Determination of genetic relatedness from low‐coverage human genome sequences using pedigree simulations |
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Authors: | Michael D Martin Flora Jay Sergi Castellano Montgomery Slatkin |
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Institution: | 1. Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway;2. Center for Theoretical Evolutionary Genomics, Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA;3. Laboratoire de Recherche en Informatique, CNRS UMR 8623, Université Paris‐Sud, Paris‐Saclay, France;4. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany |
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Abstract: | We develop and evaluate methods for inferring relatedness among individuals from low‐coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate and the presence of contamination from present‐day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present‐day contamination and sequencing error. The model is validated by a simulation study as well as the analysis of aligned sequences from present‐day human genomes. We then apply the method to the recently published genome sequences of ancient Europeans, developing a statistical treatment to determine confidence in assigned relatedness that is, in some cases, more precise than previously reported. As the majority of ancient specimens are from animals, this method would be applicable to investigate kinship in nonhuman remains. The developed software grups (Genetic Relatedness Using Pedigree Simulations) is implemented in Python and freely available. |
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Keywords: | ancient DNA computer simulation DNA genetics genome genomics humans pedigree polymorphism relatedness single nucleotide |
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