Genome-wide detection and characterization of positive selection in human populations Public Deposited

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Creator
  • Hostetter, Elizabeth
    • Other Affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
  • Sabeti, Pardis C.
    • Other Affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
  • Byrne, Elizabeth H.
    • Other Affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
  • Schaffner, Stephen F.
    • Other Affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
  • Xie, Xiaohui
    • Other Affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
  • Cotsapas, Chris
    • Other Affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA; Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
  • The International HapMap Consortium
  • McCarroll, Steven A.
    • Other Affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA; Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
  • Fry, Ben
    • Other Affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
  • Lohmueller, Jason
    • Other Affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
  • Lander, Eric S.
    • Other Affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA; Department of Biology, MIT, Cambridge, Massachusetts 02139, USA; Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
  • Varilly, Patrick
    • Other Affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
  • Gaudet, Rachelle
    • Other Affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
  • Li, Yun
    • Affiliation: School of Medicine, Department of Genetics, Gillings School of Global Public Health, Department of Biostatistics
Abstract
  • With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used ‘long-range haplotype’ methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population: LARGE and DMD, both related to infection by the Lassa virus3, in West Africa; SLC24A5 and SLC45A2, both involved in skin pigmentation in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.
Date of publication
Identifier
  • doi:10.1038/nature06250
  • 2-s2.0-35349012592
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Resource type
  • Article
Rights statement
  • In Copyright
Journal title
  • Nature
Journal volume
  • 449
Journal issue
  • 7164
Page start
  • 913
Page end
  • 918
Language
  • English
Version
  • Postprint
ISSN
  • 1476-4687
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