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

Author:

Sudmant Peter H.1,Mallick Swapan23,Nelson Bradley J.1,Hormozdiari Fereydoun1,Krumm Niklas1,Huddleston John14,Coe Bradley P.1,Baker Carl1,Nordenfelt Susanne23,Bamshad Michael5,Jorde Lynn B.6,Posukh Olga L.78,Sahakyan Hovhannes910,Watkins W. Scott11,Yepiskoposyan Levon10,Abdullah M. Syafiq12,Bravi Claudio M.13,Capelli Cristian14,Hervig Tor15,Wee Joseph T. S.16,Tyler-Smith Chris17,van Driem George18,Romero Irene Gallego19,Jha Aashish R.19,Karachanak-Yankova Sena20,Toncheva Draga20,Comas David21,Henn Brenna22,Kivisild Toomas23,Ruiz-Linares Andres24,Sajantila Antti25,Metspalu Ene926,Parik Jüri9,Villems Richard9,Starikovskaya Elena B.27,Ayodo George28,Beall Cynthia M.29,Di Rienzo Anna19,Hammer Michael F.30,Khusainova Rita3132,Khusnutdinova Elza3132,Klitz William33,Winkler Cheryl34,Labuda Damian35,Metspalu Mait9,Tishkoff Sarah A.36,Dryomov Stanislav2737,Sukernik Rem2738,Patterson Nick23,Reich David2339,Eichler Evan E.14

Affiliation:

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.

3. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

4. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

5. Department of Pediatrics, University of Washington, Seattle, WA 98119, USA.

6. Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.

7. Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.

8. Novosibirsk State University, Novosibirsk 630090, Russia.

9. Estonian Biocentre, Evolutionary Biology Group, Tartu 51010, Estonia.

10. Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan 0014, Armenia.

11. Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.

12. Raja Isteri Pengiran Anak Saleha (RIPAS) Hospital, Bandar Seri Begawan, Brunei Darussalam.

13. 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.

14. Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.

15. Department of Clinical Science, University of Bergen, Bergen 5021, Norway.

16. National Cancer Centre Singapore, Singapore.

17. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.

18. Institute of Linguistics, University of Bern, Bern CH-3012, Switzerland.

19. Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

20. Department of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia 1431, Bulgaria.

21. 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.

22. Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA.

23. Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK.

24. Department of Genetics, Evolution and Environment, University College London, WC1E 6BT, UK.

25. University of Helsinki, Department of Forensic Medicine, Helsinki 00014, Finland.

26. University of Tartu, Department of Evolutionary Biology, Tartu 5101, Estonia.

27. Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.

28. Center for Global Health and Child Development, Kisumu 40100, Kenya.

29. Department of Anthropology, Case Western Reserve University, Cleveland, OH 44106-7125, USA.

30. Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA.

31. Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa 450054, Russia.

32. Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa 450074, Russia.

33. Integrative Biology, University of California, Berkeley, CA 94720-3140, USA.

34. Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Incorporated, Frederick National Laboratory, Frederick, MD 21702, USA.

35. Centre Hospitalier Universitaire (CHU) Sainte-Justine, Département de Pédiatrie, Université de Montréal, QC H3T 1C5, Canada.

36. Departments of Biology and Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.

37. Department of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.

38. Altai State University, Barnaul 656000, Russia.

39. Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.

Abstract

Duplications and deletions in the human genome Duplications and deletions can lead to variation in copy number for genes and genomic loci among humans. Such variants can reveal evolutionary patterns and have implications for human health. Sudmant et al. examined copy-number variation across 236 individual genomes from 125 human populations. Deletions were under more selection, whereas duplications showed more population-specific structure. Interestingly, Oceanic populations retain large duplications postulated to have originated in an ancient Denisovan lineage. Science , this issue 10.1126/science.aab3761

Funder

NSF

NIH

Howard Hughes Medical Institute

National Cancer Institute

Simons Foundation

Paul G. Allen Family Foundation

Wellcome Trust

European Research Council

Ministry of Education and Science, Russian Federation

Intramural Research Program of the NIH

Center for Cancer Research

ENA

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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