ArticleBioinformatics (Oxford, England)2023
Achieving improved accuracy for imputation of ancient DNA.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- MetaGLIMPSE: Meta-imputation of low-coverage sequencing data for modern and ancient genomes.American journal of human genetics · 2026Article
- Recent advances in methods to characterize archaic introgression in modern humans.Genome research · 2026Review
- Predicting Physical Appearance from Low Template: State of the Art and Future Perspectives.Genes · 2026Review
- Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Inferring Domestic Goat Demographic History Through Ancient Genome Imputation.Genome biology and evolution · 2025Article
- MetaGLIMPSE: Meta Imputation of Low Coverage Sequencing Data for Modern and Ancient Genomes.bioRxiv : the preprint server for biology · 2025Article
- The genomic footprints of migration: how ancient DNA reveals our history of mobility.Genome biology · 2025Review
- Identifying individuals with rare disease variants by inferring shared ancestral haplotypes from SNP array data.NAR genomics and bioinformatics · 2025Article
- Using feedback in pooled experiments augmented with imputation for high genotyping accuracy at reduced cost.G3 (Bethesda, Md.) · 2025Article
- Genotyping of SNPs in bread wheat at reduced cost from pooled experiments and imputation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
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Authors and funding
2 authors.
Funding
Abstract
motivationGenotype imputation has the potential to increase the amount of information that can be gained from the often limited biological material available in ancient samples. As many widely used tools have been developed with modern data in mind, their design is not necessarily reflective of the requirements in studies of ancient DNA. Here, we investigate if an imputation method based on the full probabilistic Li and Stephens model of haplotype frequencies might be beneficial for the particular challenges posed by ancient data.
resultsWe present an implementation called prophaser and compare imputation performance to two alternative pipelines that have been used in the ancient DNA community based on the Beagle software. Considering empirical ancient data downsampled to lower coverages as well as present-day samples with artificially thinned genotypes, we show that the proposed method is advantageous at lower coverages, where it yields improved accuracy and ability to capture rare variation. The software prophaser is optimized for running in a massively parallel manner and achieved reasonable runtimes on the experiments performed when executed on a GPU. AVAILABILITY AND IMPLEMENTATION: The C++ code for prophaser is available in the GitHub repository https://github.com/scicompuu/prophaser. SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.
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