Abstract
Turkmen populations remain underrepresented in genome-wide reference datasets, limiting comparative analyses of genetic diversity in Central Asia. This study provides an initial regional genome-wide characterization of self-identified Turkmen students who were studying in Kazakhstan at the time of sample collection and who reported the Dashoguz Region, Turkmenistan, as their place of birth in the questionnaire. Approximately 650,000 markers were genotyped in 25 participants, of whom 23 unrelated individuals were retained after genotype quality control and relatedness filtering. Population structure was evaluated with 600 present-day Eurasian reference individuals using principal component analysis, ADMIXTURE v1.3.0, and pairwise Weir–Cockerham FST estimates based on 17,471 linkage-disequilibrium-pruned autosomal SNPs. Runs of homozygosity, Y-chromosome haplogroups, and mitochondrial DNA haplogroups were also examined. The analyzed cohort was positioned within the Central Asian genetic landscape and showed the lowest pairwise differentiation from Uzbek, Tajik, and AADR Turkmen reference groups. Runs-of-homozygosity analysis showed mostly low-to-moderate individual burdens, although one individual had elevated long-segment homozygosity; sensitivity analyses indicated that the main autosomal results were not driven by this individual. Paternal and maternal haplogroup assignments revealed diverse uniparental lineages. These data provide a regional genome-wide resource for future comparative studies of Central Asian genetic diversity and have been deposited in the European Variation Archive.