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. 2024 Aug 21;15(8):1099.
doi: 10.3390/genes15081099.

Local Ancestry Inference Based on Population-Specific Single-Nucleotide Polymorphisms-A Study of Admixed Populations in the 1000 Genomes Project

Haoyue Fu  1 , Gang Shi  1
Affiliations

Local Ancestry Inference Based on Population-Specific Single-Nucleotide Polymorphisms-A Study of Admixed Populations in the 1000 Genomes Project

Haoyue Fu et al. Genes (Basel). .

Abstract

Human populations have interacted throughout history, and a considerable portion of modern human populations show evidence of admixture. Local ancestry inference (LAI) is focused on detecting the genetic ancestry of chromosomal segments in admixed individuals and has wide applications. In this work, we proposed a new LAI method based on population-specific single-nucleotide polymorphisms (SNPs) and applied it in the analysis of admixed populations in the 1000 Genomes Project (1KGP). Based on population-specific SNPs in a sliding window, we computed local ancestry information vectors, which are moment estimators of local ancestral proportions, for two haplotypes of an admixed individual and inferred the local ancestral origins. Then we used African (AFR), East Asian (EAS), European (EUR) and South Asian (SAS) populations from the 1KGP and indigenous American (AMR) populations from the Human Genome Diversity Project (HGDP) as reference populations and conducted the proposed LAI analysis on African American populations and American populations in the 1KGP. The results were compared with those obtained by RFMix, G-Nomix and FLARE. We demonstrated that the existence of alleles in a chromosomal region that are specific to a particular reference population and the absence of alleles specific to the other reference populations provide reasonable evidence for determining the ancestral origin of the region. Contemporary AFR, AMR and EUR populations approximate ancestral populations of the admixed populations well, and the results from RFMix, G-Nomix and FLARE largely agree with those from the Ancestral Spectrum Analyzer (ASA), in which the proposed method was implemented. When admixtures are ancient and contemporary reference populations do not satisfactorily approximate ancestral populations, the performances of RFMix, G-Nomix and FLARE deteriorate with increased error rates and fragmented chromosomal segments. In contrast, our method provides fair results.

Keywords: admixture; human populations; local ancestry inference; population-specific SNPs.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Local ancestry results of HG02052 on chromosome 1 with reference populations from AFR, AMR, EAS, EUR and SAS.
Figure 2
Figure 2
Local ancestry results of HG02330 on chromosome 18 with reference populations from AFR, AMR, EAS, EUR and SAS.
Figure 3
Figure 3
Local ancestry results of HG02107 on chromosome 1 with reference populations from AFR, AMR, EAS, EUR and SAS.
Figure 4
Figure 4
Local ancestry results of NA20299 on chromosome 1 with reference populations from AFR, AMR, EAS, EUR and SAS.
Figure 5
Figure 5
Local ancestry results of HG01893 on chromosome 2 with reference populations from AFR, AMR, EAS, EUR and SAS.
Figure 6
Figure 6
Local ancestry results of HG02272 on chromosome 3 with reference populations from AFR, EAS, EUR and SAS.
Figure 7
Figure 7
Local ancestry results of HG02272 on chromosome 3 with reference populations from AFR, AMR, EAS, EUR and SAS.
Figure 8
Figure 8
Local ancestry results of HG01880 on autosomes with reference populations from AFR, AMR, EAS, EUR and SAS. The analysis was conducted by ASA.
Figure 9
Figure 9
Local ancestry results of HG01944 on autosomes with reference populations from AFR, AMR, EAS, EUR and SAS. The analysis was conducted by ASA.
Figure 10
Figure 10
Computational time for ASA, RFMix, G-Nomix and FLARE.
See this image and copyright information in PMC

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