A second generation human haplotype map of over 3.1 million SNPs

Frazer, K. A., Ballinger, D. G., Cox, D. R., Hinds, D. A., Stuve, L. L., Gibbs, R. A., Belmont, J. W., Boudreau, A., Hardenbol, P., Leal, S. M., Pasternak, S., Wheeler, D. A., Willis, T. D., Yu, F. L., Yang, H. M., Zeng, C. Q., Gao, Y., Hu, H. R., Hu, W. T., Li, C. H., Lin, W., Liu, S. Q., Pan, H., Tang, X. L., Wang, J., Wang, W., Yu, J., Zhang, B., Zhang, Q. R., Zhao, H. B., Zhao, H., Zhou, J., Gabriel, S. B., Barry, R., Blumenstiel, B., Camargo, A., Defelice, M., Faggart, M., Goyette, M., Gupta, S., Moore, J., Nguyen, H., Onofrio, R. C., Parkin, M., Roy, J., Stahl, E., Winchester, E., Ziaugra, L., Altshuler, D., Shen, Y., Yao, Z. J., Huang, W., Chu, X., He, Y. G., Jin, L., Liu, Y. F., Shen, Y. Y., Sun, W. W., Wang, H. F., Wang, Y., Wang, Y., Xiong, X. Y., Xu, L., Waye, M. M. Y., Tsui, S. K. W., Wong, J. T. F., Galver, L. M., Fan, J. B., Gunderson, K., Murray, S. S., Oliphant, A. R., Chee, M. S., Montpetit, A., Chagnon, F., Ferretti, V., Leboeuf, M., Olivier, J. F., Phillips, M. S., Roumy, S., Sallee, C., Verner, A., Hudson, T. J., Kwok, P. Y., Cai, D. M., Koboldt, D. C., Miller, R. D., Pawlikowska, L., Taillon-Miller, P., Xiao, M., Tsui, L. C., Mak, W., Song, Y. Q., Tam, P. K. H., Nakamura, Y., Kawaguchi, T., Kitamoto, T., Morizono, T., Nagashima, A., Ohnishi, Y., Sekine, A. (October 2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449 (7164). 851-U3. ISSN 0028-0836

URL: https://www.ncbi.nlm.nih.gov/pubmed/17943122
DOI: 10.1038/nature06258

Abstract

We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r(2) of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r(2) of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.

Item Type: Paper
Uncontrolled Keywords: GENOME-WIDE ASSOCIATION LINKAGE DISEQUILIBRIUM NATURAL-SELECTION MEIOTIC RECOMBINATION GENETIC ASSOCIATION HUMAN-POPULATIONS RECESSIVE TRAITS HAPMAP PROJECT HOT-SPOTS TAG SNPS
Subjects: bioinformatics > genomics and proteomics > databases > database construction
bioinformatics > genomics and proteomics > databases > database optimization
bioinformatics > genomics and proteomics > Mapping and Rendering
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism > haplotype
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism
CSHL Authors:
Communities: CSHL labs > Stein lab
Depositing User: CSHL Librarian
Date: October 2007
Date Deposited: 15 Nov 2011 19:40
Last Modified: 23 Mar 2018 20:30
PMCID: PMC2689609
Related URLs:
URI: http://repository.cshl.edu/id/eprint/23017

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