A set of novel SNP loci for differentiating continental populations and three Chinese 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.

Ancestral Information Analysis of Chinese Korean Ethnic Group via a Novel Multiplex DIP System

Deletion/insertion polymorphism (DIP) is one of the more promising genetic markers in the field of forensic genetics for personal identification and biogeographic ancestry inference. In this research, we used an in-house developed ancestry-informative marker-DIP system, including 56 autosomal diallelic DIPs, three Y-chromosomal DIPs, and an Amelogenin gene, to analyze the genetic polymorphism and ancestral composition of the Chinese Korean group, as well as to explore its genetic relationships with the 26 reference populations. The results showed that this novel panel exhibited high genetic polymorphism in the studied Korean group and could be effectively applied for forensic individual identification in the Korean group. In addition, the results of multiple population genetic analyses indicated that the ancestral component of the Korean group was dominated by northern East Asia. Moreover, the Korean group was more closely related to the East Asian populations, especially to the Japanese population in Tokyo. This study enriched the genetic data of the Korean ethnic group in China and provided information on the ancestry of the Korean group from the perspective of population genetics.

Determining the Area of Ancestral Origin for Individuals From North Eurasia Based on 5,229 SNP Markers

Currently available genetic tools effectively distinguish between different continental origins. However, North Eurasia, which constitutes one-third of the world’s largest continent, remains severely underrepresented. The dataset used in this study represents 266 populations from 12 North Eurasian countries, including most of the ethnic diversity across Russia’s vast territory. A total of 1,883 samples were genotyped using the Illumina Infinium Omni5Exome-4 v1.3 BeadChip. Three principal components were computed for the entire dataset using three iterations for outlier removal. It allowed the merging of 266 populations into larger groups while maintaining intragroup homogeneity, so 29 ethnic geographic groups were formed that were genetically distinguishable enough to trace individual ancestry. Several feature selection methods, including the random forest algorithm, were tested to estimate the number of genetic markers needed to differentiate between the groups; 5,229 ancestry-informative SNPs were selected. We tested various classifiers supporting multiple classes and output values for each class that could be interpreted as probabilities. The logistic regression was chosen as the best mathematical model for predicting ancestral populations. The machine learning algorithm for inferring an ancestral ethnic geographic group was implemented in the original software “Homeland” fitted with the interface module, the prediction module, and the cartographic module. Examples of geographic maps showing the likelihood of geographic ancestry for individuals from different regions of North Eurasia are provided. Validating methods show that the highest number of ethnic geographic group predictions with almost absolute accuracy and sensitivity was observed for South and Central Siberia, Far East, and Kamchatka. The total accuracy of prediction of one of 29 ethnic geographic groups reached 71%. The proposed method can be employed to predict ancestries from the populations of Russia and its neighbor states. It can be used for the needs of forensic science and genetic genealogy.

Development and Performance Evaluation of a Novel Ancestry Informative DIP Panel for Continental Origin Inference

Ancestry informative markers (AIMs) are useful to infer individual biogeographical ancestry and to estimate admixture proportions of admixed populations or individuals. Although a growing number of AIM panels for forensic ancestry origin analyses were developed, they may not efficiently infer the ancestry origins of most populations in China. In this study, a set of 52 ancestry informative deletion/insertion polymorphisms (AIDIPs) were selected with the aim of effectively differentiate continental and partial Chinese populations. All of the selected markers were successfully incorporated into a single multiplex PCR panel, which could be conveniently and efficiently detected on capillary electrophoresis platforms. Genetic distributions of the same 50 AIDIPs in different continental populations revealed that most loci showed high genetic differentiations between East Asian populations and other continental populations. Population genetic analyses of different continental populations indicated that these 50 AIDIPs could clearly discriminate East Asian, European, and African populations. In addition, the 52 AIDIPs also exhibited relatively high cumulative discrimination power in the Eastern Han population, which could be used as a supplementary tool for forensic investigation. Furthermore, the Eastern Han population showed close genetic relationships with East Asian populations and high ancestral components from East Asian populations. In the future, we need to investigate genetic distributions of these 52 AIDIPs in Chinese Han populations in different regions and other ethnic groups, and further evaluate the power of these loci to differentiate different Chinese populations.

Development a multiplex panel of AISNPs, multi-allelic InDels, microhaplotypes and Y-SNP/InDel loci for multiple forensic purposes via the NGS

Recently, next generation sequencing showed the promising application value in forensic research. In this study, we constructed a multiplex system of different molecular genetic markers based on the previous selected AISNPs, multi-allelic InDels, microhaplotypes and Y-SNP/InDel loci and evaluated forensic efficiencies of the system in Chinese Shaanxi Han, Hui and Mongolian groups via the NGS platform. Ancestry informative analyses of Shaanxi Han, Hui and Mongolian groups revealed that most Mongolian individuals could be differentiated from Shaanxi Hans and Huis based on the selected AISNPs. Multi-allelic InDels and microhaplotypes showed the multiple allele variations and possessed relatively high genetic polymorphisms in these three groups, indicating these loci could also provide higher forensic efficiencies for individual identification and paternity testing. Based on Y-SNPs, different haplogroup distributions were observed among Shaanxi Han, Hui and Mongolian groups. In conclusion, the self-developed system could be used to simultaneously carry out the individual identification, paternity analysis, mixture deconvolution, forensic ancestry information analysis and Y chromosomal haplogroup inference, which could provide more investigative clues in forensic practices. This article is protected by copyright. All rights reserved.

Genetic structure analyses and ancestral information inference of Chinese Kyrgyz group via a panel of 39 AIM-DIPs

Ancestry informative markers have extensive uses and advantages in inferring ancestral origins and estimating ancestral genetic information components of admixed populations. With the characteristics of highly cultural exchange and the admixed genetic structure of the Kyrgyz group, it is essential to enrich the genetic data of the Kyrgyz group. In this study, we used a self-developed ancestry informative marker-deletion/insertion polymorphic (AIM-DIP) panel to explore ancestral components of Chinese Kyrgyz group and population genetic relationships between the Kyrgyz group and reference populations. Results showed that all AIM-DIP loci were conformed to Hardy-Weinberg equilibrium. There were 36 AIM-DIP loci that contributed significantly to genetic information inference. Multiple statistical analyses revealed that Chinese Kyrgyz group had a closer genetic relationship with Chinese Uyghur group. The ancestral components of the Kyrgyz group, being mostly composed of genetic components of European and East Asian populations, were more similar to the ancestral components of Chinese Uyghur group.

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.

Genetic Polymorphisms and Forensic Efficiencies of a Set of Novel Autosomal InDel Markers in a Chinese Mongolian Group

Insertion/deletion (InDel) markers have been treated as a prospective and helpful aid in the fields of forensic human identifications and biogeography origin researches for the past few years. In this study, we analyzed genetic polymorphisms and forensic efficiencies of 35 InDels in a novel multiplex PCR-InDel panel in a Chinese Mongolian group. All these 35 InDel loci were observed to conform to Hardy–Weinberg equilibrium and linkage equilibrium. The mean values of expected heterozygosity and observed heterozygosity were 0.4788 and 0.4852, respectively. Besides, the interpopulation differentiations and genetic distributions based on 35 InDels found that the Chinese Mongolian group might have closer genetic relationships and similar population genetic structures with East Asian populations.