Targeted sequencing of high-density SNPs provides an enhanced tool for forensic applications and genetic landscape exploration in Chinese Korean ethnic group

Abstract

Background: In this study, we present a NGS-based panel designed for sequencing 1993 SNP loci for forensic DNA investigation. This panel addresses unique challenges encountered in forensic practice and allows for a comprehensive population genetic study of the Chinese Korean ethnic group. To achieve this, we combine our results with datasets from the 1000 Genomes Project and the Human Genome Diversity Panel.

Results: We demonstrate that this panel is a reliable tool for individual identification and parentage testing, even when dealing with degraded DNA samples featuring exceedingly low SNP detection rates. The performance of this panel for complex kinship determinations, such as half-sibling and grandparent-grandchild scenarios, is also validated by various kinship simulations. Population genetic studies indicate that this panel can uncover population substructures on both global and regional scales. Notably, the Han population can be distinguished from the ethnic minorities in the northern and southern regions of East Asia, suggesting its potential for regional ancestry inference. Furthermore, we highlight that the Chinese Korean ethnic group, along with various Han populations from different regional areas and certain northern ethnic minorities (Daur, Tujia, Japanese, Mongolian, Xibo), exhibit a higher degree of genetic affinities when examined from a genomic perspective.

Conclusion: This study provides convincing evidence that the NGS-based panel can serve as a reliable tool for various forensic applications. Moreover, it has helped to enhance our knowledge about the genetic landscape of the Chinese Korean ethnic group.

Keywords: Chinese Korean ethnic group; Forensic application; Genetic structure; Next-generation sequencing; Single nucleotide polymorphism.

Fig. 1

Estimating the efficiencies of the 1946 SNP loci for kinship analyses by simulating different kinships. A Box plots displaying the distributions of Log₁₀ (LR) for different kinships based on 1946 SNP loci. PC, parent–child pair; FS, full sibling pair; HS, half sibling pair; GG, grandparent-grandchild pair; B Log₁₀ (LR) distributions for FS and unrelated individuals (UI); C Log₁₀ (LR) distributions for HS and unrelated individuals (UI); D Log₁₀ (LR) distributions for GG and unrelated individuals (UI)

Fig. 2

Forensic applications of the 1706 SNP loci in individual identification and ancestry inference. A Heatmap of the allele frequencies for the 1706 SNP loci in the 76 populations; B Distribution of PD and I_{n_1} values of the 1706 SNPs to distinguish among the overall eight intercontinental populations C Distribution of PD and I_{n_2} values of the 1706 SNPs to distinguish between Asia populations; D Distribution of PD and I_{n_3} values of the 1706 SNPs to distinguish between East Asia populations. The I_{n_1} denotes that the SNP loci are used to distinguish between the overall 76 intercontinental populations. The I_{n_2} is calculated to show the efficiency of the SNP locus to distinguish between East Asia, South Asia, Central South Asia and Middle East populations. The I_{n_3} is estimated to show the efficiency of the SNP locus in distinguishing between East Asia populations

Fig. 3

Pairwise F_ST values among different populations. A Heat map of the F_ST values estimated among different intercontinental populations, including Africa, Europe, East Asia, South Asia, America, Central South Asia, Middle East and Oceania populations. The color ranges from red to blue, corresponding to F_ST values from low to high. B Bar plot of the F_ST values between the Chinese Korean ethnic group and the reference populations. Populations labeled with the same color indicate they are from the same continents; C ADMIXTURE results for K = 9. The genetic components of different populations are represented in different colors

Fig. 4

Population genetic structures revealed by principal component analyses. Each dot represents a single individual and is colored according to its continental origin. A, B PCA of the overall individuals with the first three principal components (PC) involved, which reveals the population genetic structures of the intercontinental populations from eight major global regions; C, D PCA of the individuals from East Asia, South Asia, Central South Asia and Middle East with the first three PCs involved, which reveals the population genetic structures of these populations; E, F PCA of the individuals from East Asia with the first three PCs involved, which reveals the population genetic structures of East Asia populations. The individuals from East Asia are categorized into the Han populations, northern ethnic minorities and southern ethnic minorities

Fig. 5

Gene flow estimated among the Chinese Korean ethnic group and the reference populations. A Pairwise outgroup-f₃ of the Chinese Korean ethnic group and the reference populations. The color gradient ranges from green to red, corresponding to outgroup-f₃ values from low to high. The map shows the approximate geographic distribution for each population; B Pairwise outgroup-f₃ of the Chinese Korean ethnic group and the East Asian reference populations; C–E Distribution of f₄ values from Dstats tests under the model of [Mbuti, Korean_C; X, Y], where X represents the Han populations of different regions, Y represents different East Asian populations and the Mbuti population serves as an outgroup

Fig. 6

Phylogenetic relatedness of the Chinese Korean ethnic group and the reference populations. A Population-level maximum-likelihood phylogenetic tree; B Individual-level maximum-likelihood phylogenetic tree; C Population-level maximum likelihood tree and pairwise residuals for the phylogenies after accounting for four migration events. The scale bar shows the average standard error of the entries in the covariance matrix