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Sci Rep. 2015 Dec 2;5:17453. doi: 10.1038/srep17453.

High level of inbreeding in final phase of 1000 Genomes Project.

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INSERM, IAME, UMR 1137, F-75018 Paris, France.
Plateforme de génomique constitutionnelle du GHU Nord, Assistance Publique des Hôpitaux de Paris (APHP), Hôpital Bichat, F-75018 Paris, France.
Fondation Jean Dausset CEPH, F-75010 Paris, France.
INSERM, Genetic variability and human diseases, UMR 946, F-75010 Paris, France.
Univ Paris-Diderot, UMR 946, Sorbonne Paris Cité, F-75010 Paris, France.
INSERM, UMR 1078, Génétique, Génomique fonctionnelle et Biotechnologies, F-29218 Brest, France.
Centre Hospitalier Régional Universitaire de Brest, F-29200 Brest, France.


The 1000 Genomes Project provides a unique source of whole genome sequencing data for studies of human population genetics and human diseases. The last release of this project includes more than 2,500 sequenced individuals from 26 populations. Although relationships among individuals have been investigated in some of the populations, inbreeding has never been studied. In this article, we estimated the genomic inbreeding coefficient of each individual and found an unexpected high level of inbreeding in 1000 Genomes data: nearly a quarter of the individuals were inbred and around 4% of them had inbreeding coefficients similar or greater than the ones expected for first-cousin offspring. Inbred individuals were found in each of the 26 populations, with some populations showing proportions of inbred individuals above 50%. We also detected 227 previously unreported pairs of close relatives (up to and including first-cousins). Thus, we propose subsets of unrelated and outbred individuals, for use by the scientific community. In addition, because admixed populations are present in the 1000 Genomes Project, we performed simulations to study the robustness of inbreeding coefficient estimates in the presence of admixture. We found that our multi-point approach (FSuite) was quite robust to admixture, unlike single-point methods (PLINK).

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