Ancient human trio (Koszyce). Imputation of ancient genomes

Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we downsample and impute 43 ancient genomes, 42 of which are high-coverage (above 10x) and three constitute a trio (mother, father and son). We assess imputation accuracy across ancestry, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. We impute 36 of the 42 1x genomes with low error rates (below 5%) and estimate higher error rates for African genomes. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel’s rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method with potential improve ancient DNA studies.

受死后DNA降解与微生物定植影响，绝大多数古基因组（ancient genomes）的测序深度（depth of coverage）较低，这会阻碍基因型分型（genotype calling）工作的开展。基因型填充（Genotype imputation）可提升低测序深度基因组的分型精度。然而，目前学界尚未明确古DNA基因型填充的精度水平，以及该步骤是否会为下游分析引入偏倚。本研究对43个古基因组开展降采样与基因型填充操作：其中42个为原始高测序深度（>10x）样本，且该42个样本中的3个构成一家三口家系（母亲、父亲与儿子）。研究团队从祖先背景、时间维度、测序深度以及测序技术四个维度对基因型填充精度展开评估，发现古DNA与现代DNA的基因型填充精度相当。我们将42个高测序深度样本降采样至1x测序深度后，对其中36个进行基因型填充，其错误率低于5%；同时发现非洲古基因组的填充错误率更高。本研究借助该古人类家系数据与基于孟德尔遗传定律的正交验证方法，对基因型填充与单体型分型（phasing）结果进行了验证。我们进一步对比了填充后基因组与高测序深度基因组的下游分析结果，具体涵盖主成分分析（principal component analysis）、遗传聚类以及纯合子连续区域（runs of homozygosity）。结果显示，除非洲古基因组外，当测序深度低至0.5x时，两类样本的分析结果均保持一致。综上结果表明，针对绝大多数人群以及低至0.5x的测序深度样本，基因型填充是一种可靠的分析手段，有望推动古基因组研究领域的发展。