Imputation of ancient genomes

Abstract

25 Due to postmortem DNA degradation, most ancient genomes sequenced to date have low depth of 26 coverage, preventing the true underlying genotypes from being recovered. Genotype imputation has 27 been put forward to improve genotyping accuracy for low-coverage genomes. However, it is 28 unknown to what extent imputation of ancient genomes produces accurate genotypes and whether 29 imputation introduces bias to downstream analyses. To address these questions, we downsampled 30 43 ancient genomes, 42 of which are high-coverage (above 10x) and three constitute a trio (mother, 31 father and son), from different times and continents to simulate data with coverage in the range of 32 0.1x-2.0x and imputed these using state-of-the-art methods and reference panels. We assessed 33 imputation accuracy across ancestries and depths of coverage. We found that ancient and modern 34 DNA imputation accuracies were comparable. We imputed most of the 42 high-coverage genomes 35 downsampled to 1x with low error rates (below 5%) and estimated higher error rates for African 36 genomes, which are underrepresented in the reference panel. We used the ancient trio data to 37 validate imputation and phasing results using an orthogonal approach based on Mendel’s rules of 38 inheritance. This resulted in imputation and switch error rates of 1.9% and 2.0%, respectively, for 1x 39 genomes. We further compared the results of downstream analyses between imputed and high- 40 coverage genomes, notably principal component analysis (PCA), genetic clustering, and runs of 41 homozygosity (ROH). For these three approaches, we observed similar results between imputed 42 and high-coverage genomes using depths of coverage of at least 0.5x, except for African genomes, 43 for which the decreased imputation accuracy impacted ROH estimates. Altogether, these results 44 suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable 45 method with potential to expand and improve ancient DNA studies. 46