Investigating the effectiveness of forensic genetics and population genetic diversity using a multi-InDel system in Chinese Hezhou and Southern Shaanxi Han populations.

INTRODUCTION: Multiple insertion-deletion (multi-InDel) has greater potential in forensic genetics than InDel, and its efficacy in kinship testing, individual identification, DNA mixture detection and ancestry inference remains to be explored. METHODS: Consequently, we designed an efficient and robust system consisting of 41 multi-InDels to evaluate its efficacy in forensic applications in Chinese Hezhou Han (HZH) and Southern Shaanxi Han (SNH) populations and explore the genetic relationships between the SNH, HZH, and 26 reference populations. RESULTS AND CONCLUSION: The obtained results showed that 38 out of the 41 multi-InDels had fairly high genetic variations. The the cumulative probability of discrimination and exclusion values of the multi-InDels (except MI38) in HZH and SNH populations both exceeded 1-e-25 and 1-e-6, correspondingly. The genetic compositions of HZH and SNH individuals were similar to that of East Asians and the Naive Bayes model could well distinguish East Asians, Africans and Americans. These results indicated that the multi-InDel systerm can serve as an effective tool to provide important evidence for the development of multi-InDels in forensic practice and better analyse the genetic background of the Han Chinese populations.

Joint application of A-InDels and miniSTRs for forensic personal, full and half sibling identifications, and genetic differentiation analyses in two populations from China.

BACKGROUND: Previously, a novel multiplex system of 64 loci was constructed based on capillary electrophoresis platform, including 59 autosomal insertion/deletions (A-InDels), two Y-chromosome InDels, two mini short tandem repeats (miniSTRs), and an Amelogenin gene. The aim of this study is to evaluate the efficiencies of this multiplex system for individual identification, paternity testing and biogeographic ancestry inference in Chinese Hezhou Han (CHH) and Hubei Tujia (CTH) groups, providing valuable insights for forensic anthropology and population genetics research. RESULTS: The cumulative values of power of discrimination (CDP) and probability of exclusion (CPE) for the 59 A-InDels and two miniSTRs were 0.99999999999999999999999999754, 0.99999905; and 0.99999999999999999999999999998, 0.99999898 in CTH and CHH groups, respectively. When the likelihood ratio thresholds were set to 1 or 10, more than 95% of the full sibling pairs could be identified from unrelated individual pairs, and the false positive rates were less than 1.2% in both CTH and CHH groups. Biogeographic ancestry inference models based on 35 populations were constructed with three algorithms: random forest, adaptive boosting and extreme gradient boosting, and then 10-fold cross-validation analyses were applied to test these three models with the average accuracies of 86.59%, 84.22% and 87.80%, respectively. In addition, we also investigated the genetic relationships between the two studied groups with 33 reference populations using population statistical methods of FST, DA, phylogenetic tree, PCA, STRUCTURE and TreeMix analyses. The present results showed that compared to other continental populations, the CTH and CHH groups had closer genetic affinities to East Asian populations. CONCLUSIONS: This novel multiplex system has high CDP and CPE in CTH and CHH groups, which can be used as a powerful tool for individual identification and paternity testing. According to various genetic analysis methods, the genetic structures of CTH and CHH groups are relatively similar to the reference East Asian populations.

Systematic analyses of AISNPs screening and classification algorithms based on genome-wide data for forensic biogeographic ancestry inference.

Identifying the biogeographic ancestral origin of biological sample left at a crime scene can provide important evidence for judicial case, as well as clue for narrowing down suspect. Ancestry informative single nucleotide polymorphism (AISNP) has become one of the most important genetic markers in recent years for screening ancestry information loci and analyzing the population genetic background and structure due to their high number and wide distributions in the human genome. In this study, based on data from 26 populations in the 1000 Genomes Project Phase 3, a Random Forest classification model was constructed with one-vs-rest classification strategy for embedded feature selection in order to obtain a panel with a small number of efficient AISNPs. The research aim was to clarify differentiations of population genetic structures among continents and subregions of East Asia. ADMIXTURE results showed that based on the 58 AISNPs selected by the machine learning algorithm, the 26 populations involved in the study could be categorized into six intercontinental ancestry components: North East Asia, South East Asia, Africa, Europe, South Asia, and America. The 24 continental-specific AISNPs and 34 East Asian-specific AISNPs were finally obtained, and used to construct the ancestry prediction model using XGBoost algorithm, resulting in the Matthews correlation coefficients of 0.94 and 0.89, and accuracies of 0.94 and 0.92, respectively. The machine learning models that we constructed using population-specific AISNPs were able to accurately predict the ancestral origins of continental and intra-East Asian populations. To summarize, screening a set of high-perform AISNPs to infer biogeographical ancestral information using embedded feature selection has potential application in creating a layered inference system that accurately differentiates from intercontinental populations to local subpopulations.

Focus on studying the effects of different exposure durations on the microbial structures and characteristics of three types of body fluids.

BACKGROUND: Body fluid traceability inferences can provide important clues to the investigation of forensic cases. Microbiome has been proven to be well applied in forensic body fluid traceability studies. Most of the specimens at crime scenes are often exposed to the external environment when collected, so it is extremely important to exploring the structure characteristics of microbial communities of body fluid samples under different exposure durations for tracing the origin of body fluids based on microorganisms. METHODS: Full-length 16S rRNA sequencing technology and multiple data analysis methods were used to explore the microbial changes in three types of body fluid samples at five different exposure time points. RESULTS: With increasing exposure time, the Proteobacteria abundance gradually increased in the negative control and body fluid samples, and the Bacteroidetes and Firmicutes abundance decreased gradually, but the relative abundance of dominant genera in each body fluid remained dynamically stable. The microbial community structures of those samples from the same individual at different exposure durations were similar, and there were no significant differences in the microbial community structures among the different exposure time points. LEfSe and random forest analyses were applied to screen stable and differential microbial markers among body fluids, such as Streptococcus thermophilus, Streptococcus pneumoniae and Haemophilus parainfluenzae in saliva; Lactobacillus iners and Streptococcus agalactiae in vaginal fluid. CONCLUSIONS: There were no significant differences in microbial community structures of the three types of body fluid samples exposed to the environment for various time periods, although the relative abundance of some microbes in these samples would change. The exposed samples could still be traced back to their source of the body fluid samples using the microbial community structures.

Using two self-developed InDel panels to explore forensic traits and ancestral components in the Hui group.

To address the challenges faced by forensic examiners in degraded DNA analysis, we have developed two different panels for various forensic applications, encompassing an AIM-InDel panel for ancestry inference and a Multi-InDel panel for individual identification, respectively. Herein, the efficiencies of these two panels were tested in the Chinese Hui group. By calculating forensic parameters and simulating family relationships, we verified that the Multi-InDel panel could be an effective tool for individual identification, paternity testing, and could assist in kinship identification in the Hui group. For full siblings, the true positive rate of kinship discrimination was 96.553%, when the threshold of log10LR was 1. The cumulative probability of matching as well as cumulative probability of exclusion were 3.8117 × 10-26 and 0.999999722, respectively. Meanwhile, we found that the AIM-InDel panel was effective for bio-geographic ancestry inference, with the vast majority of loci contributing significantly to distinguish East Asian, African, and European populations. By studying the population structure of the Hui ethnic minority, the genetic distance to the Beijing Han population was the closest among the 26 reference populations, which was similar to previous reports. In summary, we have developed two panels which can be effectively applied to the Hui group for individual identification, parentage testing and bio-geographic ancestry inference.

Retrospective Analysis of Death Cases of Oral Diphenidol Hydrochloride Poisoning.

OBJECTIVES: To explore the characteristics of postmortem examination, chemical examination and scene investigation of deaths caused by oral diphenidol hydrochloride poisoning, and so as to provide a reference for proper settlement and prevention of such deaths. METHODS: The data of 22 deaths caused by oral diphenidol hydrochloride poisoning in a city from January 2018 to August 2020 were collected, including case details, scene investigations, autopsies, chemical examinations and digital evidence. Thirty-one cases of deaths caused by oral diphenidol hydrochloride poisoning reported in previous literature were also collected. RESULTS: In the 53 oral diphenidol hydrochloride poisoning death cases, 50 cases were suicide, 2 cases were accidental, while 1 case was undetermined. Fifty-two cases were found in the medical records or crime scene investigation reports with doses ranging from 775 mg to 12 500 mg, and 23 deceased were detected with postmortem blood concentrations ranging from 2.71 mg/L to 83.1 mg/L. Clinical symptoms were recorded in 6 patients, including conscious disturbance and convulsion. Among the 45 cases which were performed with external examination, 23 cases autopsied. CONCLUSIONS: Most of the deceased of oral diphenidol hydrochloride poisoning were suicide. No significant correlation was found between dose and blood concentration through the retrospective analysis of cases.

Selection and validation of a novel set of specific differential methylation markers and construction of a random forest prediction model for the accurate tissue origin identifications of body fluids involving young and middle-aged group of Chinese Han population.

The identification of tissue origin of body fluid is helpful to the determination of the case nature and the reproduction of the case process. It has been confirmed that tissue-specific differential methylation markers could be used to identify the tissue origins of different body fluids. To select suitable tissue-specific differential methylation markers and establish the efficient typing system which could be applied to the identifications of body fluids in forensic cases involving Chinese Han individuals of young and middle-aged group, a total of 125 body fluids (venous blood, semen, vaginal fluid, saliva, and menstrual blood) were collected from healthy Chinese Han volunteers aged 20-45 years old. After genome-wide explorations of DNA methylation patterns in these five kinds of body fluids based on the Illumina Infinium Methylation EPIC BeadChip, 15 novel body fluid-specific differential CpGs were selected and verified based on the pyrosequencing method. And these identification efficiencies for target body fluids were verified by ROC curves. The pyrosequencing results indicated that the average methylation rates of nine CpGs were consistent with those of DNA methylation chip detection results, and the other five CpGs (except for cg12152558) were still helpful for the tissue origin identifications of target body fluids. Finally, a random forest classification prediction model based on these 14 CpGs was constructed to successfully identify five kinds of body fluids, and the tested accuracy rates all reached 100%.

Exploration of the ancestral inference effectiveness of 126 AI-SNPs and the genetic feature of Inner Mongolian Manchu group.

In addition to the validated ancestry-informative single nucleotide polymorphisms (AI-SNPs) in classic panels, there are many new potential AI-SNPs yet to be explored. Moreover, the search for AI-SNPs with highly discriminative power for ancestry inference in inter- and intra-continental populations has become a realistic need. In this study, 126 novel AI-SNPs were selected to distinguish the African, European, Central/South Asian and East Asian populations, and a random forest model was introduced to assess the performance of the AI-SNP set. This panel was further used in the genetic analysis of the Manchu group in Inner Mongolia, China, based on 79 reference populations from seven continental regions. Results showed that the 126 AI-SNPs were able to achieve the ancestry informative inference for African, East Asian, European, and Central/South Asian populations. Population genetic analyses indicated that the Manchu group in Inner Mongolia was genetically typical of East Asian populations and was more closely related to the northern Han Chinese and Japanese than to other Altaic-speaking populations. Overall, this study provided a selection of new promising loci of ancestry inference for major intercontinental populations and intracontinental subgroups, as well as genetic insights and valuable data for dissecting the genetic structure of the Inner Mongolian Manchu group.

A self-developed AIM-InDel panel designed for degraded DNA analysis: Forensic application characterization and genetic landscape investigation in the Han Chinese population.

To assist in forensic DNA investigation, we developed a new panel capable of simultaneously amplifying 56 ancestry-informative InDels, three Y-InDels and the Amelogenin locus in one PCR reaction. The fragment lengths of the InDel amplicons in this panel were restricted to <200 bp to benefit degraded DNA analysis. In this study, we explored the efficiency of this new panel for forensic applications in the Han Chinese population, and further shed light on the genetic structures of Han populations. We showed that the new panel could be served as an efficient tool for ancestry inference of intercontinental populations. Especially, the Han individuals in different regions could be 100% correctly predicted to be of East Asian origin with this new panel. The Han populations in different regions shared similar ancestry components in their genetic structures. Besides, we also revealed that the new panle could be useful for individual identification in different Han Chinese populations. In conclusion, we have provided the necessary evidence that the self-constructed new panel could play an important role in forensic DNA investigation.

Comprehensive evaluations of individual discrimination, kinship analysis, genetic relationship exploration and biogeographic origin prediction in Chinese Dongxiang group by a 60-plex DIP panel.

BACKGROUND: Dongxiang group, as an important minority, resides in Gansu province which is located at the northwest China, forensic detection system with more loci needed to be studied to improve the application efficiency of forensic case investigation in this group. METHODS: A 60-plex system including 57 autosomal deletion/insertion polymorphisms (A-DIPs), 2 Y chromosome DIPs (Y-DIPs) and the sex determination locus (Amelogenin) was explored to evaluate the forensic application efficiencies of individual discrimination, kinship analysis and biogeographic origin prediction in Gansu Dongxiang group based on the 60-plex genotype results of 233 unrelated Dongxiang individuals. The 60-plex genotype results of 4582 unrelated individuals from 33 reference populations in five different continents were also collected to analyze the genetic background of Dongxiang group and its genetic relationships with other continental populations. RESULTS: The system showed high individual discrimination power, as the cumulative power of discrimination (CPD), cumulative power of exclusion (CPE) for trio and cumulative match probability (CMP) values were 0.99999999999999999999997297, 0.999980 and 2.7029E- 24, respectively. The system could distinguish 98.12%, 93.78%, 82.18%, 62.35% and 39.32% of full sibling pairs from unrelated individual pairs, when the likelihood ratio (LR) limits were set as 1, 10, 100, 1000 and 10,000 based on the simulated family samples, respectively. Additionally, Dongxiang group had the close genetic distances with populations in East Asia, especially showed the intimate genetic relationships with Chinese Han populations, which were concluded from the genetic affinities and genetic background analyses of Dongxiang group and 33 reference populations. In terms of the effectiveness of biogeographic origin inference, different artificial intelligent algorithms possessed different efficacies. Among them, the random forest (RF) and extreme gradient boosting (XGBoost) algorithm models could accurately predict the biogeographic origins of 99.7% and 90.59% of three and five continental individuals, respectively. CONCLUSION: This 60-plex system had good performance for individual discrimination, kinship analysis and biogeographic origin prediction in Dongxiang group, which could be used as a powerful tool for case investigation.

Systematically exploring the performance of a self-developed Multi-InDel system in forensic identification, ancestry inference and genetic structure analysis of Chinese Manchu and Mongolian groups.

The insertion/deletion (InDel) polymorphism has promising applications in forensic DNA analysis. However, the insufficient forensic efficiencies of the present InDel-based systems restrict their applications in parentage testing, due to the lower genetic polymorphism of the biallelic InDel locus and the limited number of InDel loci in a multiplex amplification system. Here, we introduced an in-house developed system which contained 41 polymorphic Multi-InDel markers (equivalent to 82 InDels in total), to serve as an efficient and reliable tool for different forensic applications in the Manchu and Mongolian groups. We demonstrated that the new system exhibited potential efficiencies for personal identification, parentage testing, two-person DNA mixture interpretation and ancestry inference of intercontinental populations. Meanwhile, we explored the genetic backgrounds of the Manchu and Mongolian groups by conducting a series of population genetic analyses. We showed that the Manchu and Mongolian groups shared closer genetic relationships with East Asian populations, especially Han Chinese populations in northern China. Moreover, more similar genetic compositions were detected between the Manchu group and the northern Han populations in this study, suggesting that the Manchu group had higher genetic affinities with northern Han populations than the Mongolian group. Overall. this study provided the necessary evidence that these Multi-InDel genetic markers could play an important role in forensic applications.

Allelic and haplotypic polymorphisms and paternal genetic analysis of Chinese Shaanxi Han population utilizing a multiplex Y-STR set.

BACKGROUND: The analysis of Y chromosomal genetic markers is of great significance in human genetic fields related to male individuals. The Han nationality is the most populous ethnic group. It is critical to investigate the Y-chromosome short tandem repeat (Y-STR) genetic informativeness of Han nationalities in different Chinese regions in order to gain a comprehensive understanding of their paternal genetic relationships and origin. AIM: To assess the allelic and haplotypic polymorphisms of the novel AGCU Y SUPP STR amplification system containing seven Y-STRs in the maximal dataset of the Y-STR Haplotype Reference Database (YHRD) and 17 newly included Y-STRs, and explore the genetic relationships among the Shaanxi Han population and 12 reference populations from China. SUBJECTS AND METHODS: A total sample of 220 Han male subjects were obtained from the Shaanxi Province, China, and genotyped by the novel AGCU Y SUPP STR amplification system. Multiplex population genetic analyses derived from the same 16 Y-STR loci were carried out among the Shaanxi Han population and 12 reference populations from China. RESULTS: The gene diversities (GD) ranged from the maximum value of 0.9609 (DYS385a,b) to the minimum value of 0.5441 (DYS531). Besides, 217 distinct haplotypes were detected wholly in 220 individuals, of which 214 (98.62%) were exclusive. The entire haplotype diversity (HD) and discrimination capacity (DC) were 0.9999 and 0.9864, respectively, while the haplotype match probability (HMP) was 0.0045. Among the reference populations, the obtained results of population genetic analyses revealed that the Shaanxi Han population had the largest genetic distance with the Guangxi Yao group, but the smallest genetic distance with the Hunan Tujia group. CONCLUSIONS: These Y-STR loci in the AGCU Y SUPP STR amplification system were of high genetic polymorphisms and the amplification system could be used as a prospective complementary tool for forensic application and paternal genetics in the Shaanxi Han population.

A bibliometrics and visualization analysis of cannabidiol research from 2004 to 2021.

Cannabidiol, a non-psychoactive component extracted from the plant cannabis sativa, has gained growing focus in recent years since its extensive pharmacology effects have been founded. The purpose of this study intends to reveal the hot spots and frontiers of cannabidiol research using bibliometrics and data visualization methods. A total of 3,555 publications with 106,793 citations from 2004 to 2021 related to cannabidiol were retrieved in the Web of Science database, and the co-authorships, research categories, keyword burst, and reference citations in the cannabidiol field were analyzed and visualized by VOSviewer and Citespace software. Great importance has been attached to the pharmacology or pharmacy values of cannabidiol, especially in the treatment of neuropsychiatric disorders, such as epilepsy, anxiety, and schizophrenia. The mechanisms or targets of the cannabidiol have attracted the extreme interest of the researchers, a variety of receptors including cannabinoids type 1, cannabinoids type 2, 5-hydroxytriptamine1A, and G protein-coupled receptor 55 were involved in the pharmacology effects of cannabidiol. Moreover, the latest developed topic has focused on the positive effects of cannabidiol on substance use disorders. In conclusion, this study reveals the development and transformation of knowledge structures and research hotspots in the cannabidiol field from a bibliometrics perspective, exploring the possible directions of future research.

Forensic Characteristics and Genetic Background Dissections of Chinese Manchu and Zhuang Groups Using 59 Autosomal Diallelic InDels and 2 miniSTRs.

BACKGROUND: The latest development in molecular biology has offered an opportunity to construct multiplex panel with better applicability for forensic purpose, and a self-developed 64-plex panel, including 59 autosomal diallelic InDels, 2 miniSTRs, 2 Y-InDels, and an Amelogenin gene, was validated to be an effective forensic tool in the previous study. METHODS: By applying the 64-plex panel for DNA profiling, the obtained genotypes and the corresponding frequency data were used to investigate the forensic characteristics and population genetic structures of the Chinese Manchu group from the Inner Mongolia Autonomous Region and the Chinese Zhuang group from the Yunnan province. RESULTS: The 64-plex panel was qualified to perform human identification and paternity testing with the combined powers of discrimination of 0.99999999999999999999999999758 and 0.99999999999999999999999999691; and cumulative probabilities of exclusion of 0.99999866 and 0.99999880 in the studied Manchu and Zhuang groups, respectively. Relatively closer genetic relationships were found between the Chinese Manchu group and Han population in Beijing; and between the Chinese Zhuang group and Vietnamese Kinh population. CONCLUSIONS: It could be indicated from the results that, with the preliminary ability to distinguish ancestral components from all the studied groups, the 64-plex panel can not only serve as a robust forensic panel in the Manchu and Zhuang groups, but also offer genetic insights into the genetic differentiations and substructures of these populations.

Genetic Background of Kirgiz Ethnic Group From Northwest China Revealed by Mitochondrial DNA Control Region Sequences on Massively Parallel Sequencing.

The mitochondrial DNA (mtDNA) has been used to trace population evolution and apply to forensic identification due to the characteristics including lack of recombination, higher copy number and matrilineal inheritance comparing with nuclear genome DNA. In this study, mtDNA control region sequences of 91 Kirgiz individuals from the Northwest region of China were sequenced to identify genetic polymorphisms and gain insight into the genetic background of the Kirgiz ethnic group. MtDNA control region sequences of Kirgiz individuals presented relatively high genetic polymorphisms. The 1,122 bp sequences of mtDNA control region could differ among unrelated Kirgiz individuals, which suggested the mtDNA control region sequences have a good maternal pedigree tracing capability among different Kirgiz individuals. The neutrality test, mismatch distribution, Bayesian phylogenetic inference, Bayesian skyline analysis, and the median network analyses showed that the Kirgiz group might occurred population expansion, and the expansion could be observed at about ∼53.41 kilo years ago (kya) when ancestries of modern humans began to thrive in Eurasia. The pairwise population comparisons, principal component analyses, and median network analyses were performed based on haplogroup frequencies or mtDNA control region sequences of 5,886 individuals from the Kirgiz group and the 48 reference populations all over the world. And the most homologous haplotypes were found between Kirgiz individuals and the East Asian individuals, which indicated that the Kirgiz group might have gene exchanges with the East Asian populations.

New Advances, Challenges and Opportunities in Forensic Applications of Microbiomics.

The succession of microbiota is closely associated with several essential factors, including race, sex, health condition, lifestyle, postmortem interval, etc., and it has great potential application value in forensic medicine. This paper summarizes recent studies on the forensic applications of the microbiome, including individual identification, geographical feature identification, origin identification of the tissue or body fluid, and postmortem interval estimation, and introduces the current machine learning algorithms for microbiology research based on next-generation sequencing data. In addition, the current problems facing forensic microbiomics such as the extraction and preservation of samples, construction of standardization and database, ethical review and practical applicability are discussed. Future multi-omics studies are expected to explore micro ecosystems from a comprehensive and dynamic perspective, to promote the development of forensic microbiomics application.