Genetic Ancestry and Affinity of a Local Population in Southern Thailand Using Whole-Exome Sequencing

Population-specific genomic references remain limited for many Southeast Asian communities, particularly in Southern Thailand. We characterized the broad genetic affinity of 24 unrelated adults from Che He Subdistrict, Tak Bai District, Narathiwat Province, using whole-exome sequencing. Reads were processed against GRCh38, and population structure was assessed using reference-defined principal component analysis (PCA), ADMIXTURE, pairwise FST, EthSEQ, and KING-based relatedness analysis. A mean of 114.5 million reads per participant was retained (99.03%), with 99.98–99.99% mapping and a mean depth of 117.07× across the manufacturer-defined Agilent V8 targets. Joint genotyping identified 421,801 PASS variants. For expanded analysis, 24 Che He samples were compared with 3380 high-quality unrelated HGDP–1000 Genomes references. Group-specific missingness control retained 183,930 callable autosomal SNPs; reference-only minor-allele-frequency filtering and LD pruning retained 43,353 SNPs for projection. Che He clustered within the East Asian reference space, with its centroid closest to Cambodian across higher-dimensional summaries. Unpruned Weir–Cockerham FST was also lowest versus Cambodian (0.00256), followed by Dai (0.00892), KHV (0.00956), CDX (0.01149), and Lahu (0.01202). These results indicate relative genetic proximity within the available reference panel and should not be interpreted as definitive ancestry or ethnicity assignment.