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Data obtained with the use of massive parallel sequencing (MPS) can be valuable in population genetics studies. In particular, such data harbor the potential for distinguishing samples from different populations, especially from those coming from adjacent populations of common origin. Machine learning (ML) techniques seem to be especially well suited for analyzing large datasets obtained using MPS. The Slavic populations constitute about a third of the population of Europe and inhabit a large area of the continent, while being relatively closely related in population genetics terms. In this proof-of-concept study, various ML techniques were used to classify DNA samples from Slavic and non-Slavic individuals. The primary objective of this study was to empirically evaluate the feasibility of discerning the genetic provenance of individuals of Slavic descent who exhibit genetic similarity, with the overarching goal of categorizing DNA specimens derived from diverse Slavic population representatives. Raw sequencing data were pre-processed, to obtain a 1200 character-long binary vector. A total of three classifiers were used—Random Forest, Support Vector Machine (SVM), and XGBoost. The most-promising results were obtained using SVM with a linear kernel, with 99.9% accuracy and F1-scores of 0.9846–1.000 for all classes. [ABSTRACT FROM AUTHOR]

This review focuses on the study of biogeographic ancestry using the Accurate Ancestry Identification Panel. Autosomal markers may provide little information about the nature of an individual's admixture due to ongoing human recombination and migration. Biogeographic ancestry assessment (BGA) is a term used to describe ancestry through DNA testing. This is usually accomplished by testing specific regions of DNA called ancestry information markers (AIMs). AIMs are chosen because they expose significantly different frequencies between different populations in different parts of the world. The panels of these AIMs can be assessed using next-generation sequencing (NGS) to predict the geographical origins of a person of interest's ancestors, usually in terms of continent of origin, and sometimes by smaller geographic regions. The use of ancestry informative markers (AIM) to identify genomic ancestry can be useful for a variety of studies in evolutionary genetics, biomedical research, and forensic analyses. However, there remains a major challenge in determining AIMs for populations with complex and highly mixed ancestry.

Data obtained with the use of massive parallel sequencing (MPS) can be valuable in population genetics studies. In particular, such data harbor the potential for distinguishing samples from different populations, especially from those coming from adjacent populations of common origin. Machine learning (ML) techniques seem to be especially well suited for analyzing large datasets obtained using MPS. The Slavic populations constitute about a third of the population of Europe and inhabit a large area of the continent, while being relatively closely related in population genetics terms. In this proof-of-concept study, various ML techniques were used to classify DNA samples from Slavic and non-Slavic individuals. The primary objective of this study was to empirically evaluate the feasibility of discerning the genetic provenance of individuals of Slavic descent who exhibit genetic similarity, with the overarching goal of categorizing DNA specimens derived from diverse Slavic population representatives. Raw sequencing data were pre-processed, to obtain a 1200 character-long binary vector. A total of three classifiers were used—Random Forest, Support Vector Machine (SVM), and XGBoost. The most-promising results were obtained using SVM with a linear kernel, with 99.9% accuracy and F1-scores of 0.9846–1.000 for all classes.

Biogeographical ancestry analysis is valuable in forensic investigations, especially in missing person cases or crimes without eyewitnesses, as it helps to infer geographic origins from genetic markers. This approach enhances forensic efforts by providing essential clues for identifying individuals with limited direct evidence. Slavic-speaking populations are poorly distinguishable based on human genome variability. However, recent studies show that even populations with close biogeographic origin could be differentiated based on salivary microbiomes. Nevertheless, the salivary microbiomes of Slavs have not been characterized yet. Therefore, this study aimed to compare the composition of the salivary microbiomes of Western and Southern Slavs' representatives. 16S rRNA libraries from salivary microbiomes of 40 Poles (Western Slavs) and 40 Serbians (Southern Slavs) were prepared via PCR and sequenced on the MiSeq FGx platform (Illumina), giving approximately 100,000 reads per sample. Bioinformatic and statistical analyses were performed to assess the alpha and beta diversity of microbiomes and determine the differences in the abundance of bacterial genera between the groups studied. Analyses of alpha (ACE, Chao1, Shannon, and Simpson) and beta (Jaccard and Bray-Curtis dissimilarity) diversities in the salivary microbiomes clearly distinguished between Poles and Serbians. Alpha and beta diversity metrics were significantly higher in the Serbian population. Fusobacterium, Lautropia, Porphyromonas, Actinobacillus, Capnocytophaga, and Kingella were the most significantly increased genera in Serbians, whereas Veillonella, Selenomonas, Megasphaera, and Atopobium were more prevalent in Poles. In summary, our study identified significant differences in the salivary microbiomes of Poles and Serbians, with distinct microbial signatures associated with each population. These findings highlight the potential of salivary microbiome analysis as a tool for predicting biogeographic ancestry. Nevertheless, further analysis extended to other Slavic-speaking populations is necessary to clarify this issue., Competing Interests: Declaration of Competing Interest The authors declare no competing interests., (Copyright © 2024. Published by Elsevier B.V.)

This research was designed to assess the operational effectiveness of Biogeographical Ancestry (BGA) and Externally Visible Characteristics (EVCs) Massively Parallel Sequencing (MPS) for criminal cases. Engaging with end users to assess new DNA technology is a novel approach for Queensland, and considered necessary given the investment required to develop this capability. Detectives were presented with MPS intelligence from four real Queensland criminal cases in a workshop setting, and were asked to assess its utility. Detectives were also asked to determine whether they could use the MPS intelligence to prioritize (include/exclude) persons of interest (POIs). The results from this research showed the detectives had confidence in MPS intelligence and its value in providing avenues for investigation. There was a high rate of correct interpretation and use of the MPS results; however, the frequency of errors suggest that detectives need support from a trained forensic biologist to ensure accurate result interpretation. Detectives excluded on average 30% of POIs, demonstrating the potential use of MPS intelligence to prioritize POIs. Although this workshop did not accurately replicate an active criminal investigation, the results of this research are encouraging and suggest that MPS intelligence is operationally effective and could be used in Queensland as a valuable investigative tool. [ABSTRACT FROM AUTHOR]

Objective: Differences between self‐perceived biogeographic ancestry and estimates derived from DNA are potentially informative about the formation of ethnic identities in different sociohistorical contexts. Here, we compared self‐estimates and DNA‐estimates in New Mexico, where notions of shared ancestry and ethnic identity have been shaped by centuries of migration and admixture. Materials and Methods: We asked 507 New Mexicans of Spanish‐speaking descent (NMS) to list their ethnic identity and to estimate their percentages of European and Native American ancestry. We then compared self‐estimates to estimates derived from 291,917 single nucleotide polymorphisms (SNPs), and we examined how differences between the estimates varied by ethnic identity. Results: Most NMS (94%) predicted that they had non‐zero percentages of European and Native American ancestry. Self‐estimates and SNP‐estimates were positively correlated (rEuropean = 0.38, rNative‐American = 0.36, p < 0.001). The correlations belie systematic patterns of underestimation and overestimation based on ethnic identity. NMS with ancestral ties to 20th century immigrants, who identified as Mexican or Mexican American, often underestimated their European ancestry (self‐estimate < SNP‐estimate) and overestimated their Native American ancestry. The pattern was reversed for NMS who emphasized deep connections to colonial New Mexico and identified as Spanish or Spanish American. Discussion: While NMS accurately predicted that they had European and Native American ancestry, they predicted ancestry percentages with only moderate accuracy. Differences between self‐estimated and SNP‐estimated ancestry were associated with ethnic identities that were shaped by migration to the region over the past 400 years. We connect ethnic identities and patterns of ancestry estimation to resistance to colonial hegemony and discuss the implications of our results for the construction of ethnic identities, now and in the past. [ABSTRACT FROM AUTHOR]

PurposeWe determined if quantitative measurements of biogeographic ancestry (BGA) correlate with variations in optic disc area, corneal thickness (CCT), and retinal nerve fiber layer (RNFL) thickness.MethodsData were obtained from 656 participants in the African Descent and Glaucoma Evaluation Study (ADAGES) cohort who consented to BGA testing. Data for CCT, optic disc area, and RNFL thickness were obtained from subjects in the ADAGES study who also had participated in the current substudy. A total of 31 ancestry informative markers (AIMs) with large allele frequencies differences between populations was used to calculate admixture proportion (implemented in STRUCTURE). Correlations with BGA adjusted for diagnosis, age, and sex for CCT and optic disc area using the whole group and RNFL thickness adjusted for age and sex for the normal study participants were determined.ResultsThe mean percentage of African admixture was 79.6% in the self-described African Descent (AD) group and 3.5% in the European Descent (ED) group. Percent African ancestry was significantly correlated with CCT (ρ = -0.27, P < 0.0001) and disc area (ρ = 0.15, P < 0.0001), but only marginally associated with RNFL thickness (ρ = 0.20, P = 0.092) in adjusted models.ConclusionsThe BGA correlates with variation in ocular features that significantly differ across racial groups and that have been associated with the development of glaucoma. While BGA can provide an objective measurement of the biologic component of self-described race for ocular research, for most nongenetic epidemiologic studies, self-described race may adequately describe the associations with these ocular characteristics. (ClinicalTrials.gov number, NCT00221923.).

The phenotype is the result of the interaction of the genotype with epigenetic factors and the environment. It has been considered that genetics is responsible for >70% of facial phenotype. Interestingly, besides sequencing nucleic acids, it is possible to generate DNA methylation maps of ancient remains, to determine phenotypes. Other application areas are medicine, forensics and law-enforcement. Thus, breakthroughs in nucleic-acid analyses are allowing to determine the phenotype from genotypic data. That is also being facilitated by developments in software (including parallel processing) and hardware, including neural engines (neural-network hardware). New strategies involving artificial intelligence and machine learning have been also deployed to reach such a goal. Phenotyping is a challenging task, on the edge of current technology. Promising results have already been obtained, including prediction of Neanderthal (Homo sapiens neanderthalensis) and Denisovan (Homo sapiens denisova) faces. The future is promising in this research area, in which ethical and legal implications should also be considered. [ABSTRACT FROM AUTHOR]

The phenotype is the result of the interaction of the genotype with epigenetic factors and the environment. It has been considered that genetics is responsible for >70% of facial phenotype. Interestingly, besides sequencing nucleic acids, it is possible to generate DNA methylation maps of ancient remains, to determine phenotypes. Other application areas are medicine, forensics and law-enforcement. Thus, breakthroughs in nucleic-acid analyses are allowing to determine the phenotype from genotypic data. That is also being facilitated by developments in software (including parallel processing) and hardware, including neural engines (neural-network hardware). New strategies involving artificial intelligence and machine learning have been also deployed to reach such a goal. Phenotyping is a challenging task, on the edge of current technology. Promising results have already been obtained, including prediction of Neanderthal (Homo sapiens neanderthalensis) and Denisovan (Homo sapiens denisova) faces. The future is promising in this research area, in which ethical and legal implications should also be considered. [ABSTRACT FROM AUTHOR]

Direct-to-consumer DNA testing is increasingly affordable and accessible, and the potential implications from these tests are becoming more important. As additional people partake in DNA testing, larger population groups and information will cause further refinement of results and more extensive databases, resulting in further potential opportunities to connect biological relatives and increased chances of testers potentially having their identities re-aligned, reinforced or solidified. The effects of DNA testing were explored through 16 semi-structured in-depth interviews conducted with participants who had received their DNA test results. These participants came from diverse groups, genders and ethnic backgrounds. A thematic analysis found that notions of family were frequently challenged with unexpected DNA test results causing shifts in personal and social identities, especially in their family and biological identities. Discrepancies in DNA test results prompted re-negotiation of these identities and affected their feelings of belonging to their perceived social groups. Participants’ identities were important to them in varying degrees, with some feeling stronger connections with specific identities, thus having significant re-alignment of these identities and feelings of belonging. This article discusses the thematic analysis’s findings and explores how identities of the participants, many of whom took the test for genealogical purposes, were affected by DNA test results. As more people undertake DNA testing, it is important to explore how it may change the notions of family in the future and how their biological and family identities are affected.

• Custom-built ancestry panel of 111 AIM-SNPs developed for North African and Middle Eastern populations ('NAME' panel). • Independent evaluation and validation in three European member laboratories of the EUROFORGEN consortium. • Maximum differentiation of six major geographical regions obtained with 237 AIM-SNPs (combined NAME and Global AIMs panels). Inference of biogeographic origin is an important factor in clinical, population and forensic genetics. The information provided by AIMs (Ancestry Informative Markers) can allow the differentiation of major continental population groups, and several AIM panels have been developed for this purpose. However, from these major population groups, Eurasia covers a wide area between two continents that is difficult to differentiate genetically. These populations display a gradual genetic cline from West Europe to South Asia in terms of allele frequency distribution. Although differences have been reported between Europe and South Asia, Middle East populations continue to be a target of further investigations due to the lack of genetic variability, therefore hampering their genetic differentiation from neighboring populations. In the present study, a custom-built ancestry panel was developed to analyze North African and Middle Eastern populations, designated the 'NAME' panel. The NAME panel contains 111 SNPs that have patterns of allele frequency differentiation that can distinguish individuals originating in North Africa and the Middle East when combined with a previous set of 126 Global AIM-SNPs. [ABSTRACT FROM AUTHOR]

Graphical abstract Health related off-target-phenotypes (OTPs) associated with SNP (single nucleotide polymorphism) markers used in forensic DNA phenotyping (FDP) and biogeographic ancestry inference (BGA). Highlights • 27 of 1766 SNPs used in FDP and BGA reveal health-related information. • Effect sizes for a small subset of the SNPs are considerable. • Off-target phenotypes: disposition to develop cancer, alcohol dependence, asthma. • We provide a list of off-target associations of BGA and FDP SNPs as a resource. Abstract With recent advances in DNA sequencing technologies it has become feasible and cost effective to genotype larger marker sets for forensic purposes. Two technologies that make use of the larger marker sets have come into focus in forensic research and applications; inference of biogeographic ancestry (BGA) and forensic DNA phenotyping (FDP). These methods hold the promise to reveal information about a yet unknown perpetrator from a DNA sample. In contrast, DNA-profiling, that is a standard practice in case work, relies on matching DNA-profiles between crime scene material and suspects on a database of DNA-profiles. Markers for DNA-profiling were developed under the premise to reveal as little additional information about the human source of the profile as possible, the rationale being that personal privacy rights have to be balanced against the public interest in solving a crime. The same argument holds for markers used in BGA and FDP; these markers might also reveal information on off-target phenotypes (OTPs), that go beyond BGA and the phenotypes targeted in FDP. In particular, health related OTPs might shift the balance between privacy protection and public interest. However, to our knowledge, there is currently no convenient resource available to incorporate knowledge on OTPs in BGA and FDP assay design and application. In order to provide such a resource, we performed a systematic search for OTPs associated with a comprehensive set of markers (1766 SNPs) used or suggested to be used for BGA inference and FDP. In this set, we identified a relatively small number of 27 SNPs (1.53%) that convey information on diverse health related OTPs such as cancer risk, induced asthma, or risk of alcoholism. Some of these SNPs are commonly used for FDP and BGA across different marker sets. We conclude that the effects of SNP markers used in FDP and BGA on OTPs are currently limited, with few exceptions that should be considered in a balanced decision on assay design and application. [ABSTRACT FROM AUTHOR]

DNA methylation based age prediction is a new method in the toolbox of forensic genetics. Typically, the method is applied in the course of police investigation e.g. to predict the age of an unknown person that has left a biological trace at a crime scene. The method can also be used to answer other forensic questions, for example to estimate the age of unknown human bodies in the course of the identification process. In the present study, we tested for a potential impact of biogeographic ancestry (BGA) on age predictions using five age dependent methylated CpG sites within the genetic regions of ELOVL2, MIR29B2CHG, FHL2, KLF14 and TRIM59. We collected 102 blood samples each from donors living in Iraq, Middle East (ME) and Germany, Central Europe (EU). Both sample sets were matched in sex and age ranging from 18 to 68 years with exactly one male and female sample per year of age. All samples were analyzed by bisulfite pyrosequencing applying a multiplex pre-amplification strategy based on a single input of 35 ng converted DNA in the PCR. For the CpGs in MIR29B2CHG , FHL2 and KLF14 , we observed significantly different methylation levels between the two populations. While we were able to train two highly accurate prediction models for the respective population with mean absolute deviations between predicted and actual ages (MAD) of 3.34 years for the ME model, and 2.72 years for the EU model, we found an absolute prediction difference between the two population specific models of more than 4 years. A combined model for both populations compensated the methylation difference between the two populations, providing MADs of prediction of only 3.81 years for ME and 3.31 years for EU samples. In total, the results of the present study strongly support the benefit of BGA information for more reliable methylation based age predictions. • Significant methylation differences between EU and ME samples were found for MIR29B2CHG , FHL2 and KLF14. • Population specific CpG methylation caused more than four years prediction differences between EU and ME samples. • Population specific age prediction models lead to great prediction errors when applied to samples with different ancestry. • A combined model compensated for population specific methylation differences but underperformed population specific models. • Biogeographic ancestry has been identified as a relevant co-variable for reliable DNA methylation based age predictions. [ABSTRACT FROM AUTHOR]

Forensic genetics is a rapidly developing discipline. Nowadays, human genetic identification relies on the application of complex solutions ensuring high sensitivity and resistance to the inhibition and degradation of biological traces, and revealing maximum information which has relevance for the justice system. However, recent improvements in forensic DNA identification testing are associated with problems including secondary transfer, DNA mixtures and incompleteness of DNA profiles, which were formerly less significant. It also seems that the potential of the national DNA database in Poland has not been fully developed, and it is necessary to implement an appropriate information policy in order to improve it. Novel methods that can be applied at the level of investigation include analysis of biogeographic ancestry, prediction of visible traits, and estimation of human chronological age. Moreover, next-generation sequencing has a potential to entirely replace capillary electrophoresis in forensic genetics. Further works are necessary to ensure a proper implementation of uniform standards of data interpretation and evaluation of DNA evidence in forensic genetics. In order to maintain proper standards of forensic DNA assessment, continuous training of DNA experts and appropriate information policy for recipients of DNA assessments are required.

Short Tandem Repeat (STR) genotyping is currently the primary DNA-based method for human identification, however it can have limited success when applied to degraded human remains. Massively parallel sequencing (MPS) provides new opportunities to obtain genetic data for hundreds of loci in a single assay with higher success from degraded samples. However, due to the extra requirement for specialised equipment, expertise and resources, routine use of MPS may not be feasible or necessary for many forensic cases. Here we describe the development of a mini-multiplex SNaPshot screening tool (Miniplex) for human samples which allows the qualitative comparison of short mitochondrial and nuclear DNA targets, as well as the interrogation of biogeographic ancestry, lineage, and phenotype single nucleotide polymorphisms (SNPs). This tool is useful to triage samples based on sample quality prior to downstream identification workflows and provides broad biological profile data for intelligence purposes. [ABSTRACT FROM AUTHOR]

Forensic DNA Phenotyping (FDP) comprises the prediction of a person's externally visible characteristics regarding appearance, biogeographic ancestry and age from DNA of crime scene samples, to provide investigative leads to help find unknown perpetrators that cannot be identified with forensic STR-profiling. In recent years, FDP has advanced considerably in all of its three components, which we summarize in this review article. Appearance prediction from DNA has broadened beyond eye, hair and skin color to additionally comprise other traits such as eyebrow color, freckles, hair structure, hair loss in men, and tall stature. Biogeographic ancestry inference from DNA has progressed from continental ancestry to sub-continental ancestry detection and the resolving of co-ancestry patterns in genetically admixed individuals. Age estimation from DNA has widened beyond blood to more somatic tissues such as saliva and bones as well as new markers and tools for semen. Technological progress has allowed forensically suitable DNA technology with largely increased multiplex capacity for the simultaneous analysis of hundreds of DNA predictors with targeted massively parallel sequencing (MPS). Forensically validated MPS-based FDP tools for predicting from crime scene DNA i) several appearance traits, ii) multi-regional ancestry, iii) several appearance traits together with multi-regional ancestry, and iv) age from different tissue types, are already available. Despite recent advances that will likely increase the impact of FDP in criminal casework in the near future, moving reliable appearance, ancestry and age prediction from crime scene DNA to the level of detail and accuracy police investigators may desire, requires further intensified scientific research together with technical developments and forensic validations as well as the necessary funding. • Advances in DNA prediction of appearance, ancestry and age increase impact of Forensic DNA Phenotyping. • Appearance DNA prediction broadened beyond eye, hair, skin color to include more traits. • Ancestry DNA prediction progressed beyond continental levels to sub-regional and admixture resolution. • Age DNA prediction widened beyond blood to more somatic tissues and semen. • FDP tools with improved multiplexing capacity based on massively parallel sequencing are emerging. [ABSTRACT FROM AUTHOR]

Forensic DNA phenotyping (FDP) includes biogeographic ancestry (BGA) inference and externally visible characteristics (EVCs) prediction directly from an evidential DNA sample as alternatives to provide valuable intelligence when conventional DNA profiling fails to achieve identification. In this context, the application of Massively Parallel Sequencing (MPS) methodologies, which enables simultaneous typing of multiple samples and hundreds of forensic markers, has been gradually implemented in forensic genetic casework. The Precision ID Ancestry Panel (Thermo Fisher Scientific, Waltham, USA) is a forensic multiplex assay consisting of 165 autosomal SNPs designed to provide biogeographic ancestry information. In this work, a sample of 250 individuals from Rio Grande do Sul (RS) State, southern Brazil, apportioned into four main population groups (African-, European-, Amerindian-, and Admixed-derived Gauchos), was evaluated with this panel, to assess the feasibility of this approach in a highly heterogeneous population. Forensic descriptive parameters estimated for each population group revealed that this panel has enough polymorphic and informative SNPs to be used as a supplementary instrument in forensic individual identification and kinship testing regardless of ethnicity. No statistically significant deviation from Hardy-Weinberg equilibrium was observed after Bonferroni correction. However, seven loci pairs displayed linkage disequilibrium in pairwise LD testing (p < 3.70 × 10−6). Interpopulation comparisons by F ST analysis, MDS plot, and STRUCTURE analysis among the four RS population groups apart and along with 89 reference worldwide populations demonstrated that Admixed- and African-derived Gauchos present the highest levels of admixture and population stratification, whereas European- and Amerindian-derived exhibit a more homogeneous genetic conformation. • 250 samples from four South Brazilian population groups were typed for 165 AISNPs. • All loci were in HW equilibrium, with association between seven loci pairs. • South Amerindians show greater miscegenation than European-derived Gauchos. • Admixed and African-derived present the highest levels of population stratification. • The panel is a promising tool for biogeographical ancestry and human identification. [ABSTRACT FROM AUTHOR]

Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling. • Single nucleotide polymorphisms (SNPs) can provide forensic intelligence. • Existing forensic SNP panels are inflexible and may perform poorly on degraded DNA. • We developed and tested a customisable, SNP hybridisation enrichment panel. • The panel provides valuable biological profiles and forensic intelligence. [ABSTRACT FROM AUTHOR]

During every criminal investigation, it is vital to extract as much information as possible from every piece of evidence. When it comes to DNA testing, simple short tandem repeat (STR) typing may soon become a relic because it is now possible to genotype more characteristics. Ancestry informative markers are receiving attention from the forensic community because individuals can be assigned to their population or territory of origin based on their analysis. Many panels of this kind have been proposed so far, yet most of them require typing of a large number of loci. In many cases it is crucial to pick a minimal set of the most informative markers due to the limited amount of material available for analysis. In this study, we demonstrate that 14 carefully picked SNPs combined in two multiplex assays are capable of fast, robust and cost effective three-way differentiation of East Asians, Europeans and Africans. [ABSTRACT FROM AUTHOR]

Purpose Racial/ethnic disparities in the incidence of type 2 diabetes mellitus (T2DM) are well documented, and many researchers have proposed that biogeographical ancestry (BGA) may play a role in these disparities. However, studies examining the role of BGA on T2DM have produced mixed results to date. Therefore, the objective of this research was to quantify the contribution of BGA to racial/ethnic disparities in T2DM incidence controlling for the mediating influences of socioeconomic factors. Methods We analyzed data from the Boston Area Community Health Survey, a prospective cohort with approximately equal numbers of black, Hispanic, and white participants. We used 63 ancestry-informative markers to calculate the percentages of participants with West African and Native American ancestry. We used logistic regression with G-computation to analyze the contribution of BGA and socioeconomic factors to racial/ethnic disparities in T2DM incidence. Results We found that socioeconomic factors accounted for 44.7% of the total effect of T2DM attributed to black race and 54.9% of the effect attributed to Hispanic ethnicity. We found that BGA had almost no direct association with T2DM and was almost entirely mediated by self-identified race/ethnicity and socioeconomic factors. Conclusions It is likely that nongenetic factors, specifically socioeconomic factors, account for much of the reported racial/ethnic disparities in T2DM incidence. [ABSTRACT FROM AUTHOR]

Abstract: Marked differences in Y-SNP allele frequencies between continental populations can be used to predict the biogeographic origin of a man''s ancestral paternal lineage. Using 627 samples collected from individuals within the UK with pale-skinned Caucasian, dark-skinned Caucasian, African/Caribbean, South Asian, East Asian or Middle Eastern appearance we demonstrate that an individual''s Y-SNP haplogroup is also strongly correlated with their physical appearance. Furthermore, experimental evaluation of the Marligen Signet™ Y-SNP kit in conjunction with the Luminex 100 detection instrument indicates that reliable and reproducible haplogrouping results can be obtained from 1ng or more of target template derived from a variety of forensic evidence types including, blood, saliva and post-coital vaginal swabs. The test proved highly male-specific with reliable results being generated in the presence of a 1000-fold excess of female DNA, and no anomalous results were observed during degradation studies despite a gradual loss of typable loci. Hence, Y-SNP haplogrouping has considerable potential forensic utility in predicting likely ethnic appearance. [Copyright &y& Elsevier]

Human facial morphology is a combination of many complex traits and is determined by a large number of genes and enhancers. Here, we report a Copy Number Variation (CNV) study of enhancer hs1431 in populations of Central European and South Siberian ancestry. Central European samples included 97 Poles, while South Siberian samples included 78 Buryats and 27 Tuvinians. CNVs were detected by real-time PCR, using ViiA™ 7 Real-Time PCR System (Applied Biosystems). We revealed significant differences in CNV of hs1431 enhancer between Polish and Buryat population (p=0.0378), but not between Central European and South Siberian population (p=0.1225). Our results suggest that an increase in copy number variation of hs1431 enhancer is associated with biogeographic ancestry. However, this result needs extending and replicating in larger cohorts. This is the first study revealing the presence of copy number variation of enhancer hs1431 in humans., (Copyright © 2022 by PTMSiK.)

Skin pigmentation is one of the most prominent and variable phenotypes in humans. We compared the alleles of 163 SNPs and indels from the Human Pigmentation (HuPi) AmpliSeq™ Custom panel, and biogeographic ancestry with the quantitative skin pigmentation levels on the upper arm, lower arm, and forehead of 299 Pakistani individuals from three subpopulations: Baloch, Pashtun, and Punjabi. The biogeographic ancestry of each individual was estimated using the Precision ID Ancestry Panel. All individuals were mainly of mixed South-Central Asian and European ancestry. However, the Baloch individuals also had an average proportion of Sub-Saharan African ancestry of approximately 10%, whereas it was <1% in the Punjabi and Pashtun individuals. The pairwise genetic distances between the Pashtun, Punjabi, and Baloch subpopulations based on the ancestry markers were statistically significantly different. Individuals from the Pashtun subpopulation had statistically significantly lower skin pigmentation than individuals from the Punjabi and Baloch subpopulations (p < 0.05). The proportions of European and Sub-Saharan African ancestry and five SNPs (rs1042602, rs10831496, rs1426654, rs16891982, and rs12913832) were statistically significantly associated with skin pigmentation at either the upper arm, lower arm or forehead in the Pakistani population after correction for multiple testing (p < 10−3). A model based on four of these SNPs (rs1426654, rs1042602, rs16891982, and rs12913832) explained 33% of the upper arm skin pigmentation. The four SNPs and the proportions of European and Sub-Saharan African ancestry explained 37% of the upper arm skin pigmentation. Our results indicate that the four likely causative SNPs, rs1426654, rs1042602, rs16891982, and rs12913832 located in SLC24A5, TYR, SLC45A2, and HERC2, respectively, are essential for skin color variation in the admixed Pakistani subpopulations. [ABSTRACT FROM AUTHOR]

In 1932, seven burials were discovered on a Texas plantation that was originally the site of a 17th-century Caddo Indian village. Of the seven excavated graves, one set of remains (an adult male) was notably buried in a manner inconsistent with traditional Caddoan burial practices and has long been purported to be the remains of Sieur de Marle (a member of the French explorer La Salle's last expedition). Diary accounts of La Salle's expedition scribe report that Sieur de Marle died along a river near an Indian village during a trek to Canada to find help for colonists left behind at the ill-fated Fort St. Louis. Additionally, two lead projectiles recovered from the grave were ballistically analyzed and determined to be consistent with ammunition used in 17th-century weaponry. In the 1980s, anthropologists requested access to the remains for study, but the skull was missing. Cranial measurements recorded in 1940 and 1962 (by two independent anthropologists) were used to investigate the ancestry of this individual; and the Giles-Elliot (G-E) discriminant function was calculated to be 18.1, within the Anglo-European range. Dietary isotope testing on non-cranial skeletal elements determined that this unknown male's diet was rich in animal/marine protein sources, which differs appreciably from Caddo Indian populations of that time period. In order to genetically assess this individual's biogeographic ancestry and to provide further support that this individual is of European descent, mitochondrial DNA (mtDNA) sequencing was performed using the Applied Biosystems™ Precision ID mtDNA Whole Genome Panel. mtDNA sequencing of multiple sections from two different long bones yielded compiled results consistent with either Haplogroup H or R, both predominantly European mtDNA haplogroups. Further anthropological calculations were conducted using cranial measurements, FORDISC™ software, and discriminant function analysis. Two-way, four-way, and multigroup discriminant function analyses further classify this set of unidentified remains as being White (European) in origin, with posterior probabilities of 0.999, 0.881 and 0.986, respectively. Combined with historical records of Sieur de Marle's death, as well as overlays of historical and contemporary maps which demonstrate that the plantation site aligns with Joutel's diary accounts of de Marle's burial, these collective results support that these remains are of a European male and may possibly belong to this prominent member of La Salle's expedition team. [ABSTRACT FROM AUTHOR]

In 1995, the historical shipwreck of La Belle was discovered off the coast of Texas. One partial human skeleton was recovered from alongside cargo in the rear portion of the ship; a second (complete) skeleton was found atop coiled anchor rope in the bow. In late 2015, comprehensive forensic genetic testing began on multiple samplings from each set of remains. For the partial skeleton recovered from the ship's rear cargo area, results were obtained for 26/27 Y-STRs using traditional CE; with MPS technology, results were obtained for 18/24 Y-STRs, 56/56 ancestry-informative SNPs (aiSNPs), 22/22 phenotype-informative SNPs (piSNPs), 22/27 autosomal STRs, 4/7 X-STRs, and 94/94 identity-informative SNPs (iiSNPs). For the complete skeleton of the second individual, results were obtained for 7/17 Y-STRs using traditional CE; with MPS technology, results were obtained for 5/24 Y-STRs, 49/56 aiSNPs, 18/22 piSNPs, 15/27 autosomal STRs, 1/7 X-STRs, and 66/94 iiSNPs. Biogeographic ancestry for each set of skeletal remains was predicted using the ancestry feature and metapopulation tool of the Y-STR Haplotype Reference Database (YHRD), Haplogroup Predictor, and the Forensic Research/Reference on Genetics knowledge base (FROG-kb). Phenotype prediction was performed using piSNP data and the HIrisplex eye color and hair color DNA phenotyping webtool. mtDNA whole genome sequencing also was performed successfully. This study highlights the sensitivity of current forensic laboratory methods in recovering DNA from historical and archaeological human remains. Using advanced sequencing technology provided by MiSeq™ FGx (Verogen) and Ion S5™ (Thermo Fisher Scientific) instrumentation, degraded skeletal remains can be characterized using a panel of diverse and highly informative markers, producing data which can be useful in both forensic and genealogical investigations. [ABSTRACT FROM AUTHOR]

The Centre of Forensic Sciences has validated the Precision ID Ancestry Panel on the Ion S5™ Massively Parallel Sequencing instrument for use in forensic casework. The focus of this paper is the development of reporting guidelines for implementation of the biogeographic ancestry inference service based on the Admixture Prediction results produced using the Torrent Suite™ Software (Thermo Fisher Scientific). The Admixture Prediction algorithm estimates the genetic ancestry of a sample using seven root populations (Europe, East Asia, Oceania, America, Africa, South Asia, and Southwest Asia). For individuals that declared a single ancestry, there was a high correlation between the declared ancestry and the ancestry predicted by the algorithm. However, some individuals with declared ancestries of Southern Europe, Southwest Asia, South Asia and Horn of Africa had Admixture Predictions that were composed of two or more root populations at 20% or greater. For individuals with known admixed ancestry, the major component of their declaration was included in their results in all but one case. Based on these results, reporting guidelines were developed and subsequently evaluated using the Admixture Predictions of additional samples. This paper discusses the development and evaluation of these reporting guidelines, along with an implementation plan for forensic casework., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

An accurate, up-to-date, detailed and global phylogenetic tree of human mitochondrial DNA (mtDNA) is essential for various forensic mtDNA applications including data quality control and haplogroup assignment for biogeographic ancestry inference. PhyloTree ( http://www.phylotree.org ) is widely accepted as the reference phylogeny for human mtDNA. Here, a new update of PhyloTree, Build 17, is introduced, comprising nearly 5.5 thousand haplogroups. [ABSTRACT FROM AUTHOR]