Characterisation of identity-informative genetic markers in the Australian population with European ancestry

Identity-informative single nucleotide polymorphisms (iiSNPs) are valuable genetic markers for human identification and kinship testing in forensic casework, especially when the quality and quantity of DNA evidence is not suitable for routine short tandem repeat (STR) profiling. This study analysed 105 buccal samples representing the Australian population with European ancestry in order to assign allele frequencies and conduct population genetic analyses for 94 iiSNPs and 20 STRs. The markers were assessed by calculating relevant forensic statistics and testing for deviations from Hardy-Weinberg and linkage equilibrium. No linkage of statistical significance was observed between any of the pair-wise combinations of the combined 114 identity-informative markers and only one STR exhibited deviation from Hardy-Weinberg equilibrium (D8S1179). The probability of matching genotypes being observed within this population was of the order of 10-23 for STRs, 10-38 for iiSNPs and 10-60 for the combined identity-informative marker panel, improving the ability to discriminate between individuals when calculating likelihood ratios in direct or indirect matching scenarios. Further, the addition of iiSNPs will facilitate identifications when suboptimal STR profiles are recovered from compromised or challenging samples and aid comparisons to genetic relatives for familial or kinship testing.

Advancement and the existing landscape of forensic medicine in Africa: A comparison with developed countries

This article explores the development and challenges of forensic medicine in Africa, comparing it to developed countries. It addresses limited resources, funding, and a shortage of trained professionals. The growth of forensic investigation capabilities and the challenges of funding and technology access are discussed. Training and education have improved, but disparities remain. Partnerships with developed countries and international organizations are crucial to bridge the gap. A comprehensive legal framework is important, but disparities exist among African countries. Harmonizing forensic laws would enhance cooperation. The role of forensic medicine in the criminal justice system is examined, emphasizing the need to build trust in forensic evidence. International collaboration and capacity building are key to advancing forensic medicine in Africa. Investments in infrastructure, funding, training, and legal frameworks are required. By leveraging partnerships, Africa can develop its forensic medicine capabilities for a fair and effective criminal justice system.

A game theoretic approach to balance privacy risks and familial benefits

As recreational genomics continues to grow in its popularity, many people are afforded the opportunity to share their genomes in exchange for various services, including third-party interpretation (TPI) tools, to understand their predisposition to health problems and, based on genome similarity, to find extended family members. At the same time, these services have increasingly been reused by law enforcement to track down potential criminals through family members who disclose their genomic information. While it has been observed that many potential users shy away from such data sharing when they learn that their privacy cannot be assured, it remains unclear how potential users' valuations of the service will affect a population's behavior. In this paper, we present a game theoretic framework to model interdependent privacy challenges in genomic data sharing online. Through simulations, we find that in addition to the boundary cases when (1) no player and (2) every player joins, there exist pure-strategy Nash equilibria when a relatively small portion of players choose to join the genomic database. The result is consistent under different parametric settings. We further examine the stability of Nash equilibria and illustrate that the only equilibrium that is resistant to a random dropping of players is when all players join the genomic database. Finally, we show that when players consider the impact that their data sharing may have on their relatives, the only pure strategy Nash equilibria are when either no player or every player shares their genomic data.

Gattaca as a lens on contemporary genetics: marking 25 years into the film's "not-too-distant" future

The 1997 film Gattaca has emerged as a canonical pop culture reference used to discuss modern controversies in genetics and bioethics. It appeared in theaters a few years prior to the announcement of the "completion" of the human genome (2000), as the science of human genetics was developing a renewed sense of its social implications. The story is set in a near-future world in which parents can, with technological assistance, influence the genetic composition of their offspring on the basis of predicted life outcomes. The current moment-25 years after the film's release-offers an opportunity to reflect on where society currently stands with respect to the ideas explored in Gattaca. Here, we review and discuss several active areas of genetic research-genetic prediction, embryo selection, forensic genetics, and others-that interface directly with scenes and concepts in the film. On its silver anniversary, we argue that Gattaca remains an important reflection of society's expectations and fears with respect to the ways that genetic science has manifested in the real world. In accompanying supplemental material, we offer some thought questions to guide group discussions inside and outside of the classroom.

Sociotechnical safeguards for genomic data privacy

Recent developments in a variety of sectors, including health care, research and the direct-to-consumer industry, have led to a dramatic increase in the amount of genomic data that are collected, used and shared. This state of affairs raises new and challenging concerns for personal privacy, both legally and technically. This Review appraises existing and emerging threats to genomic data privacy and discusses how well current legal frameworks and technical safeguards mitigate these concerns. It concludes with a discussion of remaining and emerging challenges and illustrates possible solutions that can balance protecting privacy and realizing the benefits that result from the sharing of genetic information.

Forensic genetics through the lens of Lewontin: population structure, ancestry and race

In his famous 1972 paper, Richard Lewontin used 'classical' protein-based markers to show that greater than 85% of human genetic diversity was contained within, rather than between, populations. At that time, these same markers also formed the basis of forensic technology aiming to identify individuals. This review describes the evolution of forensic genetic methods into DNA profiling, and how the field has accounted for the apportionment of genetic diversity in considering the weight of forensic evidence. When investigative databases fail to provide a match to a crime-scene profile, specific markers can be used to seek intelligence about a suspect: these include inferences on population of origin (biogeographic ancestry) and externally visible characteristics, chiefly pigmentation of skin, hair and eyes. In this endeavour, ancestry and phenotypic variation are closely entangled. The markers used show patterns of inter- and intrapopulation diversity that are very atypical compared to the genome as a whole, and reinforce an apparent link between ancestry and racial divergence that is not systematically present otherwise. Despite the legacy of Lewontin's result, therefore, in a major area in which genetics coincides with issues of public interest, methods tend to exaggerate human differences and could thereby contribute to the reification of biological race. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.

Forensic Feature Exploration and Comprehensive Genetic Insights Into Yugu Ethnic Minority and Northern Han Population via a Novel NGS-Based Marker Set

The MPS technology has expanded the potential applications of DNA markers and increased the discrimination power of the targeted loci by taking variations in their flanking regions into consideration. Here, a collection of nuclear and extranuclear DNA markers (totally six kinds of nuclear genetic markers and mtDNA hypervariable region variations) were comprehensively and systematically assessed for polymorphism detections, further employed to dissect the population backgrounds in the Yugu ethnic group from Gansu province (Yugu) and Han population from the Inner Mongolia Autonomous Region (NMH) of China. The elevated efficiencies of the marker set in separating full sibling and challenging half sibling determination cases in parentage tests (iiSNPs), as well as predicting ancestry origins of unknown individuals from at least four continental populations (aiSNPs) and providing informative characteristic-related clues for Chinese populations (piSNPs) are highlighted in the present study. To sum up, different sets of DNA markers revealed sufficient effciencies to serve as promising tools in forensic applications. Genetic insights from the perspectives of autosomal DNA, Y chromosomal DNA, and mtDNA variations yielded that the Yugu ethnic group was genetically close related to the Han populations of the northern region. But we admit that more reference populations (like Mongolian, Tibetan, Hui, and Tu) should be incorporated to gain a refined genetic background landscape of the Yugu group in future studies.

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.

Avoiding genetic racial profiling in criminal DNA profile databases

DNA profiling has become an essential tool for crime solving and prevention, and CODIS (Combined DNA Index System) criminal investigation databases have flourished at the national, state and even local level. However, reports suggest that the DNA profiles of all suspects searched in these databases are often retained, which could result in racial profiling. Here, we devise an approach to both enable broad DNA profile searches and preserve exonerated citizens' privacy through a real-time privacy-preserving procedure to query CODIS databases. Using our approach, an agent can privately and efficiently query a suspect's DNA profile device in the field, learning only whether the profile matches against any database profile. More importantly, the central database learns nothing about the queried profile, and thus cannot retain it. Our approach paves the way to implement privacy-preserving DNA profile searching in CODIS databases and any CODIS-like system.

Pedigrees and Perpetrators: Uses of DNA and Genealogy in Forensic Investigations

In the past few years, cases with DNA evidence that could not be solved with direct matches in DNA databases have benefited from comparing single-nucleotide polymorphism data with private and public genomic databases. Using a combination of genome comparisons and traditional genealogical research, investigators can triangulate distant relatives to the contributor of DNA data from a crime scene, ultimately identifying perpetrators of violent crimes. This approach has also been successful in identifying unknown deceased persons and perpetrators of lesser crimes. Such advances are bringing into focus ethical questions on how much access to DNA databases should be granted to law enforcement and how best to empower public genome contributors with control over their data. The necessary policies will take time to develop but can be informed by reflection on the familial searching policies developed for searches of the federal DNA database and considerations of the anonymity and privacy interests of civilians.

Next generation sequencing of a set of ancestry-informative SNPs: ancestry assignment of three continental populations and estimating ancestry composition for Mongolians

When traditional short tandem repeat profiling fails to provide valuable information to arrest the criminal, forensic ancestry inference of the biological samples left at the crime scene will probably offer investigative leads and facilitate the investigation process of the case. That is why there are consistent efforts in developing panels for ancestry inference in forensic science. Presently, a 30-plex next generation sequencing-based assay was exploited in this study by assembling well-differentiated single nucleotide polymorphisms for ancestry assignment of unknown individuals from three continental populations (African, European and East Asian). And meanwhile, relatively balanced population-specific differentiation values were maintained to avoid the over-estimation or under-estimation of co-ancestry proportions in individuals with admixed ancestry. The principal component analysis and STRUCTURE analysis of reference populations, test populations and the studied Mongolian group indicated that the novel assay was efficient enough to determine the ancestry origin of an unknown individual from the three continental populations. Besides, ancestry membership proportion estimations for the Mongolian group revealed that a large fraction of the ancestry was contributed by East Asian genetic component (approximately 83.9%), followed by European (approximately 12.6%) and African genetic components (approximately 3.5%), respectively. And next generation sequencing technology applied in this study offers possibility to incorporate more single nucleotide polymorphisms for individual identification and phenotype prediction into the same assay to provide as many as possible investigative clues in the future.

Mind the gap: resources required to receive, process and interpret research-returned whole genome data

Most genotype-phenotype studies have historically lacked population diversity, impacting the generalizability of findings and thereby limiting the ability to equitably implement precision medicine. This well-documented problem has generated much interest in the ascertainment of new cohorts with an emphasis on multiple dimensions of diversity, including race/ethnicity, gender, age, socioeconomic status, disability, and geography. The most well known of these new cohort efforts is arguably All of Us, formerly known as the Precision Medicine Cohort Initiative Program. All of Us intends to ascertain at least one million participants in the United States representative of the multiple dimensions of diversity. As an incentive to participate, All of Us is offering the return of research results, including whole genome sequencing data, as well as the opportunity to contribute to the scientific process as non-scientists. The scale and scope of the proposed return of research results are unprecedented. Here, we briefly review possible return of genetic data models, including the likely data file formats and modes of data transfer or access. We also review the resources required to access and interpret the genetic or genomic data once received by the average participant, highlighting the nuanced anticipated barriers that will challenge both the digitally, computationally literate and illiterate participant alike. This inventory of resources required to receive, process, and interpret return of research results exposes the potential for access disparities and warns the scientific community to mind the gap so that all participants have equal access and understanding of the benefits of human genetic research.