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

Dissecting the genetic admixture and forensic signatures of ethnolinguistically diverse Chinese populations via a 114-plex NGS InDel panel

Comprehensive characterizations of genetic diversity and demographic models of ethnolinguistically diverse Chinese populations are essential for elucidating their forensic characteristics and evolutionary past. We developed a 114-plex NGS InDel panel to genotype 114 genome-wide markers and investigated the genetic structures of Zhuang, Hui, Miao, Li, Tibetan, Yi, and Mongolian populations, encompassing five language families. This panel demonstrated robust performance, with exceptional potential for forensic individual identification and paternity testing, evidenced by the combined power of discrimination for 77 autosomal InDels (ranged from 1-3.6400 × 10-30 to 1-3.5713 × 10-32) and the combined power of exclusion (ranged from 1-2.1863 × 10-6 to 1-2.1261 × 10-7). The cumulative mean exclusion chance for 32 X-chromosomal InDels varied between 0.99996 and 0.99999 for trios and 0.99760 to 0.99898 for duos. We also analyzed genetic similarities and differences between these populations and 27 global populations, revealing distinct clusters among African, South Asian, East Asian, and European groups, with a close genetic affinity to East Asians. Notably, we identified geography-related genetic substructures: Inner Mongolia Mongolians and Gansu Huis formed a northern branch, Tibetans and Yis from Sichuan constituted a highland branch, and Guangxi Zhuangs exhibited close ties with Hainan Lis and Guangxi Miaos in the southern branch. Additionally, many InDels proved to be ancestry-informative markers for biogeographic ancestry inference. Collectively, these findings underscore the utility of the 114-plex NGS InDel panel as a complementary tool for forensic investigations and as a source of insights into the genetic architecture of ethnolinguistically distinct Chinese populations.

Characterization of sequence variations in the extended flanking regions using massively parallel sequencing in 21 A-STRs and 21 Y-STRs

In forensic genetics, utilizing massively parallel sequencing (MPS) to analyze short tandem repeats (STRs) has demonstrated several advantages compared to conventional capillary electrophoresis (CE). Due to the current technical limitations, although flanking region polymorphisms had been mentioned in several previous studies, most studies focused on the core repeat regions of STRs or the variations in the adjacent flanking regions. In this study, we developed an MPS system consisting of two sets of multiplex PCR systems to detect not only the STR core repeat regions but also to observe variants located at relatively distant positions in the flanking regions. The system contained 42 commonly used forensic STRs, including 21 autosomal STRs (A-STRs) and 21 Y-chromosomal STRs (Y-STRs), and a total of 350 male individuals from a Chinese Han population were genotyped. The length and sequence variants per locus were tallied and categorized based on length (length-based, LB), sequence without flanking region (core repeat regions sequence-based, RSB), and sequence with flanking region (core repeat and flanking regions sequence-based, FSB), respectively. Allele frequencies, Y-haplotype frequencies, and forensic parameters were calculated based on LB, RSB, and FSB, respectively, to evaluate the improvement in discrimination power, heterozygosity, and effectiveness of forensic systems. The results suggested the sequence variations have more influence on A-STRs and could improve the identification ability of MPS-STR genotyping. Concordance between MPS and CE methods was confirmed by using commercial CE-based STR kits. The impact of flanking region variations on STR genotype analysis and potential factors contributing to discordances were discussed. A total of 58 variations in the flanking regions (53 SNPs/SNVs and 5 InDels) were observed and most variations (48/58) were distributed in A-STRs. In summary, this study delved deeper into the genetic information of forensic commonly used STR and advanced the application of massively parallel sequencing in forensic genetics.

Applications and Performance of Precision ID GlobalFiler NGS STR, Identity, and Ancestry Panels in Forensic Genetics

Short Tandem Repeat (STR) testing via capillary electrophoresis is undoubtedly the most popular forensic genetic testing method. However, its low multiplexing capabilities and limited performance with challenging samples are among the factors pushing scientists towards new technologies. Next-generation sequencing (NGS) methods overcome some of these limitations while also enabling the testing of Single-Nucleotide Polymorphisms (SNPs). Nonetheless, these methods are still under optimization, and their adoption into practice is limited. Among the available kits, Thermo Fisher Scientific (Waltham, MA, USA) produces three Precision ID Panels: GlobalFiler NGS STR, Identity, and Ancestry. A clear review of these kits, providing information useful for the promotion of their use, is, however, lacking. To close the gap, a literature review was performed to investigate the popularity, applications, and performance of these kits. Following the PRISMA guidelines, 89 publications produced since 2015 were identified. China was the most active country in the field, and the Identity Panel was the most researched. All kits appeared robust and useful for low-quality and low-quantity samples, while performance with mixtures varied. The need for more population data was highlighted, as well as further research surrounding variables affecting the quality of the sequencing results.

Hungarian legislation regarding implementing a forensic DNA elimination database

The inception of forensic DNA elimination database represents a pivotal advancement in forensic science, aiming to streamline the process of distinguishing between DNA found at crime scenes and that of individuals involved in the investigation process, such as law enforcement personnel and forensic lab staff. In subsequent phases, once familiarity with the database is achieved by its administrators and other stakeholders, and they have accrued sufficient experience, the possibility of expanding the database to encompass first responders-including firefighters, paramedics, emergency medical technicians, and other emergency services personnel-can be contemplated. Key challenges in managing these databases encompass the grounds for collecting samples, ensuring the integrity of both samples and profiles, along with the duration of retention, access to the database, and the protocols to follow when a match is found in the database. This paper outlines the conceptual and detailed legislative framework in Hungary, where the forensic DNA elimination database was introduced in 2022.

The Evolution of Forensic Genomics: Regulating Massively Parallel Sequencing

Forensic genomics now enables law enforcement agencies to undertake rapid and detailed analysis of suspect samples using a technique known as massively parallel sequencing (MPS), including information such as physical traits, biological ancestry, and medical conditions. This article discusses the implications of MPS and provides ethical analysis, drawing on the concept of joint rights applicable to genomic data, and the concept of collective moral responsibility (understood as joint moral responsibility) that are applicable to law enforcement investigations that utilize genomic data. The widespread and unconstrained use of this technology without appropriate legal protections of individual moral rights and associated accountability mechanisms, could potentially not only involve violations of individual moral rights but also lead to an unacceptable shift in the balance of power between governments and the citizenry. We argue that in light of the rights of victims and the security benefits for society, there is a collective moral responsibility for individuals to submit their DNA to law enforcement and for MPS to be used where other, less invasive techniques are not effective. However, this application should be limited by legislation, including that any data obtained should be directly relevant to the investigation and should be destroyed at the conclusion of the investigation.

Global survey on evaluative reporting on DNA evidence with regard to activity-level propositions

For many criminal cases, the source of who deposited the DNA is not what the prosecutor and the defense are trying to dispute. In court, the question may be how the DNA was deposited at the crime scene rather than who the DNA came from. Although laboratories in many countries have begun to evaluate DNA evidence given formal activity-level propositions (ALPs), it is unknown how much other forensic practitioners know and what they think about activity-level evaluative reporting (ALR). To collect this information, a survey with 21 questions was submitted to international forensic science organizations across Europe, Australia, South America, Canada, Asia, and Africa. The survey combined open-ended and multiple-choice questions and received 162 responses. Responses revealed a wide range of knowledge on the topic. Overall, most respondents were somewhat knowledgeable about ALR, ALP, and current practices in court and expressed their support of the concept. A majority of participants identified gaps and obstacles regarding ALR they would like to see addressed. Examples include (1) need for more education/training at all stakeholder levels, (2) need for more DNA evidence-related data under realistic case scenarios, (3) need to internally implement and validate a formalized and objective approach for reporting, and (4) in some countries the need to achieve court admissibility. This global survey gathered the current concerns of forensic DNA practitioners and outlined several operational concerns. The information can be used to advance the implementation of ALR in laboratories and court testimony worldwide.

Microbiome-Based Stain Analyses in Crime Scenes

Recent advances in next-generation sequencing technologies (NGS) coupled with machine learning have demonstrated the potential of microbiome-based analyses in applied areas such as clinical diagnostics and forensic sciences. Particularly in forensics, microbial markers in biological stains left at a crime scene can provide valuable information for the reconstruction of crime scene cases, as they contain information on bodily origin, the time since deposition, and donor(s) of the stain. Importantly, microbiome-based analyses provide a complementary or an alternative approach to current methods when these are limited or not feasible. Despite the promising results from recent research, microbiome-based stain analyses are not yet employed in routine casework. In this review, we highlight the two main gaps that need to be addressed before we can successfully integrate microbiome-based analyses in applied areas with a special focus on forensic casework: one is a comprehensive assessment of the method's strengths and limitations, and the other is the establishment of a standard operating procedure. For the latter, we provide a roadmap highlighting key decision steps and offering laboratory and bioinformatic workflow recommendations, while also delineating those aspects that require further testing. Our goal is to ultimately facilitate the streamlining of microbiome-based analyses within the existing forensic framework to provide alternate lines of evidence, thereby improving the quality of investigations.

A Systematic Review on Commercially Available Integrated Systems for Forensic DNA Analysis

This systematic review describes and discusses three commercially available integrated systems for forensic DNA analysis, i.e., ParaDNA, RapidHIT, and ANDE. A variety of aspects, such as performance, time-to-result, ease-of-use, portability, and costs (per analysis run) of these three (modified) rapid DNA analysis systems, are considered. Despite their advantages and developmental progress, major steps still have to be made before rapid systems can be broadly applied at crime scenes for full DNA profiling. Aspects in particular that need (further) improvement are portability, performance, the possibility to analyze a (wider) variety of (complex) forensic samples, and (cartridge) costs. Moreover, steps forward regarding ease-of-use and time-to-result will benefit the broader use of commercial rapid DNA systems. In fact, it would be a profit if rapid DNA systems could be used for full DNA profile generation as well as indicative analyses that can give direction to forensic investigators which will speed up investigations.

American forensic DNA practitioners' opinion on activity level evaluative reporting

The technical advancements made in DNA profiling now allow for very low DNA amounts to be analyzed. Accordingly, the argument often made in criminal courts is not who the DNA belongs to but rather how it was deposited. Despite the complexity of the relevant DNA transfer, persistence, prevalence, and recovery issues, forensic laboratories in some European countries have used evaluative reports with activity level propositions, while this is not current practice in the United States. The purpose of this study was to gain an overview of the opinions about activity level reporting (ALR) held by forensic biologists in the United States. A seventeen-question survey was distributed to members of the American Society of Crime Laboratory Directors and U.S. members of the International Society for Forensic Genetics. The survey included multiple-choice and open-response questions and received 54 responses. The majority of responses expressed moderate support of ALR. Participants mentioned six major concerns to be addressed prior to implementing ALR in the United States: (1) effect of number of variables involved; (2) need of education for practitioners/legal system; (3) inadequate number of activity studies with realistic scenarios; (4) difficulty of achieving admissibility in court; (5) need for standardized approaches/guidelines; and (6) requisite shift in perspective as to the validity of ALR. Overall, this small segment of U.S. forensic DNA practitioners appear to be willing to implement ALR once these concerns are fully addressed and resolved. As a follow-up, it would be worthwhile exploring these and other questions with a larger group and also other disciplines.

Review of direct PCR and Rapid DNA approaches to streamline sexual assault kit testing

Crime laboratories have been faced with large casework backlogs due to lengthy processing times, limited resources and scientists, and rising crime rates. Evidence related to sexual assault crimes, specifically sexual assault kits (SAKs), heavily contribute to the reported backlogs. Although more sensitive, faster chemistries and automated techniques have been implemented over the years, the traditional STR workflow remains relatively unchanged. Enhanced workflows such as direct PCR and Rapid DNA have the potential to streamline the processing of forensic evidence items including those commonly submitted in SAKs, but the FBI QAS guidelines restrict CODIS-approved labs from implementing these methods for forensic samples. Recent studies have shown decreased turnaround times and improved or comparable profiling success with both approaches. However, review of the literature shows a lack of in-depth research comparing traditional DNA workflows to faster and more sensitive direct PCR and/or Rapid DNA approaches for evidentiary samples, especially for SAKs. By providing the forensic science and criminal justice communities with the strengths and limitations of direct PCR and Rapid DNA methods, stakeholders and policy makers may be better informed.

Development of the first DNA database and identification portal for identification of Unidentified bodies in India - UMID

Identifying missing persons and unidentified dead bodies is a well-documented global problem in recent years. To curb this issue, countries such as the USA, UK, and Australia already have well-established DNA databases. Considering the alarming number of unidentified/unclaimed dead bodies reported in India every year, it is evident that the current practices are not sufficient to establish their identities. Forensic medicine professionals are ethically, morally, and dutybound to collect information about missing and unidentified persons and work with the government agencies to determine their identity. Concerning the social and public interest, we have developed the first-ever identification portal and DNA database of unidentified dead bodies autopsied at the Department of Forensic Medicine and Toxicology, AIIMS, New Delhi, India. After the investigation officer's informed consent, biological samples from unidentified dead bodies and a detailed phenotypic description, anthropological data and other visual characteristics of the deceased are recorded at the time of autopsy. This information is uploaded on our database which is available for public access, and the genotypic information generated through STR analysis is only available for internal usage.Claimants (biological relatives) may browse through the URL (https://umid-aiims.icmr.org.in/), and if they wish to claim an unidentified dead body, they may approach as per the given guidelines. The DNA profiles generated include a total of 16 STRs (15 autosomal tetranucleotide microsatellite STRs and 1 Sex Chromosome Specific STR). The claimant's STR profile is run through the questioned database to look for a potential match. If positive, the investigating officer of that particular case is informed for further necessary action. Until December 2020, our database consisted the information of 255 individuals and two unidentified cadavers were identified. This project's success can also lead to a pioneering National DNA database of unidentified and missing persons in India.

The development of forensic DNA analysis: New debates on the issue of fundamental human rights

Before the advent of forensic DNA profiling, forensic techniques such as fingerprint examination and blood type comparison were used in the identification of suspects. DNA profiling has since become the gold standard of forensic science, and forensic DNA analysis techniques continue to evolve. Recent developments such as familial searching and phenotyping have raised ethical questions and concerns reflecting those expressed in the late 1980s when forensic DNA analysis was first introduced. At that time, attempts to use DNA evidence in criminal trials were met with challenges to its evidential value and admissibility. A common concern was whether the probative value of the evidence would outweigh its potentially prejudicial effect. This gave rise to a complex three-way debate, which revolved around first, the admissibility of the scientific principles in criminal courts; second, the scientific process involved in analysing DNA samples; and third, the impact that forensic DNA analysis may have on fundamental human rights. Ultimately, debates about the scientific process and the admissibility of such evidence in criminal trials overshadowed the debate about potential infringements of fundamental human rights. This resulted in a lack of critical discussion around the erosion of civil liberties through the use of scientific technologies. This paper revisits the early debates on the development of forensic DNA analysis. It draws parallels with current developments and analyses the potential for current and future human rights infringements, highlighting that the libertarian model offers a necessary counterbalance to the other arguments, due to its concern for maintaining fundamental rights.

Developments in forensic DNA analysis

The analysis of DNA from biological evidence recovered in the course of criminal investigations can provide very powerful evidence when a recovered profile matches one found on a DNA database or generated from a suspect. However, when no profile match is found, when the amount of DNA in a sample is too low, or the DNA too degraded to be analysed, traditional STR profiling may be of limited value. The rapidly expanding field of forensic genetics has introduced various novel methodologies that enable the analysis of challenging forensic samples, and that can generate intelligence about the donor of a biological sample. This article reviews some of the most important recent advances in the field, including the application of massively parallel sequencing to the analysis of STRs and other marker types, advancements in DNA mixture interpretation, particularly the use of probabilistic genotyping methods, the profiling of different RNA types for the identification of body fluids, the interrogation of SNP markers for predicting forensically relevant phenotypes, epigenetics and the analysis of DNA methylation to determine tissue type and estimate age, and the emerging field of forensic genetic genealogy. A key challenge will be for researchers to consider carefully how these innovations can be implemented into forensic practice to ensure their potential benefits are maximised.

Commercial DNA tests and police investigations: a broad bioethical perspective

Over 30 million people worldwide have taken a commercial at-home DNA test, because they were interested in their genetic ancestry, disease predisposition or inherited traits. Yet, these consumer DNA data are also increasingly used for a very different purpose: to identify suspects in criminal investigations. By matching a suspect's DNA with DNA from a suspect's distant relatives who have taken a commercial at-home DNA test, law enforcement can zero in on a perpetrator. Such forensic use of consumer DNA data has been performed in over 200 criminal investigations. However, this practice of so-called investigative genetic genealogy (IGG) raises ethical concerns. In this paper, we aim to broaden the bioethical analysis on IGG by showing the limitations of an individual-based model. We discuss two concerns central in the debate: privacy and informed consent. However, we argue that IGG raises pressing ethical concerns that extend beyond these individual-focused issues. The very nature of the genetic information entails that relatives may also be affected by the individual customer's choices. In this respect, we explore to what extent the ethical approach in the biomedical genetic context on consent and consequences for relatives can be helpful for the debate on IGG. We argue that an individual-based model has significant limitations in an IGG context. The ethical debate is further complicated by the international, transgenerational and commercial nature of IGG. We conclude that IGG should not only be approached as an individual but also-and perhaps primarily-as a collective issue.

Evaluation of OpenArray™ as a Genotyping Method for Forensic DNA Phenotyping and Human Identification

A custom plate of OpenArray™ technology was evaluated to test 60 single-nucleotide polymorphisms (SNPs) validated for the prediction of eye color, hair color, and skin pigmentation, and for personal identification. The SNPs were selected from already validated subsets (Hirisplex-s, Precision ID Identity SNP Panel, and ForenSeq DNA Signature Prep Kit). The concordance rate and call rate for every SNP were calculated by analyzing 314 sequenced DNA samples. The sensitivity of the assay was assessed by preparing a dilution series of 10.0, 5.0, 1.0, and 0.5 ng. The OpenArray™ platform obtained an average call rate of 96.9% and a concordance rate near 99.8%. Sensitivity testing performed on serial dilutions demonstrated that a sample with 0.5 ng of total input DNA can be correctly typed. The profiles of the 19 SNPs selected for human identification reached a random match probability (RMP) of, on average, 10⁻⁸. An analysis of 21 examples of biological evidence from 8 individuals, that generated single short tandem repeat profiles during the routine workflow, demonstrated the applicability of this technology in real cases. Seventeen samples were correctly typed, revealing a call rate higher than 90%. Accordingly, the phenotype prediction revealed the same accuracy described in the corresponding validation data. Despite the reduced discrimination power of this system compared to STR based kits, the OpenArray™ System can be used to exclude suspects and prioritize samples for downstream analyses, providing well-established information about the prediction of eye color, hair color, and skin pigmentation. More studies will be needed for further validation of this technology and to consider the opportunity to implement this custom array with more SNPs to obtain a lower RMP and to include markers for studies of ancestry and lineage.

Relative Protein Abundances and Biological Ageing in Whole Skeletal Elements

Establishing biological age is an integral part of forensic investigations, currently achieved through morphological methods with varying degrees of accuracy. Furthermore, biological ageing is much easier in juveniles than in adults, at which point traditional ageing methods struggle. Therefore, biomolecular approaches are considered of great interest, with several protein markers already recognized for their potential forensic significance. However, previous studies have typically relied on subsampling different parts of skeletal elements. Here, we attempt to evaluate the proteome of complete elements using a rat model. In the analysis of specimens spanning beyond adulthood (1 week to 1.5 years), we observed 729 unique proteins across 33 samples (three for each sex for each of the five (female) or six (male)), five of which represent newly identified proteins in relation to age estimation: vimentin, osteopontin, matrilin-1, apolipoprotein A-I, and prothrombin. Most of these follow the trend of decreasing abundance through age, with the exception of prothrombin that increases. We consider the combined use of these relative abundances, along with those of previously noted fetuin-A, biglycan, albumin, and chromogranin-A signatures, as being of potential value to the development of an age estimation tool worthy of further evaluation in forensic contexts.

The STRidER Report on Two Years of Quality Control of Autosomal STR Population Datasets

STRidER, the STRs for Identity ENFSI Reference Database, is a curated, freely publicly available online allele frequency database, quality control (QC) and software platform for autosomal Short Tandem Repeats (STRs) developed under the endorsement of the International Society for Forensic Genetics. Continuous updates comprise additional STR loci and populations in the frequency database and many further STR-related aspects. One significant innovation is the autosomal STR data QC provided prior to publication of datasets. Such scrutiny was lacking previously, leaving QC to authors, reviewers and editors, which led to an unacceptably high error rate in scientific papers. The results from scrutinizing 184 STR datasets containing >177,000 individual genotypes submitted in the first two years of STRidER QC since 2017 revealed that about two-thirds of the STR datasets were either being withdrawn by the authors after initial feedback or rejected based on a conservative error rate. Almost no error-free submissions were received, which clearly shows that centralized QC and data curation are essential to maintain the high-quality standard required in forensic genetics. While many errors had minor impact on the resulting allele frequencies, multiple error categories were commonly found within single datasets. Several datasets contained serious flaws. We discuss the factors that caused the errors to draw the attention to redundant pitfalls and thus contribute to better quality of autosomal STR datasets and allele frequency reports.

Interpreting Mixture Profiles: Comparison between Precision ID GlobalFiler™ NGS STR Panel v2 and Traditional Methods

Forensic investigation for the identification of offenders, recognition of human remains, and verification of family relationships requires the analysis of particular types of highly informative DNA markers, which have high discriminatory power and are efficient for typing degraded samples. These markers, called STRs (Short Tandem Repeats), can be amplified by multiplex-PCR (Polymerase Chain Reaction) allowing attainment of a unique profile through which it is possible to distinguish one individual from another with a high statistical significance. The rapid and progressive evolution of analytical techniques and the advent of Next-Generation Sequencing (NGS) have completely revolutionized the DNA sequencing approach. This technology, widely used today in the diagnostic field, has the advantage of being able to process several samples in parallel, producing a huge volume of data in a short time. At this time, although default parameters of interpretation software are available, there is no general agreement on the interpretation rules of forensic data produced via NGS technology. Here we report a pilot study aimed for a comparison between NGS (Precision ID GlobalFiler™ NGS STR Panel v2, Thermo Fisher Scientific, Waltham, MA, USA) and traditional methods in their ability to identify major and minor contributors in DNA mixtures from saliva and urine samples. A quantity of six mixed samples were prepared for both saliva and urine samples from donors. A total of 12 mixtures were obtained in the ratios of 1:2; 1:4; 1:6; 1:8; 1:10; and 1:20 between minor and major contributors. Although the number of analyzed mixtures is limited, our results confirm that NGS technology offers a huge range of additional information on samples, but cannot ensure a higher sensitivity in respect to traditional methods. Finally, the Precision ID GlobalFiler™ NGS STR Panel v2 is a powerful method for kinship analyses and typing reference samples, but its use in biological evidence should be carefully considered on the basis of the characteristics of the evidence.

Comparative Analysis of ANDE 6C Rapid DNA Analysis System and Traditional Methods

Rapid DNA analysis is an ultrafast and fully automated DNA-typing system, which can produce interpretable genetic profiles from biological samples within 90 minutes. This "swab in-profile out" method comprises DNA extraction, amplification by PCR multiplex, separation and detection of DNA fragments by capillary electrophoresis. The aim of study was the validation of the Accelerated Nuclear DNA Equipment (ANDE) 6C system as a typing method for reference samples according to the ISO/IEC 17025 standard. Here, we report the evaluation of the validity and reproducibility of results by the comparison of the genetic profiles generated by the ANDE 6C System with those generated by standard technologies. A quantity of 104 buccal swabs were analyzed both through the ANDE 6C technology and the traditional method (DNA extraction and quantification, amplification and separation by capillary electrophoresis). Positive typing was observed in 97% of cases for ANDE 6C technology with only three buccal swabs failing to reveal interpretable signals. Concordance was determined by comparing the allele calls generated by ANDE 6C and conventional technology. Comparison of 2800 genotypes revealed a concordance rate of 99.96%. These results met the ISO/IEC 17025 requirements, enabling us to receive the accreditation for this method. Finally, rapid technology has certainly reached a level of reliability which has made its use in laboratories of forensic genetics a reality.