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The Structure of Haplotype Blocks in the Human Genome
Stacey B. Gabriel,1Stephen F. Schaffner,1Huy Nguyen,1Jamie M. Moore,1Jessica Roy,1Brendan Blumenstiel,1John Higgins,1Matthew DeFelice,1Amy Lochner,1Maura Faggart,1Shau Neen Liu-Cordero,12Charles Rotimi,3Adebowale Adeyemo,4Richard Cooper,5Ryk Ward,6Eric S. Lander,12Mark J. Daly,1David Altshuler17*
Haplotype-based methods offer a powerful approach to disease gene
mapping, based on the association between causal mutationsand the
ancestral haplotypes on which they arose. As part of TheSNP Consortium
Allele Frequency Projects, we characterized haplotypepatterns across
51 autosomal regions (spanning 13 megabases ofthe human genome) in
samples from Africa, Europe, and Asia. Weshow that the human genome
can be parsed objectively into haplotypeblocks: sizable regions over
which there is little evidence forhistorical recombination and within
which only a few common haplotypesare observed. The boundaries of
blocks and specific haplotypesthey contain are highly correlated
across populations. We demonstratethat such haplotype frameworks
provide substantial statisticalpower in association studies of common
genetic variation acrosseach region. Our results provide a foundation
for the constructionof a haplotype map of the human genome,
facilitating comprehensivegenetic association studies of human
disease.
1 Whitehead/MIT Center for Genome Research,
Cambridge, MA 02139, USA.
2 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 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
The editors suggest the following Related Resources on Science sites:
In Science Magazine
NEWS FOCUS
Jennifer Couzin (24 May 2002) Science296 (5572), 1391.
[DOI: 10.1126/science.296.5572.1391] |Summary »|Full Text »|PDF »
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Genetic Susceptibility Loci for Breast Cancer by Estrogen Receptor Status.
No Association of Single Nucleotide Polymorphisms in One-Carbon Metabolism Genes with Prostate Cancer Risk.
V. L. Stevens, C. Rodriguez, J. Sun, J. T. Talbot, M. J. Thun, and E. E. Calle (2008)
Cancer Epidemiol. Biomarkers Prev.
17, 3612-3614
|Abstract »|Full Text »|PDF »
Genetic susceptibility to childhood leukaemia.
A. P. Chokkalingam and P. A. Buffler (2008)
Radiat Prot Dosimetry
132, 119-129
|Abstract »|Full Text »|PDF »
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
|Abstract »|Full Text »|PDF »
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
|Abstract »|Full Text »|PDF »
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
|Abstract »|Full Text »|PDF »
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
|Abstract »|Full Text »|PDF »
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
|Abstract »|Full Text »|PDF »
The Importance of Gene--Environment Interaction: Implications for Social Scientists.
K. E. North and L. J. Martin (2008)
Sociological Methods Research
37, 164-200
|Abstract »|PDF »
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
|Abstract »|Full Text »|PDF »
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
|Abstract »|Full Text »|PDF »
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
|Abstract »|Full Text »|PDF »
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
|Abstract »|Full Text »|PDF »
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
|Abstract »|Full Text »|PDF »
The genetics of SLE: an update in the light of genome-wide association studies.
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
|Abstract »|Full Text »|PDF »
HapMap and Mapping Genes for Cardiovascular Disease.
K. Musunuru and S. Kathiresan (2008)
Circ Cardiovasc Genet
1, 66-71
|Full Text »|PDF »
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
|Abstract »|Full Text »|PDF »
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
|Abstract »|Full Text »|PDF »
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
|Abstract »|Full Text »|PDF »
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
|Abstract »|Full Text »|PDF »
Domain-Specific Regulation of Recombination in Caenorhabditis elegans in Response to Temperature, Age and Sex.
J. G. Y. Lim, R. R. W. Stine, and J. L. Yanowitz (2008)
Genetics
180, 715-726
|Abstract »|Full Text »|PDF »
