonoski

et al. 2021

Journal of Fish Biology

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“…The analysis of formalin-fixed, paraffin-embedded (FFPE) tissue can be essential when the legal process requires retrospective studies, for example, in criminal paternity testing, or cases of sudden unexplained death, or the paraffin blocks are the last and only option, e.g., identification of an unknown body, or for the purpose of determining a genetic profile [106][107][108], or even the cause and/or manner of death [109]. Formalin fixation process and subsequent storage is a perfect preservative for maintaining the integrity of tissues after death, but it causes crosslinking and degradation-fragmentation of the DNA over time, which prevents molecular PCR analysis and may cause difficulties in genotyping.…”

Section: Collection Devices and Paraffin Embedded Tissuesmentioning

confidence: 99%

Most Common Medico-Legal Autopsy-Related Human and Nonhuman Biological Samples for DNA Analysis

Pádár¹,

Zenke²,

Kozma³

2018

Post Mortem Examination and Autopsy - Current Issues From Death to Laboratory Analysis

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The identification and individualization of biological evidences is crucial to actual criminal investigations. In spite of the differences at the national level, all the legal processes attribute particular importance to forensic DNA analysis. However, none of the qualified results from any professional laboratory can produce substantive, valuable evidence with insufficient quality of samples and/or problems with provision of a pristine and controlled environment. The methodology and efficiency of sampling are distinct in case of living persons and in medico-legal autopsy and crime scenes. This chapter is a short overview from the basic introductory information up to ongoing research, and in accordance with constraints on the chapter size, it briefly discusses the important topics of sample collection at medico-legal autopsy for DNA analysis. The content sorts the major types of samples, reviews the common methods of sampling and the potential risk of poor sampling or contamination transfer. The corpses can be more or less degraded, which in special cases (e.g., paraffin embedded tissues, drowned, burning and/or buried cadaver) allow only for analysis of highly degraded samples. The samples can be associated with tissues of a corpse (e.g., blood, soft tissues, bone, tooth, hair) and/or additional extraneous tissues and remains, which are often mixed (e.g., blood, saliva, semen, vaginal fluid, debris of fingernails) on the corpse.

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“…Other potentially non-mixed, but easily containable low template DNA samples such as burned body or tissue which was subjected to a high temperature [46, [63][64][65], formalin-fixed samples [66][67][68], a piece of short hair with no root [69], or fingerprints of a touched surface and body parts [38,39,[70][71][72] often require special consideration. Depending on the complexity of various influences, and with lack of valid information concerning the initial environmental circumstances and the chemical and/or physical processes involved, the degree of damage of and/or quality of obtained DNA cannot be, at first, accurately predicted.…”

Section: Extraction Of Compound And/or Challenging Samplesmentioning

confidence: 99%

Forensic DNA Technological Advancements as an Emerging Perspective on Medico-Legal Autopsy: A Mini Review

Pádár¹,

Zenke²,

Kozma³

2018

Post Mortem Examination and Autopsy - Current Issues From Death to Laboratory Analysis

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The importance of biological traces and evidences related to a criminal matter has been recognized for a long time. The examination of the expression of genetic polymorphism has been an integral part of the multidisciplinary field of medico-legal autopsy for over a century. Since the initial application of blood group antigens for personalization of a putative perpetrator in a murder case, the discipline of forensic genetics has evolved as a standard of forensic sciences. The real breakthrough, the application of molecular tools and processes for the in-vitro replication of genetic substances, has increasingly allowed the exploitation of advances of molecular genetics for both forensic and criminal investigations. Although there are certainly many more applications and scientific fields in the medico-legal arena, the relatively fast progress of genetics, which has accelerated recently with state-of-art technologies, can provide ever more relevant information in relation to a corpse or the cause and manner that resulted in the corpse for autopsy. This topic concerns the currently accepted forensic DNA technology, and the last section reviews commonly used markers for nuclear and mitochondrial DNA analysis as well as ongoing research. This review also focuses on the increasingly important non-human sources of DNA, and shortly covers the main aspects of animal forensic DNA examination.

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A review of the optimisation of the use of formalin fixed paraffin embedded tissue for molecular analysis in a forensic post-mortem setting

Cited by 19 publications

References 52 publications

Assessing DNA for fish identifications from reference collections: the good, bad and ugly shed light on formalin fixation and sequencing approaches

Assessing DNA for fish identifications from reference collections: the good, bad and ugly shed light on formalin fixation and sequencing approaches

Most Common Medico-Legal Autopsy-Related Human and Nonhuman Biological Samples for DNA Analysis

Forensic DNA Technological Advancements as an Emerging Perspective on Medico-Legal Autopsy: A Mini Review

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