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Published Online May 23, 2002
Science DOI: 10.1126/science.1069424

Reports

Submitted on December 28, 2001
Accepted on May 13, 2002

The Structure of Haplotype Blocks in the Human Genome

Stacey B. Gabriel 1, Stephen F. Schaffner 1, Huy Nguyen 1, Jamie M. Moore 1, Jessica Roy 1, Brendan Blumenstiel 1, John Higgins 1, Mathew DeFelice 1, Amy Lochner 1, Maura Faggart 1, Shau Neen Liu-Cordero 2, Charles Rotimi 3, Adebowale Adeyemo 4, Richard Cooper 5, Ryk Ward 6, Eric S. Lander 2, Mark J. Daly 1, David Altshuler 7*

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

* To whom correspondence should be addressed. E-mail: altshuler{at}molbio.mgh.harvard.edu.

Haplotype-based methods offer a powerful approach to disease gene mapping, based on association between causal mutations and the ancestral haplotypes on which they arose. We characterized haplotype patterns across 51 autosomal regions (spanning 13Mb of the human genome) in samples from Africa, Europe and Asia. We show that the human genome can be parsed objectively into haplotype blocks: sizeable 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.


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Association of the KIAA0319 Dyslexia Susceptibility Gene With Reading Skills in the General Population.
S. Paracchini, C. D. Steer, L.-L. Buckingham, A. P. Morris, S. Ring, T. Scerri, J. Stein, M. E. Pembrey, J. Ragoussis, J. Golding, et al. (2008)
Am J Psychiatry 165, 1576-1584
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Nicotinic Receptor Gene Variants Influence Susceptibility to Heavy Smoking.
V. L. Stevens, L. J. Bierut, J. T. Talbot, J. C. Wang, J. Sun, A. L. Hinrichs, M. J. Thun, A. Goate, and E. E. Calle (2008)
Cancer Epidemiol. Biomarkers Prev. 17, 3517-3525
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A better block partition and ligation strategy for individual haplotyping.
Y. Zhao, Y. Xu, Z. Wang, H. Zhang, and G. Chen (2008)
Bioinformatics 24, 2720-2725
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Association analysis identifies TLR7 and TLR8 as novel risk genes in asthma and related disorders.
S Moller-Larsen, M Nyegaard, A Haagerup, J Vestbo, T A Kruse, and A D Borglum (2008)
Thorax 63, 1064-1069
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Genotype Score in Addition to Common Risk Factors for Prediction of Type 2 Diabetes.
J. B. Meigs, P. Shrader, L. M. Sullivan, J. B. McAteer, C. S. Fox, J. Dupuis, A. K. Manning, J. C. Florez, P. W.F. Wilson, R. B. D'Agostino Sr., et al. (2008)
N. Engl. J. Med. 359, 2208-2219
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Genetic Mapping in Human Disease.
D. Altshuler, M. J. Daly, and E. S. Lander (2008)
Science 322, 881-888
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The Importance of Gene--Environment Interaction: Implications for Social Scientists.
K. E. North and L. J. Martin (2008)
Sociological Methods Research 37, 164-200
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Identification of LTBP2 on Chromosome 14q as a Novel Candidate Gene for Bone Mineral Density Variation and Fracture Risk Association.
C.-L. Cheung, P. C. Sham, V. Chan, A. D. Paterson, K. D. K. Luk, and A. W. C. Kung (2008)
J. Clin. Endocrinol. Metab. 93, 4448-4455
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Association Studies of Common Variants in 10 Hypogonadotropic Hypogonadism Genes with Age at Menarche.
Z. K. Z. Gajdos, J. L. Butler, K. D. Henderson, C. He, P. J. Supelak, M. Egyud, A. Price, D. Reich, P. E. Clayton, L. Le Marchand, et al. (2008)
J. Clin. Endocrinol. Metab. 93, 4290-4298
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Analyses of the National Institute on Aging Late-Onset Alzheimer's Disease Family Study: Implication of Additional Loci.
J. H. Lee, R. Cheng, N. Graff-Radford, T. Foroud, R. Mayeux, and for the National Institute on Aging Late-Onset Alz (2008)
Arch Neurol 65, 1518-1526
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PXR Pharmacogenetics: Association of Haplotypes with Hepatic CYP3A4 and ABCB1 Messenger RNA Expression and Doxorubicin Clearance in Asian Breast Cancer Patients.
E. Sandanaraj, S. Lal, V. Selvarajan, L. L. Ooi, Z. W. Wong, N. S. Wong, P. C. S. Ang, E. J.D. Lee, and B. Chowbay (2008)
Clin. Cancer Res. 14, 7116-7126
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The HBS1L-MYB intergenic region on chromosome 6q23 is a quantitative trait locus controlling fetal haemoglobin level in carriers of {beta}-thalassaemia.
C-C So, Y-Q Song, S T Tsang, L-F Tang, A Y Chan, E S Ma, and L-C Chan (2008)
J. Med. Genet. 45, 745-751
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The genetics of SLE: an update in the light of genome-wide association studies.
B. Rhodes and T. J. Vyse (2008)
Rheumatology 47, 1603-1611
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Genome-wide association studies: implications for multiethnic samples.
R. S. Cooper, B. Tayo, and X. Zhu (2008)
Hum. Mol. Genet. 17, R151-R155
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Toll-like Receptor 3 and Geographic Atrophy in Age-Related Macular Degeneration.
Z. Yang, C. Stratton, P. J. Francis, M. E. Kleinman, P. L. Tan, D. Gibbs, Z. Tong, H. Chen, R. Constantine, X. Yang, et al. (2008)
N. Engl. J. Med. 359, 1456-1463
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HapMap and Mapping Genes for Cardiovascular Disease.
K. Musunuru and S. Kathiresan (2008)
Circ Cardiovasc Genet 1, 66-71
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Genetic Variation in Calcium-Sensing Receptor and Risk for Colon Cancer.
L. M. Dong, C. M. Ulrich, L. Hsu, D. J. Duggan, D. S. Benitez, E. White, M. L. Slattery, B. J. Caan, J. D. Potter, and U. Peters (2008)
Cancer Epidemiol. Biomarkers Prev. 17, 2755-2765
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Association of Toll-like Receptor 4 Gene Polymorphisms with Normal Tension Glaucoma.
E. Shibuya, A. Meguro, M. Ota, K. Kashiwagi, F. Mabuchi, H. Iijima, K. Kawase, T. Yamamoto, M. Nakamura, A. Negi, et al. (2008)
Invest. Ophthalmol. Vis. Sci. 49, 4453-4457
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Thyroid Hormone Transport and Metabolism by Organic Anion Transporter 1C1 and Consequences of Genetic Variation.
W. M. van der Deure, P. S. Hansen, R. P. Peeters, K. O. Kyvik, E. C. H. Friesema, L. Hegedus, and T. J. Visser (2008)
Endocrinology 149, 5307-5314
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Genetic variants in RUNX3 and risk of bladder cancer: a haplotype-based analysis.
Z. Zhang, S. Wang, M. Wang, N. Tong, G. Fu, and Z. Zhang (2008)
Carcinogenesis 29, 1973-1978
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