DNA and RNA analysis of blood and muscle from bodies with variable postmortem intervals

Hansen, Jakob; Lesnikova, Iana; Funder, Anette Md; Banner, Jytte

doi:10.1007/s12024-014-9567-2

Cited by 41 publications

(20 citation statements)

References 43 publications

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“…We also observed a striking lack of correlation of PMI with RIN in normal skeletal muscle, and to a similar extent the heart, supporting the tissue type-specific nature of RNA degradation. In forensic settings, RNA has been shown to be stable in muscle up to 1week after death [18]. While not addressed in this study, tissue-type specific RNA degradation has also been reported in ocular tissues with avascular structures having better RNA quality than vascularized structures such as the ciliary body [23].…”

Section: Resultsmentioning

confidence: 99%

Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program

et al. 2016

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The last decade has seen a marked rise in the use of cancer tissues obtained from research autopsies. Such resources have been invaluable for studying cancer evolution or the mechanisms of therapeutic resistance to targeted therapies. Degradation of biomolecules is a potential challenge to usage of cancer tissues obtained in the post-mortem setting and remains incompletely studied. We analysed the nucleic acid quality in 371 different frozen tissue samples collected from 80 patients who underwent a research autopsy, including eight normal tissue types, primary and metastatic tumors. Our results indicate that RNA integrity number (RIN) of normal tissues decline with the elongation of post-mortem interval (PMI) in a tissue-type specific manner. Unlike normal tissues, the RNA quality of cancer tissues is highly variable with respect to post-mortem interval. The kinetics of DNA damage also has tissue type-specific features. Moreover, while DNA degradation is an indicator of low RNA quality, the converse is not true. Finally, we show that despite RIN values as low as 5.0, robust data can be obtained by RNA sequencing that reliably discriminates expression signatures.

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Section: Resultsmentioning

confidence: 99%

Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program

et al. 2016

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“…Moreover, many studies used only tumor 6,8 or diseased 11,12,16 tissue, did not access RNA quality in a comparable manner, 7,10,15 nor were measures of outcome statistically quantified. 2,6,7,10 The importance of these previously established, and newly proposed, variables in maximizing human pancreas RNA quality have not been evaluated alone or in combination with one another. Therefore, this study was performed to identify predictors that increase the odds of obtaining high quality human pancreatic RNA in samples made available through the Network for Pancreatic Organ Donors with Diabetes (nPOD) program.…”

Section: Introductionmentioning

confidence: 99%

Factors That Influence the Quality of RNA From the Pancreas of Organ Donors

et al. 2017

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Objectives Attaining high quality RNA from the tissues or organs of deceased donors used for research can be challenging due to physiological and logistical considerations. In this investigation, Methods RNA Integrity Number (RIN) was determined in pancreatic samples from 236 organ donors and utilized to define high (≥6.5) and low (≤4.5) quality RNA. Logistic regression was used to evaluate the potential effects of novel or established organ and donor factors on RIN. Results Univariate analysis revealed donor cause of death (Odds Ratio [OR]=0.35, 95% Confidence Interval [CI]=0.15–0.77, p=0.01), prolonged tissue storage prior to RNA extraction (OR=0.65, 95%CI 0.52–0.79, p<0.01), pancreas region sampled (multiple comparisons, p<0.01), and sample type (OR=0.32, 95%CI 0.15–0.67, p<0.01) negatively influenced outcome. Conversely, duration of final hospitalization (OR=3.95, 95%CI 1.59–10.37, p<0.01) and sample collection protocol (OR=8.48, 95%CI 3.96–19.30, p<0.01) positively impacted outcome. Islet RNA obtained via laser capture microdissection improved RIN when compared to total pancreatic RNA from the same donor (∆RIN=1.3, 95%CI 0.6–2.0, p<0.01). Conclusions A multivariable model demonstrates that autopsy- and biopsy-free human pancreata received, processed, and preserved at a single center, using optimized procedures, from organ donors dying of anoxia with normal lipase levels increase the odds of obtaining high-quality RNA.

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“…Unfortunately neither sample type could be obtained from badly decomposed or charred bodies. In such cases, alternative biological samples such as muscle [22], liver [2], brain tissue [31] or a fragment of the femoral head [32,33] would need to be obtained as a DNA sample. Additionally, further research will need to be conducted in order to determine if the EasiCollect device will be effective in collecting buccal DNA samples from individuals with extraneous substances in their oral cavities.…”

Section: Methods Ofmentioning

confidence: 99%

“…Although blood was previously regarded as the standard specimen for the collection of DNA samples within the ISSN: 2330-0396 mortuary, Hansen et al found that it is not always the best specimen for use in this setting due to the potential presence of coagulation and haemolysis which may inhibit sample collection [22]. Additional issues arise with the collection of this sample type in South African mortuaries due to the lack of a pre-packaged, sterile and quality controlled kit for sample collection.…”

Section: Introductionmentioning

confidence: 99%

Efficiency of Buccal DNA Sampling Device in the Mortuary

2015

J Forensic investig

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Identification of forensic DNA samples by short tandem repeat (STR) profiling is currently an essential component of criminal investigations and can aid in linking perpetrators to crimes as well as identifying missing individuals or unidentified remains. In South Africa, recent amendments to legislation have allowed for the mandatory acquisition of reference DNA samples from certain offenders in order to populate the new National Forensic DNA Database. A novel method for the collection of buccal samples, the EasiCollect device, has been proposed to facilitate the collection of these DNA samples, replacing blood collecting devices as the standard method of DNA collection. Subsequently, this device has been introduced into South African state mortuaries to assist in the identification of deceased individuals. In order to ascertain if this device is suitable for use in the postmortem setting, an investigation was performed to compare the main methodology currently utilised within South African mortuaries, namely femoral blood transferred to 'Fast Technology for Analysis of nucleic acids' (FTA) cards, and buccal cells obtained using the EasiCollect device. DNA yields and STR genotyping results were compared between the two collection methods in thirty deceased individuals. Buccal samples provided a significantly greater DNA yield than blood samples, while no significant difference was observed between the qualities of the sample types as measured by the 260/280 nm ratio. Full STR profiles were obtained from all blood and buccal samples, with amplification efficiency showing limited DNA degradation and PCR inhibition in these samples, and only 3% of samples giving potentially disputable results. Numerous issues surrounding the collection of blood samples, however, indicated that this method is not optimal for use in the mortuary, with the EasiCollect device providing a more practical and robust method for the collection of DNA samples in the mortuary.

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DNA and RNA analysis of blood and muscle from bodies with variable postmortem intervals

Cited by 41 publications

References 43 publications

Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program

Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program

Factors That Influence the Quality of RNA From the Pancreas of Organ Donors

Efficiency of Buccal DNA Sampling Device in the Mortuary

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