ArticleNature communications2023
Imputation of ancient human genomes.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Population genomics, demography, and circum-Baltic connectivity of Early Medieval southwestern Finland.Genome biology · 2026Article
- Spatial Logic and Evolutionary Innovation in Human Placentation.bioRxiv : the preprint server for biology · 2026Article
- Archaic ancestry inference in imputed ancient human genomes.Nature communications · 2026Article
- Imputation in the Wild: Genome-Wide Robustness and Fine-Scale Limitations of Low-Coverage Genomes in Endangered Species.Molecular ecology resources · 2026Article
- A Rarefaction Approach to Identify Local Introgression in a Three Population Tree.bioRxiv : the preprint server for biology · 2026Article
- Insights into human adaptation from ancient DNA.Nature genetics · 2026Review
- Optimal Reference Panel Design in Ancient DNA Imputation from Coalescent Theory, Simulation, and Real Data Application with an Ancient Reference Panel.bioRxiv : the preprint server for biology · 2026Article
- Graph transformer for ancient ancestry inference.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking imputation accuracy in the presence or absence of a reference panel.Molecular biology and evolution · 2026Article
- A large mass grave from the Early Iron Age indicates selective violence towards women and children in the Carpathian Basin.Nature human behaviour · 2026Article
- Analysis of medieval burials from Ibiza reveals genetic and pathogenic diversity during the Islamic period.Nature communications · 2026Article
- Ancient DNA reveals 4000 years of grapevine diversity, viticulture and clonal propagation in France.Nature communications · 2026Article
- MetaGLIMPSE: Meta-imputation of low-coverage sequencing data for modern and ancient genomes.American journal of human genetics · 2026Article
- Reconstruction of the lifeways of Central European Late Bronze Age communities using ancient DNA, isotope and osteoarchaeological analyses.Nature communications · 2026Article
- AncientProxy: A catalog of ancient proxies for modern genetic variants.American journal of human genetics · 2026Article
- Robust imputation-based method for eye, hair, and skin colour prediction from low-coverage ancient DNA.Scientific reports · 2026Article
- Recent advances in methods to characterize archaic introgression in modern humans.Genome research · 2026Review
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- Structured missingness in biomedical research.Communications AI & computing · 2026Article
- A SNP panel for co-analysis of capture and shotgun ancient DNA data.bioRxiv : the preprint server for biology · 2025Article
3 more citing papers are in PubMed but not listed here.
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15 authors.
Funding
Abstract
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 re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. 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 the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.