Comparing different post-mortem human samples as DNA sources for downstream genotyping and identification

Calacal, Gayvelline C.; Apaga, Dame Loveliness T.; Salvador, Jazelyn M.; Jimenez, Joseph Andrew D.; Lagat, Ludivino J.; Villacorta, Renato Pio F.; Lim, Maria Cecilia F.; Fortun, Raquel d.R.; Datar, Francisco A.; Ungria, Maria Corazon A. De

doi:10.1016/j.fsigen.2015.07.017

Cited by 32 publications

(24 citation statements)

References 8 publications

(1 reference statement)

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“…According to the manufacturer, even 22-year-old blood samples can yield short tandem repeat (STR) profiles commonly generated in forensic genetics [14]. However, most of these studies evaluated fresh blood samples which are applied immediately on the FTA cards, although other sample types also have been reported [11,[15][16][17]. Many of these studies have targeted forensically-relevant STR markers [18,19] or single nucleotide polymorphisms (SNPs) [20], and only few studies report the results from genome wide association studies [21].…”

mentioning

confidence: 99%

DNA quality and quantity from up to 16 years old post-mortem blood stored on FTA cards

Rahikainen

Palo

Leeuw

et al. 2016

Forensic Science International

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Blood samples preserved on FTA cards offer unique opportunities for genetic research. DNA recovered from these cards should be stable for long periods of time. However, it is not well established as how well the DNA stored on FTA card for substantial time periods meets the demands of forensic or genomic DNA analyses and especially so for from post-mortem (PM) samples in which the quality can vary upon initial collection. The aim of this study was to evaluate the time-dependent degradation on DNA quality and quantity extracted from up to 16 years old post-mortem bloodstained FTA cards. Four random FTA samples from eight time points spanning 1998 to 2013 (n=32) were collected and extracted in triplicate. The quantity and quality of the extracted DNA samples were determined with Quantifiler(®) Human Plus (HP) Quantification kit. Internal sample and sample-to-sample variation were evaluated by comparing recovered DNA yields. The DNA from the triplicate samplings were subsequently combined and normalized for further analysis. The practical effect of degradation on DNA quality was evaluated from normalized samples both with forensic and pharmacogenetic target markers. Our results suggest that (1) a PM change, e.g. blood clotting prior to sampling, affects the recovered DNA yield, creating both internal and sample-to-sample variation; (2) a negative correlation between the FTA card storage time and DNA quantity (r=-0.836 at the 0.01 level) was observed; (3) a positive correlation (r=0.738 at the level 0.01) was found between FTA card storage time and degradation levels. However, no inhibition was observed with the method used. The effect of degradation was manifested clearly with functional applications. Although complete STR-profiles were obtained for all samples, there was evidence of degradation manifested as decreased peak heights in the larger-sized amplicons. Lower amplification success was notable with the large 5.1 kb CYP2D6 gene fragment which strongly supports degradation of the stored samples. According to our results, DNA stored on FTA cards is rather stable over a long time period. DNA extracted from this storage medium can be used as human identification purposes as the method used is sufficiently sensitive and amplicon sizes tend to be <400 bp. However, DNA integrity was affected during storage. This effect should be taken into account depending on the intended application especially if high quality DNA and long PCR amplicons are required.

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mentioning

confidence: 99%

DNA quality and quantity from up to 16 years old post-mortem blood stored on FTA cards

Rahikainen

Palo

Leeuw

et al. 2016

Forensic Science International

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“…When generating DNA IDs from mass disaster, forensic casework, and mass graves, it is imperative to assess each set of remains to determine the optimal types of samples to process [5,22]. Temperature, moisture, and oxygen levels in the depositional environment, soil composition, and pH affect the ability to obtain analyzable DNA from biological specimens [23].…”

Section: Resultsmentioning

confidence: 99%

Identification of human remains using Rapid DNA analysis

Turingan¹,

Brown²,

Kaplun³

et al. 2019

Int J Legal Med

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Rapid identification of human remains following mass casualty events is essential to bring closure to family members and friends of the victims. Unfortunately, disaster victim identification, missing persons identification, and forensic casework analysis are often complicated by sample degradation due to exposure to harsh environmental conditions. Following a mass disaster, forensic laboratories may be overwhelmed by the number of dissociated portions that require identification and reassociation or compromised by the event itself. The interval between the disaster and receipt of victim samples at a laboratory is critical in that sample quality deteriorates as the postmortem interval increases. When bodies decompose due to delay in collection, transport, and sample processing, DNA becomes progressively fragmented, adversely impacting identification. We have previously developed a fully automated, field-forward Rapid DNA identification system that produces STR profiles (also referred to as DNA IDs or DNA fingerprints) from buccal and crime scene samples. The system performs all sample processing and data interpretation in less than 2 h. Here, we present results on Rapid DNA identification performed on several tissue types (including buccal, muscle, liver, brain, tooth, and bone) from exposed human bodies placed above ground or stored in a morgue/cooler, two scenarios commonly encountered following mass disasters. We demonstrate that for exposed remains, buccal swabs are the sample of choice for up to 11 days exposure and bone and tooth samples generated excellent DNA IDs for the 1-year duration of the study. For refrigerated remains, all sample types generated excellent DNA IDs for the 3-month testing period.

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“…All the previous studies exhibited very good amplification on the femur bone. [ 8 19 20 21 22 23 24 25 ]…”

Section: Discussionmentioning

confidence: 99%

“…As molecular genomic analysis has been limited to long bones of the body and teeth in jaws, our study highlights the use of the STR CODIS to the jaw bone where all the sites gave good amplicon though the best amplification was seen at ramus site. This study highlights that the ramus of the mandible in the head and neck region can be substituted for femur bone[ 8 19 20 21 22 23 24 25 ] owing to its easy accessibility and feasibility for bone harvest with its ample nuclear genomic DNA from bone marrow irrespective of the DNA extraction procedure.…”

Section: Discussionmentioning

confidence: 99%

Assessment of the most reliable sites in mandibular bone for the best deoxyribonucleic acid yield for expeditive human identification in forensics

Singh¹,

Bavle

Paremala

et al. 2017

J Oral Maxillofac Pathol

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Background:In recent years, the techniques used to identify human remains post accidents, trauma or in case of criminal investigation have been expanded, improved and rendered more complex by the emergence of technologies based on deoxyribonucleic acid (DNA) analysis. In the head and neck area, tooth has been proven to be the best quantitative source for DNA but in certain cases where the mandible specimen is edentulous or the tooth is extensively destroyed with caries, large dental restorations, mobile, or if they show any perimortem or postmortem fractures, sampling of such tooth specimen is usually avoided. In such situations, bone is considered the next best site for DNA analysis. Mandible being the largest, strongest and dense cortical bone is the most prominent facial bone that can be easily disarticulated. It can be analyzed for the best short tandem repeat (STR) segment qualitative amplification using polymerase chain reaction (PCR) technique for forensic analysis which can be used for gender and age determination.Aim:The aim of this study is to determine the best site for optimum quantitative and qualitative yield of DNA for amplification using specific and standard STR segment by conventional PCR technique.Methodology:Fifteen mandibular samples exposed to different environmental conditions were collected. Bone pieces of 1 cm × 1 cm were cut from each mandible from three sites, i.e., the ramus, angle and body, wherein the genomic DNA was isolated and was subjected to PCR using restricted number of 25 cycles.Results:The STR segment D3S1358 from clone RP11-438F9 used for the study showed very good amplification in restricted number of PCR cycles in the ramus region with number of repeats in every 15th genomic region.Conclusion:This study highlights the use of mandibular bone for the expeditive human identification. As per the study, the ramus of the mandible gave high quantitative and qualitative yield of DNA with thick amplification band of the STR segment as compared to the body and angle of the mandible. Thus ramus of the mandible can be preferred over other sites for molecular forensic investigations.

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Comparing different post-mortem human samples as DNA sources for downstream genotyping and identification

Cited by 32 publications

References 8 publications

DNA quality and quantity from up to 16 years old post-mortem blood stored on FTA cards

DNA quality and quantity from up to 16 years old post-mortem blood stored on FTA cards

Identification of human remains using Rapid DNA analysis

Assessment of the most reliable sites in mandibular bone for the best deoxyribonucleic acid yield for expeditive human identification in forensics

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