ADVANCING GENOTYPE IMPUTATION IN ANCIENT GENOMES USING A REGION-SPECIFIC REFERENCE PANEL AND BENCHMARK GENOTYPES

Background: Ancient DNA datasets often suffer from low coverage and extensive missing data, hindering diploid-based analyses and constraining population genetic inference. While genotype imputation has become a popular solution to address these issues, its effectiveness is heavily reliant on the composition of the reference panel, genetic divergence, and the availability of high-coverage ancient genomes. Rigorous benchmarking has proven challenging due to the scarcity of such genomes.

Results: In this study, a region-specific reference panel, named eREF, was developed to focus on Eastern Europe. This eREF panel proved to enhance the imputation performance of low-coverage ancient genomes originating from the same region. To address the limited availability of high-coverage ancient genomes suitable for direct genotype calling, crucial for imputation quality assessment, the researchers generated proxy genotypes by imputing low-to-medium coverage (1-15X) ancient genomes.

These proxy genotypes were employed as a substitute for ground truth data when evaluating imputation accuracy in ultra-low-coverage genomes. Furthermore, the eREF-imputed data was utilized to perform downstream population genetic analyses, specifically on Late Iron Age/Medieval Estonian populations, to explore whether cultural differentiation among contemporary communities corresponded with their genetic variation.

Conclusions: The eREF reference panel significantly improves imputation accuracy for ancient genomes from North and Eastern Europe by more accurately reflecting regional genetic variation. Additionally, the study demonstrates that imputed low-to-medium coverage genomes can serve as dependable proxy-truth genotypes for benchmarking imputation performance when high-coverage ancient genomes are not accessible.

Lastly, the use of eREF-enabled imputation facilitates fine-scale analyses of genetic structure, unveiling genetic differentiation between two neighboring contemporary communities that aligns with their cultural distinctions.