Local Ancestry Inference Based on Population-Specific Single-Nucleotide Polymorphisms—A Study of Admixed Populations in the 1000 Genomes Project
Haoyue Fu, Gang Shi
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This study introduces a local ancestry inference approach that relies on population-specific SNPs (LAIVs) to analyze admixed populations in the 1000 Genomes Project. It constructs local ancestry information vectors from sliding windows of population-specific SNPs, using reference panels AFR, EAS, EUR, SAS and indigenous AMR from HGDP. The method ASA (Ancestral Spectrum Analyzer) is compared against established LAI tools (RFMix, G-Nomix, FLARE) and shows that population-specific alleles can effectively discriminate ancestral origins, particularly for ancient admixture scenarios, with ASA providing robust performance across tested settings.
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Local Ancestry Inference Based on Population-Specific Single-Nucleotide Polymorphisms—A Study of Admixed Populations in the 1000 Genomes Project
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