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Vol. 296 no. 5576 pp. 2225-2229
DOI: 10.1126/science.1069424
  • Report

The Structure of Haplotype Blocks in the Human Genome

  1. David Altshuler1,7,*
  1. 1 Whitehead/MIT Center for Genome Research, Cambridge, MA 02139, USA.
  2. 2 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
  3. 3 National Human Genome Center, Howard University, Washington, DC 20059, USA.
  4. 4 Department of Pediatrics, College of Medicine, University of Ibadan, Ibadan, Nigeria.
  5. 5 Department of Preventive Medicine and Epidemiology, Loyola University Medical School, Maywood, IL 60143, USA.
  6. 6 Institute of Biological Anthropology, University of Oxford, Oxford, England OX2 6QS.
  7. 7 Departments of Genetics and Medicine, Harvard Medical School; Department of Molecular Biology and Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA.


Haplotype-based methods offer a powerful approach to disease gene mapping, based on the association between causal mutations and the ancestral haplotypes on which they arose. As part of The SNP Consortium Allele Frequency Projects, we characterized haplotype patterns across 51 autosomal regions (spanning 13 megabases of the human genome) in samples from Africa, Europe, and Asia. We show that the human genome can be parsed objectively into haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed. The boundaries of blocks and specific haplotypes they contain are highly correlated across populations. We demonstrate that such haplotype frameworks provide substantial statistical power in association studies of common genetic variation across each region. Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease.

  • * To whom correspondence should be addressed. E-mail: altshuler{at}

  • Received for publication 28 December 2001.
  • Accepted for publication 13 May 2002.