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

  1. Francisco M. De La Vega1,12,
  2. Hadar Isaac1,
  3. Andrew Collins2,
  4. Charles R. Scafe1,
  5. Bjarni V. Halldórsson1,9,
  6. Xiaoping Su1,10,
  7. Ross A. Lippert1,11,
  8. Yu Wang1,
  9. Marion Laig-Webster1,
  10. Ryan T. Koehler1,
  11. Janet S. Ziegle1,
  12. Lewis T. Wogan1,
  13. Junko F. Stevens1,
  14. Kyle M. Leinen1,
  15. Sheri J. Olson1,
  16. Karl J. Guegler1,
  17. Xiaoqing You1,
  18. Lily H. Xu1,
  19. Heinz G. Hemken1,
  20. Francis Kalush3,
  21. Mitsuo Itakura4,
  22. Yi Zheng5,
  23. Guy de Thé6,
  24. Stephen J. O'Brien7,
  25. Andrew G. Clark8,
  26. Sorin Istrail1,
  27. Michael W. Hunkapiller1,
  28. Eugene G. Spier1, and
  29. Dennis A. Gilbert1
  1. 1 Applied Biosystems, Foster City, California 94404, USA
  2. 2 Human Genetics Division, University of Southampton, Southampton, SO16 6YD, United Kingdom
  3. 3 Celera Genomics, Rockville, Maryland 20850, USA
  4. 4 Institute for Genome Research, The University of Tokushima, Tokushima 770–8503, Japan
  5. 5 Institute of Virology, Chinese Academy of Preventive Medicine, Beijing 100052, China
  6. 6 Department of Viral Oncology–Epidemiology, Institut Pasteur, Centre National de la Recherche Scientifique, 75015 Paris, France
  7. 7 Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702, USA
  8. 8 Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA

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.

Footnotes

  • [Supplemental material is available online at www.genome.org.]

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3241705. Article published online before print in March 2005. Freely available online through the Genome Research Immediate Open Access option.

  • ↵12 Corresponding author. E-mail delavefm{at}appliedbiosystems.com; fax (650) 554-2577.

  • ↵9 Present address: deCode Genetics, 101 Reykjavik, Iceland

  • ↵10 Present address: St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA

  • ↵11 Present address: Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

    • Accepted January 12, 2005.
    • Received September 8, 2004.

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  1. Published in Advance March 21, 2005, doi: 10.1101/gr.3241705 Genome Res. 15: 454-462 Cold Spring Harbor Laboratory Press

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