Benchmarking kinship estimation tools for ancient genomes using pedigree simulations.

Autor: Aktürk Ş; Department of Biological Sciences, Middle East Technical University, Ankara, Turkey., Mapelli I; Department of Biological Sciences, Middle East Technical University, Ankara, Turkey., Güler MN; Department of Biological Sciences, Middle East Technical University, Ankara, Turkey., Gürün K; Department of Biological Sciences, Middle East Technical University, Ankara, Turkey., Katırcıoğlu B; Department of Biological Sciences, Middle East Technical University, Ankara, Turkey., Vural KB; Department of Biological Sciences, Middle East Technical University, Ankara, Turkey., Sağlıcan E; Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey., Çetin M; Department of Biological Sciences, Middle East Technical University, Ankara, Turkey., Yaka R; Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.; Centre for Palaeogenetics, Stockholm, Sweden.; Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden., Sürer E; Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey., Atağ G; Department of Biological Sciences, Middle East Technical University, Ankara, Turkey., Çokoğlu SS; Department of Biological Sciences, Middle East Technical University, Ankara, Turkey., Sevkar A; Department of Anthropology, Hacettepe University, Ankara, Turkey., Altınışık NE; Department of Anthropology, Hacettepe University, Ankara, Turkey., Koptekin D; Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey., Somel M; Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
Jazyk: angličtina
Zdroj: Molecular ecology resources [Mol Ecol Resour] 2024 Jul; Vol. 24 (5), pp. e13960. Date of Electronic Publication: 2024 Apr 27.
DOI: 10.1111/1755-0998.13960
Abstrakt: There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F 1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F 1  > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.
(© 2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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