Forensic genetic investigation of human skeletal remains recovered from the La Belle shipwreck

From flesh to bones: Multi-omics approaches in forensic science

Recent advancements in omics techniques have revolutionised the study of biological systems, enabling the generation of high-throughput biomolecular data. These innovations have found diverse applications, ranging from personalised medicine to forensic sciences. While the investigation of multiple aspects of cells, tissues or entire organisms through the integration of various omics approaches (such as genomics, epigenomics, metagenomics, transcriptomics, proteomics and metabolomics) has already been established in fields like biomedicine and cancer biology, its full potential in forensic sciences remains only partially explored. In this review, we have presented a comprehensive overview of state-of-the-art analytical platforms employed in omics research, with specific emphasis on their application in the forensic field for the identification of the cadaver and the cause of death. Moreover, we have conducted a critical analysis of the computational integration of omics approaches, and highlighted the latest advancements in employing multi-omics techniques for forensic investigations.

Improving the strategy to identify historical military remains: a literature review and Y-STR meta-analysis

The identification of historical military remains by Unrecovered War Casualties-Army (UWC-A) currently relies on Y-chromosome Short Tandem Repeat (Y-STR) testing when maternal relatives are not available, or when a mitochondrial DNA match does not provide sufficient certainty of identification. However, common Y-STR profiles (using Yfiler™) between sets of remains or families often prevent identification. To resolve these cases, an investigation of additional Y-DNA markers is needed for their potential inclusion into the DNA identification strategy. The number of genetic transmissions between missing soldiers and their living relatives needs to be considered to avoid false exclusions between paternal relatives. Analysis of 236 World War I/II (WWI/II) era pairs of relatives identified up to seven genetic transmissions between WWII soldiers and their living relatives, and nine for WWI. Previous Y-STR meta-analyses were published approximately 10 years ago when rapidly mutating markers were relatively new. This paper reports a contemporary literature review and meta-analysis of 35 studies (which includes 23 studies not previously used in meta-analysis) and 23 commonly used Y-STR's mutation rates to inform the inclusion of additional loci to UWC-A's DNA identification strategy. Meta-analysis found mutation data for a given Y-STR locus could be pooled between studies and that the mutation rates were significantly different between some loci (at P < 0.05). Based on this meta-analysis, we have identified two additional markers from PowerPlex® Y23 for potential inclusion in UWC-A's identification strategy. Further avenues for potential experimental exploration are discussed.

Key points

From 236 UWC-A pairs of relatives, we observed up to nine genetic transmissions between WWI soldiers and their living relatives, and seven for WWII.MedCalc® software for meta-analysis utilizing the Freeman-Tukey transformation was run, which analysed 35 published studies and 23 commonly used loci. Previous Y-STR mutation rate meta-analyses are now 10 years old; this paper includes 23 studies that were not included in previous meta-analyses.Through meta-analysis, we identify two markers from PowerPlex® Y23 for potential inclusion in UWC-A's historical remains identification strategy (alongside Yfiler™). We discuss potential next steps for experimental exploration of additional Y-DNA markers.

Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics

Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.

Two caseworks for one gene: successful species identification from compromised bone materials with the 12S rRNA

The availability of a reliable molecular assay in species recognition in forensic cases is of paramount importance when visual inspection or morphological methods are not exhaustive, especially from challenging samples. Here, two different caseworks involving bone samples founded during medico-legal outdoor investigations are presented. In order to exclude the human nature of the specimens and to determine the exact species they belong to, we proceeded with the molecular approach trying to generate sequences from the classical mtDNA markers cyt b and COI. However, they both gave critical results. For this reason, a short amplicon of ~ 150 bp of the 12S rRNA gene was used as an alternative.This short fragment was sufficient to identify the biological origin of the bone specimens with a high degree of certainty leading to the exclusion of their human nature. This work highlights the utility of the 12S rRNA and underlines the importance of deepen the choice of alternative shorter markers with respect to the classical ones, in order to achieve species identification even from challenging and degraded material in forensic criminal and wildlife caseworks.

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.

Validation of the Verogen ForenSeq™ DNA Signature Prep kit/Primer Mix B for phenotypic and biogeographical ancestry predictions using the Micro MiSeq® Flow Cells

In anticipation of offering phenotypic and biogeographical ancestry predictions to help resolve cases, the Verogen ForenSeq™ DNA Signature Prep kit/Primer Mix B was evaluated in the context of Micro MiSeq® Flow Cells. These flow cells were determined as the best format for a quick turnaround time response and cost effective approach compared to standard flow cells. The phenotype informative SNPs (piSNPs) and ancestry informative SNPs (aiSNPs) were thoroughly examined through sensitivity, reproducibility and repeatability, concordance, robustness (mock casework) and low level DNA mixture studies purposely selecting individuals with different phenotypes (hair and eye color) when possible and different biogeographical ancestry. SNP locus-specific interpretation thresholds were established for the Universal Analysis Software (UAS) based on surviving alleles and SNP predictor rank to minimize false homozygous genotypes and maximize the information that can be derived from an unknown sample. Dropin alleles' intensity determined an appropriate threshold to minimize false heterozygous SNP genotypes. The selection of inappropriate interpretation thresholds was shown to have major consequences on phenotypic predictions. A 3.2% and 4.8% minor DNA component contribution to a DNA mixture had no impact on ancestry predictions whereas a 9.1% contribution did. The multi-locus SNP genotypes generated using the ForenSeq™ DNA Signature Prep kit/Primer Mix B were shown to be reliable, reproducible, concordant and resulted in predictions that were also reliable, reproducible and concordant based on the limited number of donors (N = 19) used in this study.

Mitochondrial DNA analysis of the putative skeletal remains of Sieur de Marle: Genetic support for anthropological assessment of biogeographic ancestry

In 1932, seven burials were discovered on a Texas plantation that was originally the site of a 17th-century Caddo Indian village. Of the seven excavated graves, one set of remains (an adult male) was notably buried in a manner inconsistent with traditional Caddoan burial practices and has long been purported to be the remains of Sieur de Marle (a member of the French explorer La Salle's last expedition). Diary accounts of La Salle's expedition scribe report that Sieur de Marle died along a river near an Indian village during a trek to Canada to find help for colonists left behind at the ill-fated Fort St. Louis. Additionally, two lead projectiles recovered from the grave were ballistically analyzed and determined to be consistent with ammunition used in 17th-century weaponry. In the 1980s, anthropologists requested access to the remains for study, but the skull was missing. Cranial measurements recorded in 1940 and 1962 (by two independent anthropologists) were used to investigate the ancestry of this individual; and the Giles-Elliot (G-E) discriminant function was calculated to be 18.1, within the Anglo-European range. Dietary isotope testing on non-cranial skeletal elements determined that this unknown male's diet was rich in animal/marine protein sources, which differs appreciably from Caddo Indian populations of that time period. In order to genetically assess this individual's biogeographic ancestry and to provide further support that this individual is of European descent, mitochondrial DNA (mtDNA) sequencing was performed using the Applied Biosystems™ Precision ID mtDNA Whole Genome Panel. mtDNA sequencing of multiple sections from two different long bones yielded compiled results consistent with either Haplogroup H or R, both predominantly European mtDNA haplogroups. Further anthropological calculations were conducted using cranial measurements, FORDISC™ software, and discriminant function analysis. Two-way, four-way, and multigroup discriminant function analyses further classify this set of unidentified remains as being White (European) in origin, with posterior probabilities of 0.999, 0.881 and 0.986, respectively. Combined with historical records of Sieur de Marle's death, as well as overlays of historical and contemporary maps which demonstrate that the plantation site aligns with Joutel's diary accounts of de Marle's burial, these collective results support that these remains are of a European male and may possibly belong to this prominent member of La Salle's expedition team.