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

Evaluating the Usefulness of Human DNA Quantification to Predict DNA Profiling Success of Historical Bone Samples

This study assessed the usefulness of DNA quantification to predict the success of historical samples when analyzing SNPs, mtDNA, and STR targets. Thirty burials from six historical contexts were utilized, ranging in age from 80 to 800 years postmortem. Samples underwent library preparation and hybridization capture with two bait panels (FORCE and mitogenome), and STR typing (autosomal STR and Y-STR). All 30 samples generated small (~80 bp) autosomal DNA target qPCR results, despite mean mappable fragments ranging from 55-125 bp. The qPCR results were positively correlated with DNA profiling success. Samples with human DNA inputs as low as 100 pg resulted in ≥80% FORCE SNPs at 10X coverage. All 30 samples resulted in mitogenome coverage ≥100X despite low human DNA input (as low as 1 pg). With PowerPlex Fusion, ≥30 pg human DNA input resulted in >40% of auSTR loci. At least 59% of Y-STR loci were recovered with Y-target qPCR-based inputs of ≥24 pg. The results also indicate that human DNA quantity is a better predictor of success than the ratio of human to exogenous DNA. Accurate quantification with qPCR is feasible for historical bone samples, allowing for the screening of extracts to predict the success of DNA profiling.

Forensic DNA Typing From Femurs and Bones of the Foot: A Study of 3 Cases

ABSTRACT

Evidence has been accumulating in the sense that femur may not always be the best option for DNA typing of skeletal remains. Recent studies have shown that bones of the hands and feet appear to be a superior source of preserved DNA. The current study reanalyzed DNA quantitation, degradation, and short tandem repeat typing in femurs, lateral cuneiforms, and distal foot phalanges. Data from 3 human identification cases involving corpses in an advanced decomposition state were collected. We found that in the studied cases, the femur provided equal or inferior results, recovering 84.9% of true alleles. Lateral cuneiforms (99.2%) and distal foot phalanges (96.8%) yielded higher percentages. In addition, more drop-ins and drop-outs were detected in femurs than cuneiforms and phalanges. This study adds to current findings that advocate for further investigation into bone selection for use in forensic practice. The impacts of our findings are limited by the small number of individuals studied and may not apply to old and degraded bones.

Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns

The integration of massively parallel sequencing (MPS) technology into forensic casework has been of particular benefit to the identification of unknown military service members. However, highly degraded or chemically treated skeletal remains often fail to provide usable DNA profiles, even with sensitive mitochondrial (mt) DNA capture and MPS methods. In parallel, the ancient DNA field has developed workflows specifically for degraded DNA, resulting in the successful recovery of nuclear DNA and mtDNA from skeletal remains as well as sediment over 100,000 years old. In this study we use a set of disinterred skeletal remains from the Korean War and World War II to test if ancient DNA extraction and library preparation methods improve forensic DNA profiling. We identified an ancient DNA extraction protocol that resulted in the recovery of significantly more human mtDNA fragments than protocols previously used in casework. In addition, utilizing single-stranded rather than double-stranded library preparation resulted in increased attainment of reportable mtDNA profiles. This study emphasizes that the combination of ancient DNA extraction and library preparation methods evaluated here increases the success rate of DNA profiling, and likelihood of identifying historical remains.

The FORCE Panel: An All-in-One SNP Marker Set for Confirming Investigative Genetic Genealogy Leads and for General Forensic Applications

The FORensic Capture Enrichment (FORCE) panel is an all-in-one SNP panel for forensic applications. This panel of 5422 markers encompasses common, forensically relevant SNPs (identity, ancestry, phenotype, X- and Y-chromosomal SNPs), a novel set of 3931 autosomal SNPs for extended kinship analysis, and no clinically relevant/disease markers. The FORCE panel was developed as a custom hybridization capture assay utilizing ~20,000 baits to target the selected SNPs. Five non-probative, previously identified World War II (WWII) cases were used to assess the kinship panel. Each case included one bone sample and associated family reference DNA samples. Additionally, seven reference quality samples, two 200-year-old bone samples, and four control DNAs were processed for kit performance and concordance assessments. SNP recovery after capture resulted in a mean of ~99% SNPs exceeding 10X coverage for reference and control samples, and 44.4% SNPs for bone samples. The WWII case results showed that the FORCE panel could predict first to fifth degree relationships with strong statistical support (likelihood ratios over 10,000 and posterior probabilities over 99.99%). To conclude, SNPs will be important for further advances in forensic DNA analysis. The FORCE panel shows promising results and demonstrates the utility of a 5000 SNP panel for forensic applications.

Extended kinship analysis of historical remains using SNP capture

DNA-assisted identification of historical remains requires the genetic analysis of highly degraded DNA, along with a comparison to DNA from known relatives. This can be achieved by targeting single nucleotide polymorphisms (SNPs) using a hybridization capture and next-generation sequencing approach suitable for degraded skeletal samples. In the present study, two SNP capture panels were designed to target ~ 25,000 (25 K) and ~ 95,000 (95 K) nuclear SNPs, respectively, to enable distant kinship estimation (up to 4th degree relatives). Low-coverage SNP data were successfully recovered from 14 skeletal elements 75 years postmortem using an Illumina MiSeq benchtop sequencer. All samples contained degraded DNA but were of varying quality with mean fragment lengths ranging from 32 bp to 170 bp across the 14 samples. SNP comparison with DNA from known family references was performed in the Parabon Fx Forensic Analysis Platform, which utilizes a likelihood approach for kinship prediction that was optimized for low-coverage sequencing data with cytosine deamination. The 25 K panel produced 15,000 SNPs on average, which allowed for accurate kinship prediction with strong statistical support in 16 of the 21 pairwise comparisons. The 95 K panel increased the average SNPs to 42,000 and resulted in an additional accurate kinship prediction with strong statistical support (17 of 21 pairwise comparisons). This study demonstrates that SNP capture combined with massively parallel sequencing on a benchtop platform can yield sufficient SNP recovery from compromised samples, enabling accurate, extended kinship predictions.

Comparison of nuclear DNA yield and STR typing success in Second World War petrous bones and metacarpals III

DNA yield and STR typing success differ among skeletal element types and within individual bones. Consequently, it is necessary to identify the skeletal elements and their intra-skeletal parts that will most likely yield utilizable and informative endogenous DNA for human identification of skeletal remains. The petrous portion of the temporal bone has been shown to be the most suitable skeletal part for sampling archaeological skeletons, and it has also been used successfully in some forensic cases. When all representative bone types were analyzed for three complete Second World War skeletons, metatarsals and metacarpals yielded more DNA than petrous bones (which generated full profiles even if the DNA yield was lower) and, among almost 200 Second World War metatarsals and metacarpals analyzed, metacarpals III were found to be the highest-yielding bones. To further improve the sampling strategy in DNA analysis of aged skeletal remains, a comparison between 26 petrous bones and 30 metacarpals III from Second World War skeletons was made considering intra-bone DNA yield variability. In metacarpals III only epiphyses were sampled, and in petrous bones only the dense part within the otic capsule was used. To exclude the influence of taphonomic issues as much as possible, petrous bones and metacarpals III from a single Second World War mass grave were examined. The difference between petrous bones and metacarpals III was explored by measuring nuclear DNA yield and success of STR typing. After cleaning the samples, full demineralization extraction was used to decalcify 0.5 g of powdered bone. PowerQuant (Promega) was used to determine DNA content and DNA degradation rates, and STR typing was performed using the PowerPlex ESI 17 Fast System (Promega). Metacarpals III produced the same DNA yields and STR typing success as petrous bones with no intra-individual difference observed in concentration of DNA, degradation rate, percentage of successfully amplified alleles, and intensity of electrophoretic signals. Sampling and processing of metacarpal III epiphyses is consequently recommended for genetic identification of highly degraded skeletal remains in routine forensic casework and in buried non-commingled aged skeletal remains whenever metacarpals III are preserved. Metacarpals III are easy to sample and less prone to contamination with modern DNA because no saw is needed for sampling in comparison to the petrous portion of the temporal bone. The data obtained in this study further improve the sampling strategy for genetic identification of Second World War skeletal remains in Slovenia.

Development of a quantitative PCR-based method for studying temporal DNA degradation in waterlogged bone

While several studies have examined temporal DNA degradation in bones collected from terrestrial environments, studies on temporal DNA degradation in bones collected from aquatic environments are limited and mostly based on case studies. The objective of this study was to assess the impact of long-term submersion, aquatic environment, bone type and DNA extraction method on DNA quality and quantity. Bone samples (scapulae and ribs), collected every ~1000 ADD from a freshwater lake and river, underwent DNA extraction via ChargeSwitch^® gDNA Plant Kit and organic phenol-chloroform methods, and DNA quantitation using both TaqMan and SYBR Green-based quantitative PCR (qPCR) methods. Results suggest that in both bone types, quality of recovered DNA (i.e., degradation index) declined significantly with increase in submersion time. Among two bone types, quality of recovered DNA from scapulae declined faster than rib samples. There was no significant difference in recovered DNA quantity between bone types, DNA extraction methods, or locations but various interactions between these variables showed significant difference. Overall, it can be concluded that DNA can be extracted from waterlogged bone in sufficient quantity to generate an STR profile up to 4000 ADD.

Next generation sequencing of STR artifacts produced from historical bone samples

STR artifacts are commonly observed in electrophoretic data and can complicate interpretation of the profiles produced. Even when a consensus approach is applied, reproducible artifacts have the potential to convolute the analysis. DNA obtained from historical bone samples is often heavily degraded and damaged, requiring the use of more sensitive procedures to increase allele recovery. Additionally, skeletal remains exposed to environmental conditions may be afflicted with microbial DNA contamination that cross-reacts with the primers during short tandem repeat (STR) multiplex amplification. STR artifacts manifested as a result of these circumstances can be sourced and characterized using new sequencing technologies to potentially ease the analysis burden. For this study, PCR product from 17 low-quality bone samples exhibiting reproducible autosomal and Y-chromosomal STR (Y-STR) artifacts in capillary electrophoresis (CE) data were sequenced with next generation sequencing (NGS). Sequenced reads were bioinformatically sorted using STRait Razor to determine the authenticity of alleles and confirm the profile generated by CE. Sequence data from the PCR products and a subset of the associated extracts were further analyzed with Kaiju to classify the microbial species present and identify potential sources of artifact peaks. A suspected Y-STR artifact was similar in sequence to Pseudomonas sp. BAY1663, a species ubiquitously found in soil. Regions of homology were observed between the Pseudomonas genome and the presumed primer binding locations for Y-STRs included in the AmpFlSTR Y-Filer STR kit. Characterization of such supposed artifact peaks may aid in interpretation of CE data and ultimately lead to increased confidence in the reported results.

Disaster victim identification operations with fragmented, burnt, or commingled remains: experience-based recommendations

Human-made and natural disasters can result in severely fragmented, compromised, and commingled human remains. The related disaster victim identification (DVI) operations are invariably challenging, with the state of the remains potentially precluding some identifications. Practitioners involved in these DVI operations will routinely face logistical, practical, and ethical challenges. This review provides information and guidance derived from first-hand experiences to individuals tasked with managing DVI operations with fragmented human remains. We outline several key issues that should be addressed during disaster preparedness planning and at the outset of an operation, when incident-specific strategies are developed. Specific challenges during recovery and examination of fragmented remains are addressed, highlighting the importance of experienced specialists at the scene and in the mortuary. DNA sample selection and sampling techniques are reviewed, as well as downstream effects of commingling and contamination, which can complicate reconciliation and emphasise the need for rigorous quality control. We also touch on issues that may arise during communication with families. While recommendations are provided, they are not intended as proscriptive policy but rather as an addition to the general recommendations given in the International Criminal Police Organization (INTERPOL) DVI Guide, to inform preparative discussions between government officials, judiciary, police, and forensic specialists.

Key points

A DVI operation for an incident characterised by many fragmented and otherwise compromised human remains poses specific challenges that may prolong and complicate identifications.

Specialists should be consulted at the outset to address key issues related to the aim and extent of the operation.

Specialist expertise in handling compromised human remains is indispensable at the scene, in the mortuary, during reconciliation, and for quality control.

Continuous consultation between representatives from government, the judiciary, law enforcement, the media, and various forensic specialists will prevent unnecessary delay and facilitate accurate and timely communication.

The effect of chemical compromise on the recovery of DNA from skeletonized human remains: A study of three World War II era incidents recovered from tropical locations

The use of DNA extracted from skeletonized human remains is a common challenge for those working in human identification. Thermal age and chemical compromise should be considered prior to performing DNA testing on skeletonized remains. Both heat and chemical contamination may cause damage to the DNA present in the osseous materials and a subsequent increase in both the difficulty and expense of DNA testing. For this study, three World War II era mass fatality events involving the US military, the USS Oklahoma, the Battle of Tarawa, and the Cabanatuan Prison Camps, were examined for the overall success of DNA testing using five DNA modalities: Sanger sequencing of mitochondrial DNA, AmpFlSTR® MiniFiler™; PowerPlex® Fusion; a modified AmpFlSTR® Yfiler™; and a Next Generation Sequencing (NGS) protocol. Decedents from the three chosen incidents were buried in tropical environments and have the same approximate post mortem interval of 75 years, however, the chemical conditions that decedents were exposed to at each of the incidents vary. Remains from the USS Oklahoma were soaked in fuel oil and salt water immediately post-mortem; Cabanatuan Prison Camp remains were treated with a 'hardening' compound; and those from the Battle of Tarawa were not treated. Skeletal elements from each incident were compared across the 5 tested DNA modalities for success. Chemical insult to skeletal materials appears to have the greatest impact on every modality of DNA testing examined.

Determination of materials present in skeletonized human remains and the associated DNA: Development of a GC/MS protocol

DNA testing of skeletonized human remains is considered to be challenging, especially when the remains have been exposed to inhibitory materials during decomposition. Inhibitors affect the processing of DNA, either by preventing efficient extraction or interfering with down-stream PCR-based processes. Limited studies have been performed on real-world samples that have been exposed to such inhibitors. This paper presents the development of a gas chromatography/mass spectrometry (GC/MS) protocol for the evaluation of materials present in skeletonized human remains recovered from the field, as well as the DNA extracted from the same materials. Twenty-one bone samples and seventeen DNA extracts were evaluated across three solvents and multiple GC/MS parameters to determine the optimal conditions for the recovery of trace materials present. The aim of this work is to provide a technique that can determine the presence of inhibitors prior to DNA extraction, allowing analysts to optimize removal of inhibitory materials.