Abstract
In the present study, we investigated the genetic polymorphisms of 39 ancestry informative marker-insertion/deletion (AIM-InDel) loci in the Chinese Hui group using a previously self-developed panel, further clarified the genetic relationships between the Hui group and other reference populations, and assessed the ancestry inference efficiency of the AIM-InDel panel based on the worldwide population data from 1000 Genomes Phase 3. The results of the locus-specific informativeness (In) and pairwise fixation index (Fst) values, multidimensional scaling analysis, and success ratio of estimation with cross-validation showed that the novel panel could well reveal the genetic structural differentiations of the East Asian, European, African, and South Asian populations. Besides, the biogeographical ancestry origin inference both at the individual and population levels was conducted on the Chinese Hui group by principal component analysis and STRUCTURE analysis, and the results revealed that the Hui group had the East Asian origin, and the East Asian component ratio of Hui group was approximately 88.87%. Furthermore, the population genetic analyses among the Hui group and reference populations were performed based on the insertion allele frequency heat map, population pairwise Fst values and phylogenetic tree, and the results indicated that the Hui group was genetically closer to East Asian populations, especially two Chinese Han populations (CHS and CHB populations).
Highlights
In recent years, ancestry informative inference has uncovered important information and provided a new perspective in biomedical fields such as anthropological research, forensic genetic application, and genetic epidemiology study [1,2,3]
The ancestry inference synthetic efficiency and forensic practicability of this novel panel were conducted by assigning the population genotype data of the same 38 AIM-InDel loci in the 2504 worldwide individuals from the 1000 Genomes Phase 3, and the pairwise Fst and locus-specific Rosenberg’s In values, the cross-validation estimation success ratios, and the multidimensional scaling (MDS)
The ancestral origin components of the Hui group were inferred by STRUCTURE software based on an admixture ancestry model, and the results revealed that the Hui group shared the relatively higher East Asian ancestry proportion (88.87%)
Summary
Ancestry informative inference has uncovered important information and provided a new perspective in biomedical fields such as anthropological research, forensic genetic application, and genetic epidemiology study [1,2,3]. Ancestry inference based on ancestry informative genetic markers could help to correct for population stratification [4,5,6]. The accumulation of genetic differences among populations, especially for intercontinental populations, is the basis of individual ancestor information inference. In the forensic genetic field, ancestry information inference. There were still some new challenges that need to be solved in ancestry inference research, such as elucidating the genetic variation estimations within or between populations and clearing the admixture proportions in an individual of mixed origin [7]
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