Abstract
Inbreeding coefficients and consanguineous mating types are usually inferred from population surveys or pedigree studies. Here, we present a method to estimate them from dense genome-wide single-nucleotide polymorphism genotypes and apply it to 940 unrelated individuals from the Human Genome Diversity Panel (HGDP-CEPH). Inbreeding is observed in almost all populations of the panel, and the highest inbreeding levels and frequencies of inbred individuals are found in populations of the Middle East, Central South Asia and the Americas. In these regions, first cousin (1C) marriages are the most frequent, but we also observed marriages between double first cousins (2 × 1C) and between avuncular (AV) pairs. Interestingly, if 2 × 1C marriages are preferred to AV marriages in Central South Asia and the Middle East, the contrary is found in the Americas. There are thus some regional trends but there are also some important differences between populations within a region. Individual results can be found on the CEPH website at ftp://ftp.cephb.fr/hgdp_hbd/.
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Acknowledgements
We thank Jean Maccario for helpful discussions on variance components and two anonymous reviewers for their constructive comments. SG is funded by the plateforme de génomique constitutionnelle (Faculté de médecine, Univ Paris-Diderot, Paris, France).
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Data availability on the HGDP-CEPH webpage: http://www.cephb.fr/en/hgdp Consanguinity/Endogamy Resource: http://www.consang.net/index.php/Main_Page
ALFRED website: http://alfred.med.yale.edu/alfred/entity.asp?condition=populations Pangaea website: http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml FEstim Software: on request from anne-louise.leutenegger@inserm.fr
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Leutenegger, AL., Sahbatou, M., Gazal, S. et al. Consanguinity around the world: what do the genomic data of the HGDP-CEPH diversity panel tell us?. Eur J Hum Genet 19, 583–587 (2011). https://doi.org/10.1038/ejhg.2010.205
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DOI: https://doi.org/10.1038/ejhg.2010.205