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Determination of genetic relatedness from low- coverage human genome sequences using pedigree simulations

Martin, MD; Jay, F; Castellano, S; Slatkin, M; (2017) Determination of genetic relatedness from low- coverage human genome sequences using pedigree simulations. Molecular ecology , 26 (16) pp. 4145-4157. 10.1111/mec.14188. Green open access

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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.

Type: Article
Title: Determination of genetic relatedness from low- coverage human genome sequences using pedigree simulations
Open access status: An open access version is available from UCL Discovery
DOI: 10.1111/mec.14188
Publisher version: https://doi.org/10.1111/mec.14188
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: ancient DNA, computer simulation, DNA, genetics, genome, genomics, humans, pedigree, polymorphism, relatedness, single nucleotide
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health > Genetics and Genomic Medicine Dept
URI: https://discovery.ucl.ac.uk/id/eprint/10061434
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