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The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern

  1. Author:
    De La Vega, F. M.
    Isaac, H.
    Collins, A.
    Scafe, C. R.
    Halldorsson, B. V.
    Su, X. P.
    Lippert, R. A.
    Wang, Y.
    Laig-Webster, M.
    Koehler, R. T.
    Ziegle, J. S.
    Wogan, L. T.
    Stevens, J. F.
    Leinen, K. M.
    Olson, S. J.
    Guegler, K. J.
    You, X. Q.
    Xu, L. H.
    Hemken, H. G.
    Kalush, F.
    Itakura, M.
    Zheng, Y.
    de The, G.
    O'Brien, S. J.
    Clark, A. G.
    Istrail, S.
    Hunkapiller, M. W.
    Spier, E. G.
    Gilbert, D. A.

  2. Author Address

    Appl Biosyst Inc, Foster City, CA 94404 USA. Univ Southampton, Div Human Genet, Southampton SO16 6YD, Hants, England. Celera Genom, Rockville, MD 20850 USA. Univ Tokushima, Inst Genome Res, Tokushima 7708503, Japan. Chinese Acad Prevent Med, Inst Virol, Beijing 100052, Peoples R China. Inst Pasteur, CNRS, Dept Viral Oncol Epidemiol, F-75015 Paris, France. NCI, Lab Genom Divers, Frederick, MD 21702 USA. Cornell Univ, Ithaca, NY 14853 USA De la Vega, FM, Appl Biosyst Inc, 850 Lincoln Ctr Dr, Foster City, CA 94404 USA
    1. Year: 2005
    2. Date: APR
  2. Journal: Genome Research
    1. 15
    2. 4
    3. Pages: 454-462
  4. Type of Article: Article
  1. Abstract:

    The extent and patterns of linkage disequilibrium (LD) determine the feasibility of association studies to map genes that underlie complex traits. Here we present a comparison of the patterns of LD across four major human populations (African-American, Caucasian, Chinese, and Japanese) with a high-resolution single-nucleotide polymorphism (SNP) map covering almost the entire length of chromosomes 6, 21, and 22. We constructed metric LD maps formulated such that the units measure the extent of useful LD for association mapping. LD reaches almost twice as far in chromosome 6 as in chromosomes 21 or 22, in agreement with their differences in recombination rates. By all measures used, out-of-Africa populations showed over a third more LD than African-Americans, highlighting the role of the population's demography in shaping the patterns of LD. Despite those differences, the long-range contour of the LD maps is remarkably similar across the four populations, presumably reflecting common localization of recombination hot spots. Our results have practical implications for the rational design and selection of SNPs for disease association studies

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External Sources

  1. View record in Web of Science®
  2. WOS: 000228203000002

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