Expanded CODIS STR allele frequencies – Evidence for the irrelevance of race-based DNA databases

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

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

Genotyping strategies for tissues fixed with various embalming fluids for human identification, databasing, and traceability

Within anatomical willed body programs and skeletal collections, whole bodies and their disassociated limbs and organs are identified and tracked. However, if these tracking mechanisms fail, DNA recovered from the formalin-fixed tissues/organs could provide an additional layer of quality assurance. Embalming fluids preserve biological tissues; however, they also damage, fragment, and cross-link DNA and protein molecules. This project investigated the success of STR-typing from various soft tissue and bone samples that were fixed with embalming solutions with a range of formaldehyde concentrations. Formalin-fixed samples dissected from five cadavers, including skin, muscle, bone, heart, and kidney were used in Phase 1 of this study. In Phase 2, an additional 57 tissue samples from various embalmed organs and body parts were collected to demonstrate long-term fixation and direct applicability within a body donor program. DNA was extracted from the samples using the QIAamp® FFPE Tissue Kit (QIAGEN), quantified with the Investigator® QuantiPlex® Pro RGQ qPCR Kit (QIAGEN), and amplified using the Investigator® 24plex and 26plex QS Kits and the Investigator® DIPplex Kit (QIAGEN). The results show the DNA was severely damaged, degraded, and often in low amounts (after one year post-embalming). Sampling from skin and muscle tissues embalmed with ~2.5%-5% formaldehyde solutions appears to be the best strategy for identification, while also maintaining the preservation of the tissues. The results of this project can provide informative data when determining which genotyping strategy may be best suited for the identification, re-association, and establishment of a database for the provenance of formalin-fixed human remains.

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019-2022

This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.

Evaluating DNA Mixtures with Contributors from Different Populations Using Probabilistic Genotyping

It is common practice to evaluate DNA profiling evidence with likelihood ratios using allele frequency estimates from a relevant population. When multiple populations may be relevant, a choice has to be made. For two-person mixtures without dropout, it has been reported that conservative estimates can be obtained by using the Person of Interest’s population with a θ value of 3%. More accurate estimates can be obtained by explicitly modelling different populations. One option is to present a minimum likelihood ratio across populations; another is to present a stratified likelihood ratio that incorporates a weighted average of likelihoods across multiple populations. For high template single source profiles, any difference between the methods is immaterial as far as conclusions are concerned. We revisit this issue in the context of potentially low-level and mixed samples where the contributors may originate from different populations and study likelihood ratio behaviour. We first present a method for evaluating DNA profiling evidence using probabilistic genotyping when the contributors may originate from different ethnic groups. In this method, likelihoods are weighted across a prior distribution that assigns sample donors to ethnic groups. The prior distribution can be constrained such that all sample donors are from the same ethnic group, or all permutations can be considered. A simulation study is used to determine the effect of either assumption on the likelihood ratio. The likelihood ratios are also compared to the minimum likelihood ratio across populations. We demonstrate that the common practise of taking a minimum likelihood ratio across populations is not always conservative when FST=0. Population stratification methods may also be non-conservative in some cases. When FST>0 is used in the likelihood ratio calculations, as is recommended, all compared approaches become conservative on average to varying degrees.

Genetic syncretism: Latin American forensics and global indigenous organizing

In the 1970s, Latin America became a global laboratory for military interventions, the cultivation of terror, and ideological and economic transformation. In response, family groups and young scientists forged a new activist forensics focused on human rights, victim-centered justice, and state accountability, inaugurating new forms of forensic practice. We examine how this new form of forensic practice centered in forensic genetics has led to a critical engagement with Indigeneity both within and outside the lab. Drawing on ethnographic fieldwork with human rights activists and forensic scientists in Argentina, Guatemala and Mexico, this paper examines the relationship between forensic genetics, Indigenous organizing, and human rights practice. We offer the concept of ‘genetic syncretism’ to attend to spaces where multiple and competing beliefs about genetics, justice, and Indigenous identity are worked out through (1) coming together in care, (2) incorporation, and (3) ritual. Helping to unpack the uneasy and incomplete alliance of Indigenous interests and forensic genetic practice in Latin American, genetic syncretism offers a theoretical lens that is attentive to how differentials of power embedded in colonial logics and scientific practice are brokered through the coming together of seemingly incompatible beliefs and practices.

Parentage analysis using genome-wide high-density SNP microarray

OBJECTIVE

Parentage analysis is a technology that uses genetic methods to verify or exclude relationships between individuals. STR technology is often used in parentage analysis. We received three sets of samples from three families. Each set of samples consisted of a male individual and a female individual. Their test requirements were meant to determine whether they were a paternity relationship, a sibling relationship, or grandparent-grandchild relationship. However, only one STR locus mismatch was detected in each group. Other family members to assist in testing could not be identified; therefore, other methods were needed to assist in judgment. Using high-density SNP microarrays, we analyzed the feasibility of its application in paternity analysis.

RESULTS

A total of 180 samples were tested, including 100 unrelated samples, and 74 samples from 30 families, and six samples from three families. The data were analyzed, grouped according to the chromosome of SNP, and the mismatching rate was counted. The total mismatching rate of SNP in unrelated individuals was 8-10 times higher than that of parent-child individuals. Individuals with a total mismatch rate of more than 5.3% were defined as individuals with no kinship, and the individuals with a total mismatch rate of less than 0.6% were defined as the individuals with a parent-child relationship.

CONCLUSIONS

Through the use of high-density gene chips for analysis, we also completed an auxiliary analysis of the kinship of the three families. The gene chip is a better method for auxiliary analysis of the kinship between individuals.

Limited not lazy: a quasi-experimental secondary analysis of evidence quality evaluations by those who hold implausible beliefs

Past research suggests that an uncritical or ‘lazy’ style of evaluating evidence may play a role in the development and maintenance of implausible beliefs. We examine this possibility by using a quasi-experimental design to compare how low- and high-quality evidence is evaluated by those who do and do not endorse implausible claims. Seven studies conducted during 2019–2020 provided the data for this analysis (N = 746). Each of the seven primary studies presented participants with high- and/or low-quality evidence and measured implausible claim endorsement and evaluations of evidence persuasiveness (via credibility, value, and/or weight). A linear mixed-effect model was used to predict persuasiveness from the interaction between implausible claim endorsement and evidence quality. Our results showed that endorsers were significantly more persuaded by the evidence than non-endorsers, but both groups were significantly more persuaded by high-quality than low-quality evidence. The interaction between endorsement and evidence quality was not significant. These results suggest that the formation and maintenance of implausible beliefs by endorsers may result from less critical evidence evaluations rather than a failure to analyse. This is consistent with a limited rather than a lazy approach and suggests that interventions to develop analytical skill may be useful for minimising the effects of implausible claims.