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Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (5 January 2024) | Viewed by 32532

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Prof. Dr. Elena Pilli

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Forensic Molecular Anthropology Laboratory, Department of Biology, University of Florence, 50122 Florence, Italy
Interests: forensic molecular anthropology; human remains identification; DNA; STRs; SNPs; phenotyping; biogeographical ancestry; massively parallel sequencing
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Prof. Dr. Cristina Cattaneo

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Laboratorio di Antropologia e Odontologia Forense (LABANOF), Sezione di Medicina Legale, Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, 20133 Milan, Italy
Interests: forensic anthropology; forensic pathology; clinical forensic medicine; identification; migration; unidentified decedents; ambiguous loss
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Human remains identification, that is, the ability to allocate a name to an unidentified person, is an important part of a wider and complex multidisciplinary process and a crucial step for contributing to the proper and healthy functioning of a civil society and of justice. The process of identifying a person in forensic and humanitarian contexts (for example, in disaster victim identification (DVI) and missing persons identification (MPI) scenarios) does not just represent a legal necessity/duty but also a fundamental right of all individuals and their families, for administrative, criminal, civil, ethical reasons and in order to avoid the flail of ambiguous loss for relatives seeking their loved ones. The identification process implicates the comparison of information of various kinds provided by someone (a family member, a colleague, a friend) who knows the person (antemortem data) with the scientific information obtained by a range of forensic experts during the examination and study of human remains (postmortem data). Over the past twenty years, we have seen the development of new technologies in diverse scientific fields as well as an improvement of existing ones that have allowed us to obtain results that until recently were not technically feasible and affordable.

This Special Issue is aimed at investigating recent advances in human remains identification. It focuses on collecting reviews and original contributions considering the importance of a multidisciplinary approach to support the identification phases of human remains as well as innovative methodological aspects, bioinformatics and statistical tools, and future prospects of forensic/humanitarian research.

Prof. Dr. Elena Pilli
Prof. Dr. Cristina Cattaneo
Guest Editors

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Keywords

skeletal remains
missing persons
identification process
DNA analysis
forensic anthropology
forensic odontology
human rights

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17 pages, 1542 KiB

Open AccessEditor’s ChoiceArticle

A New Tool for Probabilistic Assessment of MPS Data Associated with mtDNA Mixtures

by Jennifer A McElhoe, Alyssa Addesso, Brian Young and Mitchell M Holland

Genes 2024, 15(2), 194; https://doi.org/10.3390/genes15020194 - 31 Jan 2024

Cited by 1 | Viewed by 1775

Abstract

Mitochondrial (mt) DNA plays an important role in the fields of forensic and clinical genetics, molecular anthropology, and population genetics, with mixture interpretation being of particular interest in medical and forensic genetics. The high copy number, haploid state (only a single haplotype contributed per individual), high mutation rate, and well-known phylogeny of mtDNA, makes it an attractive marker for mixture deconvolution in damaged and low quantity samples of all types. Given the desire to deconvolute mtDNA mixtures, the goals of this study were to (1) create a new software, MixtureAceMT™, to deconvolute mtDNA mixtures by assessing and combining two existing software tools, MixtureAce™ and Mixemt, (2) create a dataset of in-silico MPS mixtures from whole mitogenome haplotypes representing a diverse set of population groups, and consisting of two and three contributors at different dilution ratios, and (3) since amplicon targeted sequencing is desirable, and is a commonly used approach in forensic laboratories, create biological mixture data associated with two amplification kits: PowerSeq™ Whole Genome Mito (Promega™, Madison, WI, USA) and Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific by AB™, Waltham, MA, USA) to further validate the software for use in forensic laboratories. MixtureAceMT™ provides a user-friendly interface while reducing confounding features such as NUMTs and noise, reducing traditionally prohibitive processing times. The new software was able to detect the correct contributing haplogroups and closely estimate contributor proportions in sequencing data generated from small amplicons for mixtures with minor contributions of ≥5%. A challenge of mixture deconvolution using small amplicon sequencing is the potential generation of spurious haplogroups resulting from private mutations that differ from Phylotree. MixtureAceMT™ was able to resolve these additional haplogroups by including known haplotype/s in the evaluation. In addition, for some samples, the inclusion of known haplotypes was also able to resolve trace contributors (minor contribution 1–2%), which remain challenging to resolve even with deep sequencing. Full article

(This article belongs to the Special Issue Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods)

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18 pages, 2337 KiB

Open AccessEditor’s ChoiceArticle

Utilizing Massively Parallel Sequencing (MPS) of Human Leukocyte Antigen (HLA) Gene Polymorphism to Assess Relatedness in Deficiency Parentage Testing

by Diamanto I. Kouniaki, Konstantinos V. Fotopoulos, Katerina Tarassi and Alexandra Tsirogianni

Genes 2024, 15(2), 150; https://doi.org/10.3390/genes15020150 - 24 Jan 2024

Cited by 6 | Viewed by 1778

Abstract

In the realm of DNA testing with legal implications, the reliability and precision of genetic markers play a pivotal role in confirming or negating paternity claims. This study aimed to assess the potential utility of human leukocyte antigen (HLA) gene polymorphism through massively parallel sequencing (MPS) technology as robust forensic markers for parentage testing involving genetic deficiencies. It sought to redefine the significance of HLA genes in this context. Data on autosomal short tandem repeat (aSTR) mutational events across 18 paternity cases involving 16 commonly employed microsatellite loci were presented. In instances where traditional aSTR analysis failed to establish statistical certainty, kinship determination was pursued via HLA genotyping, encompassing the amplification of 17 linked HLA loci. Within the framework of this investigation, phase-resolved genotypes for HLA genes were meticulously generated, resulting in the definition of 34 inherited HLA haplotypes. An impressive total of 274 unique HLA alleles, which were classified at either the field 3 or 4 level, were identified, including the discovery of four novel HLA alleles. Likelihood ratio (LR) values, which indicated the likelihood of the observed data under a true biological relationship versus no relationship, were subsequently calculated. The analysis of the LR values demonstrated that the HLA genes significantly enhanced kinship determination compared with the aSTR analysis. Combining LR values from aSTR markers and HLA loci yielded conclusive outcomes in duo paternity cases, showcasing the potential of HLA genes and MPS technology for deeper insights and diversity in genetic testing. Comprehensive reference databases and high-resolution HLA typing across diverse populations are essential. Reintegrating HLA alleles into forensic identification complements existing markers, creating a potent method for future forensic analysis. Full article

(This article belongs to the Special Issue Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods)

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11 pages, 4254 KiB

Open AccessEditor’s ChoiceArticle

Amplification Failure of the Amelogenin X Gene Caused by a Rare Mutation in the Primer-Binding Region

by Miwha Chang, Jong Keun Jung, Ji Hwan Park, Ju Yeon Jung, Won-Hae Lee and Joo-Young Kim

Genes 2023, 14(11), 1986; https://doi.org/10.3390/genes14111986 - 24 Oct 2023

Cited by 2 | Viewed by 1932

Abstract

The study of gender markers is essential in forensic genetic analysis. Mutations in the X or Y homologs of the amelogenin gene can be misleading, resulting in serious mistakes in forensic genetic analysis. We recently discovered two male cases of the X homolog of the amelogenin (AMELX) allelic dropout while analyzing short tandem repeat genotypes obtained from crime scene evidence. Subsequently, we evaluated the molecular characteristics of AMELX allelic dropout in this study. We used two previously reported amelogenin primers to verify a half level of amelogenin gene amplification intensity in the two male cases, which we confirmed was caused by AMELX allelic dropout. We then characterized the point mutation using Sanger sequencing and designed mutation-specific primers that could overcome AMELX allelic dropout. Short tandem repeat genotyping analysis confirmed that the AMELX allelic dropout was recovered by the mutation-specific primer designed specifically for this case. The sequencing of the AMELX allele revealed a single-point variant from A→G at base position 7 downstream from the 3′ end in the amelogenin forward primer-binding region. This point mutation was identically found in two different male cases, resulting in AMELX allelic dropout. To our knowledge, these mutations and the X homolog amplification failure of amelogenin have not been reported in the Korean population. Our study provides a reliable approach to AMELX allelic dropout due to rare case mutations and could enable the better interpretation of gender markers for forensic samples. Full article

(This article belongs to the Special Issue Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods)

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11 pages, 459 KiB

Open AccessArticle

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

by Jezerka Inkret, Tomaž Zupanc and Irena Zupanič Pajnič

Genes 2023, 14(7), 1449; https://doi.org/10.3390/genes14071449 - 14 Jul 2023

Cited by 1 | Viewed by 1959

Abstract

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. Full article

(This article belongs to the Special Issue Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods)

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14 pages, 1369 KiB

Open AccessArticle

Comparing Genetic and Physical Anthropological Analyses for the Biological Profile of Unidentified and Identified Bodies in Milan

by Elena Pilli, Andrea Palamenghi, Alberto Marino, Nicola Staiti, Eugenio Alladio, Stefania Morelli, Anna Cherubini, Debora Mazzarelli, Giulia Caccia, Daniele Gibelli and Cristina Cattaneo

Genes 2023, 14(5), 1064; https://doi.org/10.3390/genes14051064 - 11 May 2023

Cited by 4 | Viewed by 2275

Abstract

When studying unknown human remains, the estimation of skeletal sex and ancestry is paramount to create the victim’s biological profile and attempt identification. In this paper, a multidisciplinary approach to infer the sex and biogeographical ancestry of different skeletons, using physical methods and routine forensic markers, is explored. Forensic investigators, thus, encounter two main issues: (1) the use of markers such as STRs that are not the best choice in terms of inferring biogeographical ancestry but are routine forensic markers to identify a person, and (2) the concordance of the physical and molecular results. In addition, a comparison of physical/molecular and then antemortem data (of a subset of individuals that are identified during our research) was evaluated. Antemortem data was particularly beneficial to evaluate the accuracy rates of the biological profiles produced by anthropologists and classification rates obtained by molecular experts using autosomal genetic profiles and multivariate statistical approaches. Our results highlight that physical and molecular analyses are in perfect agreement for sex estimation, but some discrepancies in ancestry estimation were observed in 5 out of 24 cases. Full article

(This article belongs to the Special Issue Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods)

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15 pages, 2706 KiB

Open AccessArticle

The Baron Pasquale Revoltella’s Will in the Forensic Genetics Era

by Paolo Fattorini, Carlo Previderè, Serena Bonin, Solange Sorçaburu Ciglieri, Pierangela Grignani, Paola Pitacco, Monica Concato, Barbara Bertoglio and Irena Zupanič Pajnič

Genes 2023, 14(4), 851; https://doi.org/10.3390/genes14040851 - 31 Mar 2023

Cited by 2 | Viewed by 1754

Abstract

In this article, we describe multiple analytical strategies that were first developed for forensic purposes, on a set of three bone samples collected in 2011. We analyzed a single bone sample (patella) collected from the artificially mummified body of the Baron Pasquale Revoltella (1795–1869), as well two femurs which allegedly belonged to the Baron’s mother (Domenica Privato Revoltella, 1775–1830). Likely due to the artificial mummification procedures, the inner part of the Baron’s patella allowed the extraction of high-quality DNA yields, which were successfully used for PCR-CE and PCR-MPS typing of autosomal, Y-specific, and mitochondrial markers. The samples extracted from the trabecular inner part of the two femurs yielded no typing results by using the SNP identity panel, whereas the samples extracted from the compact cortical part of the same bone samples allowed genetic typing, even by the employment of PCR-CE technology. Altogether, 10/15 STR markers, 80/90 identity SNP markers, and HVR1, HVR2, and HVR3 regions of the mtDNA were successfully typed from the Baron’s mother’s remains by the combined use of PCR-CE and PCR-MPS technologies. The kinship analysis showed a likelihood ratio of at least 9.1 × 10⁶ (corresponding to a probability of maternity of 99.9999999%), and thus confirmed the identity of the skeletal remains as those of the Baron’s mother. This casework represented a challenging trial for testing forensic protocols on aged bones samples. It highlighted the importance of accurately sampling from the long bones, and that DNA degradation is not blocked by freezing at −80 °C. Full article

(This article belongs to the Special Issue Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods)

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22 pages, 8657 KiB

Open AccessArticle

How Physical and Molecular Anthropology Interplay in the Creation of Biological Profiles of Unidentified Migrants

by Elena Pilli, Andrea Palamenghi, Stefania Morelli, Debora Mazzarelli, Danilo De Angelis, Richard L. Jantz and Cristina Cattaneo

Genes 2023, 14(3), 706; https://doi.org/10.3390/genes14030706 - 13 Mar 2023

Cited by 10 | Viewed by 2612

Abstract

The skeletal sex and ancestry of unidentified human crania can be inferred both from physical and from molecular features. This paper depicts and discusses the experiences of physical and molecular anthropologists on a set of commingled crania from the largest Mediterranean shipwreck disaster on 18 April 2015, in order to facilitate identification of human crania. Twenty-one disarticulated crania that were recovered from the above-mentioned shipwreck were analyzed to estimate skeletal sex and ancestry, following a physical and a molecular pipeline. The physical analyses applied morphological and metric methods that provided posterior probabilities for the crania to be classified into a sex or ancestral group. The molecular analyses were performed on petrous bones via a shotgun sequencing approach that allowed us to determine the sex of each individual and to retrieve the complete mitochondrial genome, Y chromosome single nucleotide polymorphisms, up to 597573 SNPs across the human genome from each individual. The morphometric sex analyses showed that most crania belonged to male individuals, although some estimations remained uncertain or undetermined. Inconsistent results were obtained for ancestry estimation as well, since morphological methods classified the crania mostly as European/White, in contrast to the most numerous African forms determined by craniometric analyses. This quite agreed with molecular analyses that identified only African males. Overall, undetermined and contrasting results were obtained between disciplines, preventing the creation of reliable and sound biological profiles that could provide guidance on the sex and ancestral group of the victims. Therefore, the times may not be mature for a merger of physical and molecular anthropology. However, future investigations of this research avenue would pave the way to the possible development of novel tools, methods, and wider reference databases that could address the limitations of both disciplines. Full article

(This article belongs to the Special Issue Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods)

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11 pages, 1078 KiB

Open AccessArticle

Predicting Eye and Hair Color in a Turkish Population Using the HIrisPlex System

by Ilksen Sari O, Sumeyye Zulal Simsek, Gonul Filoglu and Ozlem Bulbul

Genes 2022, 13(11), 2094; https://doi.org/10.3390/genes13112094 - 11 Nov 2022

Cited by 6 | Viewed by 10630

Abstract

Forensic DNA Phenotyping (FDP) can reveal the appearance of an unknown individual by predicting the ancestry, phenotype (i.e., hair, eye, skin color), and age from DNA obtained at the crime scene. The HIrisPlex system has been developed to simultaneously predict eye and hair color. However, the prediction accuracy of the system needs to be assessed for the tested population before implementing FDP in casework. In this study, we evaluated the performance of the HIrisPlex system on 149 individuals from the Turkish population. We applied the single-based extension (SNaPshot chemistry) method and used the HIrisPlex online tool to test the prediction of the eye and hair colors. The accuracy of the HIrisPlex system was assessed through the calculation of the area under the receiver characteristic operating curves (AUC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). The results showed that the proposed method successfully predicted the eye and hair color, especially for blue (100%) and brown (95.60%) eye and black (95.23) and brown (98.94) hair colors. As observed in previous studies, the system failed to predict intermediate eye color, representing 25% in our cohort. The majority of incorrect predictions were observed for blond hair color (40.7%). Previous HIrisPlex studies have also noted difficulties with these phenotypes. Our study shows that the HIrisPlex system can be applied to forensic casework in Turkey with careful interpretation of the data, particularly intermediate eye color and blond hair color. Full article

(This article belongs to the Special Issue Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods)

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13 pages, 4630 KiB

Open AccessArticle

The Skeletal Remains of Soldiers from the Two World Wars: Between Identification, Health Research and Memorial Issues

by Marine Meucci, Emeline Verna and Caroline Costedoat

Genes 2022, 13(10), 1852; https://doi.org/10.3390/genes13101852 - 13 Oct 2022

Cited by 6 | Viewed by 3501

Abstract

After causing mass disasters that claimed the lives of tens of thousands of soldiers from countries around the world, the two Great Wars left some of them lost and missing. In France, these corpses reside in a legal vagueness where they belong neither to forensic anthropology nor archeology. Nevertheless, the process of identification and determining the cause of death requires the use of modern forensic anthropology by applying biological profiling and DNA analysis. New genomic methods also provide insight into the health statuses of these military populations, providing new perspectives on these periods of humanitarian crisis. Full article

(This article belongs to the Special Issue Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods)

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12 pages, 2611 KiB

Open AccessEditor’s ChoiceBrief Report

Long-Term Tissue Preservation at Ambient Temperature for Post-Mass Fatality Incident DNA-Based Victim Identification

by Xavier Liang Shun Chan, Shumei Michelle Lai, Danial Asyraaf bin Hamdan, Yee Bin Ng, Onn Siong Yim and Christopher Kiu Choong Syn

Genes 2024, 15(3), 373; https://doi.org/10.3390/genes15030373 - 19 Mar 2024

Viewed by 1651

Abstract

In a mass fatality incident (MFI), effective preservation of tissue samples is the cornerstone for downstream DNA-based identification of victims. This is commonly achieved through freezing of tissue samples excised from bodies/fragmented remains which may be buried or stored in refrigerated containers. This may, however, not be possible depending on the nature of the MFI; in particular, during armed conflict/war where extended periods of electrical outages would be expected. The present study compared the effectiveness of long-term tissue preservation at ambient temperatures using two commercial products (non-iodized kitchen salt and a 40% alcoholic beverage) against a chemical preservative (Allprotect™ Tissue Reagent (Qiagen, Germantown, MD, USA)) and freezing at −20 °C. Bovine muscle tissue, used as a proxy for human tissue, was treated with the four preservation methods and sampled at six different time-points over a 24-month period. All four methods were able to preserve the bovine tissue, generally yielding STR-PCR (Short Tandem Repeat-Polymerase Chain Reaction) amplicons > 200 bp in size even at the end of 24 months. Gel electrophoresis, however, indicated that salt was more effective in preserving DNA integrity with high-molecular-weight DNA clearly visible as compared to the low-molecular-weight DNA smears observed in the other methods. This study also proposes a simple process for the rapid and low-cost preservation of tissue samples for long-term storage at ambient temperatures in support of post-incident victim identification efforts. Full article

(This article belongs to the Special Issue Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods)

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