Prioritized Sampling of Bone and Teeth for DNA Analysis in Commingled Cases

Hines, David Z.C.; Vennemeyer, Matthew; Amory, Sylvain; Huel, René L.M.; Hanson, Ian; Katzmarzyk, Cheryl; Parsons, Thomas J.

doi:10.1016/b978-0-12-405889-7.00013-7

Cited by 23 publications

(22 citation statements)

References 6 publications

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“…Gross bone preservation and weathering has been shown to be unrelated to DNA preservation or degradation in some cases [19], while in others, indices of gross preservation are better correlated [20,23,24]. Differences in DNA preservation and degradation by bone type have been observed, though patterns are not consistent between studies (e.g., [9,10,[25][26][27][28]). Whether this has to do with differences in cortical and cancellous bone composition is debated.…”

Section: Introductionmentioning

confidence: 99%

Characterizing the postmortem human bone microbiome from surface-decomposed remains

et al. 2020

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Microbial colonization of bone is an important mechanism of postmortem skeletal degradation. However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It is unknown if microbial communities vary in abundance or composition between bone element types, which could help explain differences in human DNA preservation. The goals of the present study were to (1) identify the types of microbes capable of colonizing different human bone types and (2) relate microbial abundances, diversity, and community composition to bone type and human DNA preservation. DNA extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial loading and microbial community composition and structure. Random forest models were applied to predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant bacterial bone colonizers were from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Eukaryotic bone colonizers were from Ascomycota, Apicomplexa, Annelida, Basidiomycota, and Ciliophora. Bacterial loading was not a significant predictor of human DNA concentration in two out of three individuals. Random forest models were minimally successful in identifying microbes related to human DNA concentration, which were complicated by high variability in community structure between individuals and body regions. This work expands on our understanding of the types of microbes capable of colonizing the postmortem human skeleton and potentially contributing to human skeletal DNA degradation.

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Section: Introductionmentioning

confidence: 99%

Characterizing the postmortem human bone microbiome from surface-decomposed remains

et al. 2020

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“…However, other laboratories suggest that the smaller elements or non‐weight‐bearing bones may not be optimal for DNA recovery. The International Committee for Missing Persons (ICMP) recommends an ordered sampling strategy to begin with the femur and proceeding through the long bones as has the Armed Forces Medical Examiner System–Armed Forces DNA Identification Laboratory (AFMES‐AFDIL) . More recent studies recommend the removal of the petrous portion of the cranium , believed to be the densest bone in the body.…”

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confidence: 99%

Extraction of DNA from Skeletonized Postcranial Remains: A Discussion of Protocols and Testing Modalities

Edson

2019

Journal of Forensic Sciences

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This paper provides a retrospective of the DNA analysis performed by the Armed Forces Medical Examiner–Armed Forces DNA Identification Laboratory between 1990 and 2018. Over 13,000 postcranial osseous materials, comprised of wartime losses from World War II, the Korean War, and South‐East Asia, were examined by the following: mitochondrial DNA sequencing, a modified AmpFlSTR® Yfiler™, AmpFlSTR® MiniFiler™, PowerPlex® Fusion, or NGS. Four different DNA extraction protocols were used: incomplete demineralization coupled with an organic purification; complete demineralization with an organic purification; complete demineralization with an inorganic purification using QIAquick PCR Purification Kit; and a protocol designed specifically for use with next‐generation sequencing. In general, complete demineralization coupled with an organic purification was the optimal extraction protocol for sequencing of mitochondrial DNA, regardless of the osseous element tested. For STR testing, demineralization paired with an inorganic purification provided optimum results, regardless of kit used or osseous element tested.

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“…As methods to extract DNA from bones are being modified and improved, several studies have investigated the use of skeletal elements other than the more traditionally harvested femur, tibia, and humerus for the identification of human remains . In this study, nontraditional elements (radius, ulna, rib end, vertebral transverse process, broken tooth fragments, and hand and foot phalanges) yielded slightly higher concentrations and less degraded DNA ( p > 0.05), and resulted in significantly more alleles reported ( p < 0.01) compared with traditional bony elements (Fig.…”

Section: Resultsmentioning

confidence: 95%

“…However, due to the requirement of large amounts of starting material (0.5–5+ g) for some DNA extraction methods , many of these studies did not include partial tooth fragments or various smaller bony elements such as those from the hands, feet, and skull that do not meet the mass requirement, but may be more commonly recovered from human remains . A growing number of more recent studies have provided evidence that higher DNA and allele recovery may be obtained from some smaller and less frequently sampled bony elements such as phalanges of the hands and feet, as well as petrous bones in the skull . The increasing efficiency of DNA extraction methods for skeletal remains (with as little as 50 mg starting material required ), and sensitivity of STR kits have made it possible for a wider variety of sampling options that include these alternate skeletal elements.…”

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confidence: 99%

A Powder‐free DNA Extraction Workflow for Skeletal Samples

Harrel

Hughes‐Stamm

2019

Journal of Forensic Sciences

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The processing of skeletal material poses several challenges for forensic laboratories. Current methods can be laborious, time‐consuming, require dedicated equipment, and are vulnerable to contamination. In this study, various sample mass (1 × 50 mg, 3 × 50 mg, and 1 × 150 mg chip(s)) and incubation times (2, 4, and 16 h) were tested using the PrepFiler® BTA™ Forensic DNA Extraction Kit to digest whole bone chips in lieu of powdering. The most effective method was then applied to bones and tooth fragments collected from contemporary human cadavers exposed to various environmental conditions using an automated platform. Over a third of the samples tested generated full DNA profiles without having to powder the bone/tooth fragment or further alter the manufacturer's protocol. However, for most samples resulting in incomplete STR profiles due to low amounts of DNA, slightly better results were achieved with powdered tissue. Overall, this work demonstrates the potential use of a faster, nonpowdering DNA extraction method for processing skeletal samples as an effective first‐pass screening tool.

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Prioritized Sampling of Bone and Teeth for DNA Analysis in Commingled Cases

Cited by 23 publications

References 6 publications

Characterizing the postmortem human bone microbiome from surface-decomposed remains

Characterizing the postmortem human bone microbiome from surface-decomposed remains

Extraction of DNA from Skeletonized Postcranial Remains: A Discussion of Protocols and Testing Modalities

A Powder‐free DNA Extraction Workflow for Skeletal Samples

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