Bringing colour back after 70 years: Predicting eye and hair colour from skeletal remains of World War II victims using the HIrisPlex system

An optimal skeletal element for DNA testing: Evaluation of DNA quantity and quality from various bone types in routine forensic practice

For human identification, the quality and quantity of DNA must be sufficient for amplification and analysis. When DNA extraction from bone tissues and teeth is required, the optimal skeletal elements should be selected as samples for DNA extraction because DNA yield differs among elements. Recently, some studies have reported that a high quantity of high-quality DNA can be extracted from the small cancellous bones of the hands and feet. In this study, we evaluated the effectiveness of small cancellous bones in the human identification of skeletal remains in routine forensic genetic casework. Cancellous bones [phalanges, (meta)carpal bones, and (meta)tarsal bones)] and the cortical bones (femur and petrous bones) and teeth, which have generally been recommended as samples, were collected from the same individuals that needed identifying using DNA analysis in our laboratory. The quantity of DNA from small cancellous bones tended to be higher than that from cortical bones, and the quality from the former was as high as that from the latter. This study showed that in routine forensic casework, the small cancellous bones of the hands and feet should be actively selected as samples for DNA testing.

Eye and hair color prediction of human DNA recovered from Lucilia sericata larvae

Forensic entomological evidence is employed to estimate minimum postmortem interval (PMImin), location, and identification of fly samples or human remains. Traditional forensic DNA analysis (i.e., STR, mitochondrial DNA) has been used for human identification from the larval gut contents. Forensic DNA phenotyping (FDP), predicting human appearance from DNA-based crime scene evidence, has become an established approach in forensic genetics in the past years. In this study, we aimed to recover human DNA from Lucilia sericata (Meigen 1826) (Diptera: Calliphoridae) gut contents and predict the eye and hair color of individuals using the HIrisPlex system. Lucilia sericata larvae and reference blood samples were collected from 30 human volunteers who were under maggot debridement therapy. The human DNA was extracted from the crop contents and quantified. HIrisPlex multiplex analysis was performed using the SNaPshot minisequencing procedure. The HIrisPlex online tool was used to assess the prediction of the eye and hair color of the larval and reference samples. We successfully genotyped 25 out of 30 larval samples, and the most SNP genotypes (87.13%) matched those of reference samples, though some alleles were dropped out, producing partial profiles. The prediction of the eye colors was accurate in 17 out of 25 larval samples, and only one sample was misclassified. Fourteen out of 25 larval samples were correctly predicted for hair color, and eight were misclassified. This study shows that SNP analysis of L. sericata gut contents can be used to predict eye and hair color of a corpse.

Operationalisation of the ForenSeq® Kintelligence Kit for Australian unidentified and missing persons casework

Single nucleotide polymorphism (SNP) genotyping technologies can generate investigative leads for human remains identification, including estimation of biological sex, biogeographical ancestry (BGA), externally visible characteristics (EVCs), identity, uniparental lineage and extended kinship. The ForenSeq® Kintelligence Kit provides forensic laboratories with the ability to apply this suite of genetic tools to forensic samples using one panel targeting 10,230 SNPs (including 56 ancestry-informative, 24 phenotype-informative, 94 identity-informative, 106 X chromosome, 85 Y chromosome and 9867 kinship-informative SNPs) sequenced on the MiSeq FGx® Sequencing System. The ForenSeq® Kintelligence Kit has been internally validated, optimised and operationalised by the Australian Federal Police National DNA Program for Unidentified and Missing Persons (AFP Program) for coronial casework. The internal validation was conducted according to the Scientific Working Group on DNA Analysis Methods guidelines (excluding mixture analysis), focussing on sample types typically encountered in human remains identification casework, such as bones, teeth, nail, blood and hair. The workflow was optimised for a high throughput library preparation and sequencing workflow, and additional analytical thresholds were developed to improve genotyping accuracy for low DNA input samples. Additionally, the genetic intelligence generated from the kit was compared to the self-declared biological sex, EVCs and BGA of the DNA donors to assess concordance. The kit was able to produce high quality SNP profiles from 1.0 ng down to 0.1 ng of DNA, with high repeatability and reproducibility, and minimal background noise. The prediction accuracy for biological sex (95%), hair colour (58%), eye colour (74%) and BGA inferences (consistent: 74%; partially consistent: 10%; inconclusive: 16%) was determined based on self-declared data. Additionally, SNP profiles from a volunteer family group of ten related individuals were uploaded to GEDmatch PRO™ to assess kinship accuracy. The kit was capable of detecting (97%) and accurately classifying (90%) genetic relationships spanning from first to fifth degree. The Kintelligence Kit provides the AFP Program with a robust and reliable genetic intelligence tool for unidentified and missing persons investigations, which has been designed to sequence multiple challenging samples in a single multiplexed assay using existing laboratory instrumentation.

Genetic landscape of forensic DNA phenotyping markers among Mediterranean populations

Forensic DNA Phenotyping can reveal the appearance of an unknown individual by predicting the External Visible Characteristics (EVC) from DNA obtained at the crime scene. Our aim is to characterize the genetic landscape of Human identification markers responsible for EVC among Mediterranean populations compared to other worldwide groups. We conducted an exhaustive search for genes involved in EVC variation. Then, variants located on these genes were extracted from public genotypic data of Mediterranean, American, African and East Asiatic populations. The genetic landscape of these Human identification markers, their allelic distribution and admixture analyses, were determined using plink, R and ADMIXTURE softwares. Our results showed that the Mediterranean populations appear close to the Mexican populations and distinguished from sub Saharan African populations living in the USA and from East Asiatic populations. We highlighted a total of 103454 common variants shared between the studied populations and among them, 25 common variants associated with EVC. Interestingly, genotype frequencies results showed that the rs17646946, rs13016869, rs977588, rs1805008 and rs2240751 variants located respectively in the TCHH, PRKCE, OCA2, MC1R and MFSD12 genes are significantly different between the Mediterranean and Asiatic populations. The genotype frequencies of the variants rs977589 and rs7179994 located in the OCA2 gene, and of rs12913832 and rs2240751 located respectively in HERC2 and MFSD12 genes are significantly different between the Mediterranean and American populations. Our work generates a large number of EVC variants that could be a valuable resource for future studies in the forensic field.

A Multisample Approach in Forensic Phenotyping of Chronological Old Skeletal Remains Using Massive Parallel Sequencing (MPS) Technology

It is very important to generate phenotypic results that are reliable when processing chronological old skeletal remains for cases involving the identification of missing persons. To improve the success of pigmentation prediction in Second World War victims, three bones from each of the eight skeletons analyzed were included in the study, which makes it possible to generate a consensus profile. The PowerQuant System was used for quantification, the ESI 17 Fast System was used for STR typing, and a customized version of the HIrisPlex panel was used for PCR-MPS. The HID Ion Chef Instrument was used for library preparation and templating. Sequencing was performed with the Ion GeneStudio S5 System. Identical full profiles and identical hair and eye color predictions were achieved from three bones analyzed per skeleton. Blue eye color was predicted in five skeletons and brown in three skeletons. Blond hair color was predicted in one skeleton, blond to dark blond in three skeletons, brown to dark brown in two skeletons, and dark brown to black in two skeletons. The reproducibility and reliability of the results proved the multisample analysis method to be beneficial for phenotyping chronological old skeletons because differences in DNA yields in different bone types provide a greater possibility of obtaining a better-quality consensus profile.

Forensic DNA extraction methods for human hard tissue: A systematic literature review and meta-analysis of technologies and sample type

DNA identification of human remains has a valuable role in the field of forensic science and wider. Although DNA is vital in identification of unknown human remains, post-mortem environmental factors can lead to poor molecular preservation. In this respect, focus has been placed on DNA extraction methodologies for hard tissue samples, as these are the longest surviving. Despite decades of research being conducted on DNA extraction methods for bone and teeth, little consensus has been reached as to the best performing. Therefore, the aim of this study was to conduct a thorough systematic literature review to identify potential DNA extraction technique(s) which perform optimally for forensic DNA profiling from hard tissue samples. PRISMA guidelines were used, by which a search strategy was developed. This included identifying databases and discipline specific journals, keywords, and exclusion and inclusion criteria. In total, 175 articles were identified that detailed over 50 different DNA extraction methodologies. Results of the meta-analysis conducted on 41 articles - meeting further inclusion criteria - showed that statistically significant higher DNA profiling success was associated with solid-phase magnetic bead/resin methods. In addition, incorporating a demineralisation pre-step resulted in significantly higher profiling successes. For hard tissue type, bone outperformed teeth, and even though dense cortical femur samples were more frequently used across the studies, profiling success was comparable, and in some cases, higher in cancellous bone samples. Notably, incomplete data sharing resulted in many studies being excluded, thus an emphasis for minimum reporting standards is made. In conclusion, this study identifies strategies that may improve success rates of forensic DNA profiling from hard tissue samples. Finally, continued improvements to current methods can ensure faster times to resolution and restoring the identity of those who died in obscurity.

Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach

To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd to the 18th centuries AD, and for each of them at least four bone types were analyzed (for a total of 47 samples). In the second set, 24 skeletons from the Second World War were analyzed, and only petrous bones from the skulls were tested. Good-quality libraries were achieved in 83.3% of the cases for the ancient skeletons and in all Second World War petrous bones, with 94.7% and 100% of the markers, respectively, suitable for SNP typing. Consensus typing was achieved for about 91.7% of the markers in 10 out of 11 ancient skeletons, and the HIrisPlex-S webtool was then used to generate phenotypic predictions. Full predictions were achieved for 3 (27.3%) ancient skeletons and 12 (50%) Second World War petrous bones. In the remaining cases, different levels of AUC (area under the receiver operating curve) loss were computed because of no available data (NA) for 8.3% of markers in ancient skeletons and 4.2% of markers in Second World War petrous bones. Although the PCR-based approach has been replaced with new techniques in ancient DNA studies, the results show that customized forensic technologies can be successfully applied to aged bone remains, highlighting the role of the template in the success of PCR-MPS analysis. However, because several typical errors of ancient DNA sequencing were scored, replicate tests and accurate evaluation by an expert remain indispensable tools.

Identification of a Slovenian prewar elite couple killed in the Second World War

Genetic identification of a Slovenian prewar elite couple killed in 1944 was performed by typing autosomal and Y-chromosomal STRs, and phenotypic HIrisPlex SNPs for hair and eye color prediction were analyzed for the female skeleton using next-generation sequencing (NGS) technology. The clandestine grave containing the couple's skeletal remains was found in 2015 and only the partial remains were found. Living distant relatives could be found only for the male victim. Because of a lack of comparative reference samples, it was not possible to identify the female victim through autosomal and mitochondrial DNA typing. However, the possibility of comparison of eye and hair color with a painting exhibited in the City Museum of Ljubljana by the prominent Slovenian painter Ivana Kobilca existed. Nuclear DNA obtained from the samples was quantified using the PowerQuant System, and then STR typing was carried out with different autosomal and Y-STR kits. From 0.09-9.36 ng DNA/g of powder was obtained from teeth and bones analyzed. Complete autosomal and Y-STR profiles made it possible to identify the male skeleton via comparison with two nephews. For the female victim, predicted eye and hair color was compared to colors on the painting. Kobilca's painting confirms the genetically predicted eye and hair color. After more than seventy years, the skeletal remains of the couple were handed over to their relatives, who buried the victims with dignity in a family grave.

Comparative evaluation of different human dental tissues and alveolar bone for DNA quantity and quality for forensic investigation

In this study, the efficacy of dental tissues (cementum, dentine and pulp) and alveolar bone as a potential source of DNA was tested in terms of the quality and quantity using nuclear and mitochondrial markers for forensic investigation.This study found dentine as the best source of DNA with only 5.36% imbalanced (PHR<0.7) heterozygous loci. Pulp showed the highest quantity of DNA but exhibited 22.3% imbalanced (PHR<0.7) heterozygous loci. Cementum with highest (46.67%) heterozygote imbalance proved to be the last choice as a source of DNA. Alveolar bone exhibited the second-highest total yield of DNA/mg of tissue. All Global Filer™ STR loci were amplified in 70% samples of fresh alveolar bone whereas for 30% samples, only partial profile was generated along with successful sex determination. All the dental tissues and alveolar bone samples amplified non STR markers (D-loop, Cytochrome Oxidase I, SRY, AMEL). Of the alveolar bones from archival samples, one sample exhibited full STR profile whereas other alveolar bone samples gave partial profiles. This study substantiates alveolar bone as an alternate source of nuclear and mitochondrial DNA.

Ancestry and phenotype predictions from touch DNA using massively parallel sequencing

Direct PCR can be used to successfully generate full STR profiles from DNA present on the surface of objects. STR profiles are only of use in cases where a potential donor profile is available for comparison, and DNA is of sufficient DNA quality and quantity to generate a reliable profile. Often, no donor information is available and only trace DNA is present on items. As a result, alternative techniques are required to generate genetic data that can provide investigative leads. Massively parallel sequencing (MPS) offers the ability to detect trace levels of DNA and improve DNA analysis success from touched items. Here, we present the first application of direct PCR coupled with MPS to generate forensic intelligence SNP data from latent DNA. The panels assessed are (1) the HIrisplex System that targets 24 SNPs to simultaneously predict hair and eye, and (2) the Precision ID Ancestry Panel that targets 165 autosomal SNPs indicative of biogeographic ancestry. For each panel, we analysed 60 touched samples across five individuals and four substrates (glass slide, fuse, zip-lock bag and wire) using Ion AmpliSeq Library Preparation Kit on the automated Ion Chef System and Ion Torrent PGM. We examine the SNP recovery, concordance with reference samples and the genotype reproducibility from different substrates and donors. The results demonstrate the application of this approach for obtaining informative genetic from trace amounts of DNA.

Insights on hair, skin and eye color of ancient and contemporary Native Americans

Over the past few years, tools capable of predicting pigmentation phenotypes have been developed aiming to contribute for criminal and anthropological investigations. In this study, we used eight genetic systems to infer eye, hair, and skin color of ancient and contemporary Native Americans. To achieve this goal, we retrieved 61 SNPs from 42 samples available in free online repositories of DNA sequences. We performed pigmentation predictions using two freely available tools, HIrisPlex-S and Snipper, in addition to two other published models. This workflow made possible to predict all three phenotypes with at least one tool for 29 out of the 42 samples. Considering these 29 individuals, predictions for eye, hair, and skin color were obtained with HIrisPlex-S for 27, 28 and 27 individuals, respectively, while 24, 25 and 25 individuals had such predictions with Snipper. In general, ancient and contemporary Native Americans were predicted to have intermediate/brown eyes, black hair, and intermediate/darker skin pigmentation.

The challenge of predicting human pigmentation traits in degraded bone samples with the MPS-based HIrisPlex-S system

Identification of human remains is an important part of human DNA analysis studies. STR and mitochondrial DNA markers are well suited for the analysis of degraded biological samples including bone material. However, these DNA markers may be useless when reference material is not available. In these cases, predictive DNA analysis can support the process of human identification by providing investigative leads. Forensic DNA phenotyping has progressed significantly by offering new methods based on massively parallel sequencing technology, but the frequent degradation processes observed in skeletal remains can make analysis of such samples challenging. In this study, we demonstrate the usefulness of a recently established Ion AmpliSeq^TM HIrisPlex-S panel using Ion Torrent technology for analyzing bone samples that show different levels of DNA degradation. In total, 63 bone samples at post-mortem intervals up to almost 80 years were genotyped and eye, hair and skin colour predictions were performed using the HIrisPlex-S models. Following the recommended coverage thresholds, it was possible to establish full DNA profiles comprising of 41 DNA variants for 35 samples (55.6%). For 5 samples (7.9%) no DNA profiles were generated. The remaining 23 samples (36.5%) produced partial profiles and showed a clear underperformance of 3 HIrisPlex-S SNPs - rs1545397 (OCA2), rs1470608 (OCA2) and rs10756819 (BNC2), all used for skin colour prediction only. None of the 23 samples gave complete genotypes needed for skin colour prediction was obtained, and in 7 of them (25.9%) the 3 underperformed SNPs were the cause. At the same time, the prediction of eye and hair colour using complete IrisPlex and HIrisPlex profiles could be made for these 23 samples in 20 (87.0%) and 12 cases (52.2%), respectively. Complete HIrisPlex-S profiles were generated from as little as 49 pg of template DNA. Five samples for which the HIrisPlex-S analysis failed, consistently failed in standard STR analysis. Importantly, the 3 underperforming SNPs produced significantly lower number of reads in good quality samples. Nonetheless, the AUC loss resulting from missing data for these 3 SNPs is not considered large (≤0.004) and the prediction of pigmentation from partial profiles is also available in the current HPS tool. The study shows that DNA degradation and the resulting loss of data are the most serious challenge to DNA phenotyping of skeletal remains. Although the newly developed HIrisPlex-S panel has been successfully validated in the current research, primer redesign for the 3 underperforming SNPs in the MPS design should be considered in the future.

Interpol review of forensic biology and forensic DNA typing 2016-2019

This review paper covers the forensic-relevant literature in biological sciences from 2016 to 2019 as a part of the 19th Interpol International Forensic Science Managers Symposium. The review papers are also available at the Interpol website at: https://www.interpol.int/content/download/14458/file/Interpol%20Review%20Papers%202019.pdf.

Separating forensic, WWII, and archaeological human skeletal remains using ATR-FTIR spectra

ATR-FTIR spectroscopy is a fast and accessible, minimally or non-destructive technique which provides information on physiochemical characteristics of analyzed materials. In forensic and archaeological sciences, it is commonly used for answering numerous questions, including the archaeological or forensic context of the human skeletal remains. In this research, the accuracy of ATR-FTIR-obtained spectra for separation between forensic, WWII, and archaeological human skeletal remains was investigated. Building from the previously proposed methodological procedures, various ratio-based and whole spectra separation procedures were applied, carefully analyzed, and evaluated. Results showed that employing whole spectral domains works best for the separation of archaeological, WWII, and forensic samples, even with samples of highly variable origin. Principal component analysis (PCA) further highlighted the necessity of acknowledging all the major components in the remains: amides, phosphates, and carbonates for the separation. Most influential proved to be amide I, namely its secondary structure, which presented well-preserved and organized collagen structure in forensic and WWII samples, while highly degraded in archaeological samples. Using the whole spectral domain for separation between samples from different contexts proved to be fast and simple, with no manipulation beyond baseline correction and normalization of spectra necessary. However, a dataset with samples of known origin is required for the learning model and predictions. A less accurate alternative is separation based on combining ratios of peaks correlating to organics and minerals in the bone, which eliminated overlapping and managed to classify the majority of the samples correctly as archaeological, WWII, or forensic.

Population and performance analyses of four major populations with Illumina's FGx Forensic Genomics System

The MiSeq FGx Forensic Genomics System (Illumina) enables amplification and massively parallel sequencing of 59 STRs, 94 identity informative SNPs, 54 ancestry informative SNPs, and 24 phenotypic informative SNPs. Allele frequency and population statistics data were generated for the 172 SNP loci included in this panel on four major population groups (Chinese, African Americans, US Caucasians, and Southwest Hispanics). Single-locus and combined random match probability values were generated for the identity informative SNPs. The average combined STR and identity informative SNP random match probabilities (assuming independence) across all four populations were 1.75E-67 and 2.30E-71 with length-based and sequence-based STR alleles, respectively. Ancestry and phenotype predictions were obtained using the ForenSeq™ Universal Analysis System (UAS; Illumina) based on the ancestry informative and phenotype informative SNP profiles generated for each sample. Additionally, performance metrics, including profile completeness, read depth, relative locus performance, and allele coverage ratios, were evaluated and detailed for the 725 samples included in this study. While some genetic markers included in this panel performed notably better than others, performance across populations was generally consistent. The performance and population data included in this study support that accurate and reliable profiles were generated and provide valuable background information for laboratories considering internal validation studies and implementation.

Rapidly mutating Y-STR analyses of compromised forensic samples

Rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) were identified to improve differentiation of unrelated males and also to enable separating closely and distantly related males in human identity testing in forensic and other applications. RM-Yplex assay was developed as a single multiplex that is capable of simultaneously amplifying all currently known RM Y-STRs, and reproducibility and sensitivity testing were performed on reference samples. Additional analyses are necessary to test its suitability for analysing compromised forensic samples. For this purpose, we applied the RM-Yplex assay to approximately 70-year-old skeletons that were used as a model for poorly preserved, challenging forensic samples. We analysed 57 male skeletal remains (bones and teeth) from 55 skeletons excavated from the Second World War (WWII) mass graves in Slovenia. The RM-Yplex typing was successful in all 57 samples; there were 56% full profiles obtained, and in partial profiles, up to 7 locus drop-outs were observed and they appeared correlated with low DNA quantities and degradation of DNA obtained from WWII bone and tooth samples. The longest loci, DYS403S1b, DYS547, DYS627 and DYS526b, were the most often dropped-out RM Y-STRs. In spite of high frequency of drop-out events, the RM-Yplex typing was successful in all WWII samples, showing the possibility of successful amplification of at least half of the RM Y-STRs even from the most compromised samples analysed.