High-density single-nucleotide polymorphism maps of the human genome

Miller, R. D., Phillips, M. S., Jo, I., Donaldson, M. A., Studebaker, J. F., Addleman, N., Alfisi, S. V., Ankener, W. M., Bhatti, H. A., Callahan, C. E., Carey, B. J., Conley, C. L., Cyr, J. M., Derohannessian, V., Donaldson, R. A., Elosua, C., Ford, S. E., Forman, A. M., Gelfand, C. A., Grecco, N. M., Gutendorf, S. M., Hock, C. R., Hozza, M. J., Hur, S., In, S. M., Jackson, D. L., Jo, S. A., Jung, S. C., Kim, S., Kimm, K., Kloss, E. F., Koboldt, D. C., Kuebler, J. M., Kuo, F. S., Lathrop, J. A., Lee, J. K., Leis, K. L., Livingston, S. A., Lovins, E. G., Lundy, M. L., Maggan, S., Minton, M., Mockler, M. A., Morris, D. W., Nachtman, E. P., Oh, B., Park, C., Park, C. W., Pavelka, N., Perkins, A. B., Restine, S. L., Sachidanandam, R., Reinhart, A. J., Scott, K. E., Restine, S. L., Sachidanandam, R., Reinhart, A. J., Scott, K. E., Shah, G. J., Tate, J. M., Varde, S. A., Walters, A., White, J. R., Yoo, Y. K., Lee, J. E., Boyce-Jacino, M. T., Kwok, P. Y. (August 2005) High-density single-nucleotide polymorphism maps of the human genome. Genomics, 86 (2). pp. 117-126. ISSN 0888-7543

URL: https://www.ncbi.nlm.nih.gov/pubmed/15961272
DOI: 10.1016/j.ygeno.2005.04.012

Abstract

Here we report a large, extensively characterized set of single-nucleotide polymorphisms (SNPs) covering the human genome. We determined the allele frequencies of 55,018 SNPs in African Americans, Asians (Japanese-Chinese), and European Americans as part of The SNP Consortium's Allele Frequency Project. A subset of 8333 SNPs was also characterized in Koreans. Because these SNPs were ascertained in the same way, the data set is particularly useful for modeling. Our results document that much genetic variation is shared among populations. For autosomes, some 44% of these SNPs have a minor allele frequency >= 10% in each population, and the average allele frequency differences between populations with different continental origins are less than 19%. However, the several percentage point allele frequency differences among the closely related Korean, Japanese, and Chinese populations suggest caution in using mixtures of well-established populations for case-control genetic studies of complex traits. We estimate that similar to 7% of these SNPs are private SNPs with minor allele frequencies < 1%. A useful set of characterized SNPs with large allele frequency differences between populations (> 60%) can be used for admixture studies. High-density maps of high-quality, characterized SNPs produced by this project are freely available. (c) 2005 Elsevier Inc. All rights reserved.

Item Type: Paper
Uncontrolled Keywords: SNP human variation the SNP consortium pooled sequencing single-base primer extension Korean population complex disease variation search linkage disequilibrium sequence variation candidate genes SNP SNP's SNPS populations HISTORY DNA ASSOCIATION DISCOVERY admixture
Subjects: bioinformatics > genomics and proteomics > databases > database optimization
bioinformatics > genomics and proteomics > annotation > map annotation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > SNP
CSHL Authors:
Communities: CSHL labs > Sachidanandam lab
Depositing User: CSHL Librarian
Date: August 2005
Date Deposited: 09 Jan 2012 17:08
Last Modified: 24 Mar 2017 19:29
PMCID: PMC1885222
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22654

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving