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Can I read Imputation of Ancient Human Genomes on EtoBox?
Imputation of Ancient Human Genomes by 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; Olivier Delaneau is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.
What is Imputation of Ancient Human Genomes about?
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 fo
Who reads Imputation of Ancient Human Genomes?
It is typically read by researchers, students, and practitioners in Biochemistry, Genetics and Molecular Biology.
- Author
- 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; Olivier Delaneau
- Publisher
- Springer Science and Business Media LLC
- Published
- 2023
- Language
- EN
- Field
- Biochemistry, Genetics and Molecular Biology (Life Sciences)