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Genotype, haplotype and copy-number variation in worldwide human populations

Author

Listed:
  • Mattias Jakobsson

    (Center for Computational Medicine and Biology,
    Department of Human Genetics,)

  • Sonja W. Scholz

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
    Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK)

  • Paul Scheet

    (Center for Computational Medicine and Biology,
    University of Michigan, Ann Arbor, Michigan 48109, USA)

  • J. Raphael Gibbs

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
    Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK)

  • Jenna M. VanLiere

    (Center for Computational Medicine and Biology,)

  • Hon-Chung Fung

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
    Chang Gung Memorial Hospital and College of Medicine, Chang Gung University)

  • Zachary A. Szpiech

    (Center for Computational Medicine and Biology,)

  • James H. Degnan

    (Center for Computational Medicine and Biology,
    Department of Human Genetics,)

  • Kai Wang

    (University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA)

  • Rita Guerreiro

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
    Center for Neurosciences and Cell Biology, Faculty of Medicine, University of Coimbra)

  • Jose M. Bras

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
    Center for Neurosciences and Cell Biology, Faculty of Medicine, University of Coimbra)

  • Jennifer C. Schymick

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
    University of Oxford, John Radcliffe Hospital)

  • Dena G. Hernandez

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA)

  • Bryan J. Traynor

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
    Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA)

  • Javier Simon-Sanchez

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
    Unidad de Genética Molecular, Instituto de Biomedicina de Valencia-CSIC, 46010, Valencia, Spain)

  • Mar Matarin

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA)

  • Angela Britton

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA)

  • Joyce van de Leemput

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
    Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK)

  • Ian Rafferty

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA)

  • Maja Bucan

    (University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA)

  • Howard M. Cann

    (Fondation Jean Dausset – Centre d’Étude du Polymorphisme Humain (CEPH), 27 rue Juliette Dodu, 75010 Paris, France)

  • John A. Hardy

    (Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK)

  • Noah A. Rosenberg

    (Center for Computational Medicine and Biology,
    Department of Human Genetics,
    University of Michigan, Ann Arbor, Michigan 48109, USA)

  • Andrew B. Singleton

    (Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland 20892, USA
    Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia 22908, USA)

Abstract

Genetic baggage check The analysis of genome-wide patterns of variation in human populations can provide genetic evidence of patterns of human migration and adaptation across the world. Two contrasting papers in this issue illustrate the power of the method. By combining a large number of datasets, Lohmueller et al. obtain precise estimates of the number of deleterious mutations carried by each of 15 African-Americans and 20 European-Americans, resequenced across 11,000 genes. They find that individuals with a European background have more potentially damaging mutations lurking in their genomes than those with an African background. This is interpreted as a genetic legacy from the 'out-of-Africa' bottleneck that accompanied the peopling of Europe. Jakobsson et al. take a broader snapshot of human variation by examining 29 populations in the Human Genome Diversity Project. They obtain genotype data for over 500,000 markers in the human genome. Echoing the study of Americans with African and European backgrounds, these data reveal increasing linkage disequilibrium with increasing geographic distance from Africa.

Suggested Citation

  • Mattias Jakobsson & Sonja W. Scholz & Paul Scheet & J. Raphael Gibbs & Jenna M. VanLiere & Hon-Chung Fung & Zachary A. Szpiech & James H. Degnan & Kai Wang & Rita Guerreiro & Jose M. Bras & Jennifer C, 2008. "Genotype, haplotype and copy-number variation in worldwide human populations," Nature, Nature, vol. 451(7181), pages 998-1003, February.
    • Handle: RePEc:nat:nature:v:451:y:2008:i:7181:d:10.1038_nature06742
    DOI: 10.1038/nature06742
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    Citations

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    Cited by:

    1. Chaolong Wang & Sebastian Zöllner & Noah A Rosenberg, 2012. "A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations," PLOS Genetics, Public Library of Science, vol. 8(8), pages 1-16, August.
    2. Xuchao Li & Shengpei Chen & Weiwei Xie & Ida Vogel & Kwong Wai Choy & Fang Chen & Rikke Christensen & Chunlei Zhang & Huijuan Ge & Haojun Jiang & Chang Yu & Fang Huang & Wei Wang & Hui Jiang & Xiuqing, 2014. "PSCC: Sensitive and Reliable Population-Scale Copy Number Variation Detection Method Based on Low Coverage Sequencing," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-9, January.
    3. Ricardo Kanitz & Elsa G Guillot & Sylvain Antoniazza & Samuel Neuenschwander & Jérôme Goudet, 2018. "Complex genetic patterns in human arise from a simple range-expansion model over continental landmasses," PLOS ONE, Public Library of Science, vol. 13(2), pages 1-16, February.
    4. Eric R Londin & Margaret A Keller & Cathleen Maista & Gretchen Smith & Laura A Mamounas & Ran Zhang & Steven J Madore & Katrina Gwinn & Roderick A Corriveau, 2010. "CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins," PLOS ONE, Public Library of Science, vol. 5(10), pages 1-12, October.
    5. Wang Chaolong & Szpiech Zachary A & Degnan James H & Jakobsson Mattias & Pemberton Trevor J & Hardy John A & Singleton Andrew B & Rosenberg Noah A, 2010. "Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-22, January.

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