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Science. 2015 Sep 11;349(6253):aab3761. doi: 10.1126/science.aab3761. Epub 2015 Aug 6.

Global diversity, population stratification, and selection of human copy-number variation.

Author information

1
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
2
Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
3
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
4
Department of Pediatrics, University of Washington, Seattle, WA 98119, USA.
5
Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
6
Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Novosibirsk State University, Novosibirsk 630090, Russia.
7
Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia.
8
Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
9
Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia.
10
Raja Isteri Pengiran Anak Saleha (RIPAS) Hospital, Bandar Seri Begawan, Brunei Darussalam.
11
Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), Centro Científico y Tecnológico-Consejo Nacional de Investigaciones Científicas y Técnicas (CCT-CONICET) and Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), La Plata B1906APO, Argentina.
12
Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
13
Department of Clinical Science, University of Bergen, Bergen 5021, Norway.
14
National Cancer Centre Singapore, Singapore.
15
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
16
Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland.
17
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
18
Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria.
19
Institut de Biologia Evolutiva [Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra (CSIC-UPF)], Departament de Ciències Experimentals i de la Salut, UPF, Barcelona 08003, Spain.
20
Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA.
21
Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK.
22
Department of Genetics, Evolution and Environment, University College London, WC1E 6BT, UK.
23
University of Helsinki, Department of Forensic Medicine, Helsinki 00014, Finland.
24
Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia. University of Tartu, Department of Evolutionary Biology, Tartu 5101, Estonia.
25
Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.
26
Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
27
Center for Global Health and Child Development, Kisumu 40100, Kenya.
28
Department of Anthropology, Case Western Reserve University, Cleveland, OH 44106-7125, USA.
29
Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA.
30
Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia. Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia.
31
Integrative Biology, University of California, Berkeley, CA 94720-3140, USA.
32
Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Incorporated, Frederick National Laboratory, Frederick, MD 21702, USA.
33
Centre Hospitalier Universitaire (CHU) Sainte-Justine, Département de Pédiatrie, Université de Montréal, QC H3T 1C5, Canada.
34
Departments of Biology and Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.
35
Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Department of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
36
Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia. Altai State University, Barnaul 656000, Russia.
37
Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
38
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. eee@gs.washington.edu.

Abstract

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

PMID:
26249230
PMCID:
PMC4568308
DOI:
10.1126/science.aab3761
[Indexed for MEDLINE]
Free PMC Article

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