Imputation of ancient human genomes

Bárbara Sousa da Mota, Simone Rubinacci, Diana Ivette Cruz Dávalos, Carlos Eduardo G. Amorim, Martin Sikora, Niels N. Johannsen, Marzena H. Szmyt, Piotr Włodarczak, Anita Szczepanek, Marcin M. Przybyła, Hannes Schroeder, Morten E. Allentoft, Eske Willerslev, Anna-Sapfo Malaspinas () and Olivier Delaneau ()
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Bárbara Sousa da Mota: University of Lausanne
Simone Rubinacci: University of Lausanne
Diana Ivette Cruz Dávalos: University of Lausanne
Carlos Eduardo G. Amorim: California State University
Martin Sikora: University of Copenhagen
Niels N. Johannsen: Aarhus University
Marzena H. Szmyt: Adam Mickiewicz University in Poznań
Piotr Włodarczak: Polish Academy of Sciences
Anita Szczepanek: Polish Academy of Sciences
Marcin M. Przybyła: Jagiellonian University
Hannes Schroeder: University of Copenhagen
Morten E. Allentoft: University of Copenhagen
Eske Willerslev: University of Copenhagen
Anna-Sapfo Malaspinas: University of Lausanne
Olivier Delaneau: University of Lausanne

Nature Communications, 2023, vol. 14, issue 1, 1-17

Abstract: 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.

Date: 2023
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39202-0

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DOI: 10.1038/s41467-023-39202-0

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