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

Abstract

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.

Keywords: AIDIP; Eastern Han; ancestry informative marker; deletion/insertion polymorphism; forensic ancestry analysis.

FIGURE 1

Representative 500 pg of Control DNA 9948 profile amplified with the 52-AIDIP panel for 25-μl reaction volumes. Five hundred picograms of Control DNA 9948 was amplified with the developed panel for 30 cycles. One microliter of PCR product added into 12.5 μl of loading mixtures (12 μl Hi-Di formamide +0.5 μl SIZ-500 Size Standard) was electrophoresed on a 3500xL Genetic Analyzer using the default injection conditions.

FIGURE 2

Heatmap of deletion allelic frequencies of 50 ancestry informative DIPs in different continental populations.

FIGURE 3

Pairwise F _ST values of five continental populations for 50 ancestry informative DIPs.

FIGURE 4

Ancestry origin analyses of different continental populations based on 50 ancestry informative DIPs. (A) PCA of different continental populations at PC1, PC2, and PC3. (B) Population genetic structure analyses of different continental populations at K = 2–7.

FIGURE 5

Allelic frequencies and forensic parameters of 52 ancestry informative DIPs in an Eastern Han population. (A) Allelic frequency. (B) Forensic parameter.

FIGURE 6

Ancestry component analyses of the studied Eastern Han populations in comparisons with other continental populations. (A) PCA of Eastern Han and continental populations at PC1 and PC2. (B) Population genetic structure analyses of Eastern Han and continental populations at K = 3.