The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies
Open accessAbstract
Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the human genome with some regions of high LD interspersed by regions of low LD. A small fraction of SNPs (tag SNPs) is sufficient to capture most of the haplotype structure of the human genome. In this paper, we develop a method to partition haplotypes into blocks and to identify tag SNPs based on genotype data by combining a dynamic programming algorithm for haplotype block partitioning and tag SNP selection based on haplotype data with a variation of the expectation maximization (EM) algorithm for haplotype inference. We assess the effects of using either haplotype or genotype data in haplotype block identification and tag SNP selection as a function of several factors, including sample size, density or number of SNPs studied, allele frequencies, fraction of missing data, and genotyping error rate, using extensive simulations. We find that a modest number of haplotype or genotype samples will result in consistent block partitions and tag SNP selection. The power of association studies based on tag SNPs using genotype data is similar to that using haplotype data.
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Citations
Cites
The Structure of Haplotype Blocks in the Human Genome
Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., et al. (2002) · Science · doi:10.1126/science.1069424 · Cited by 5,863
Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.
(1995) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040269 · Cited by 1,950
High-resolution haplotype structure in the human genome
Daly, M. J., Rioux, J. D., Schaffner, S. F., Hudson, T. J., & Lander, E. S. (2001) · Nature Genetics · doi:10.1038/ng1001-229 · Cited by 1,717
Prospects for whole-genome linkage disequilibrium mapping of common disease genes
Kruglyak, L. (1999) · Nature Genetics · doi:10.1038/9642 · Cited by 1,416
Haplotype tagging for the identification of common disease genes
Johnson, G. C. L., Esposito, L., Barratt, B. J., Smith, A. N., Heward, J., Di Genova, G., Ueda, H., Cordell, H. J., Eaves, I. A., Dudbridge, F., et al. (2001) · Nature Genetics · doi:10.1038/ng1001-233 · Cited by 1,174
Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21
Patil, N., Berno, A. J., Hinds, D. A., Barrett, W. A., Doshi, J. M., Hacker, C. R., Kautzer, C. R., Lee, D. H., Marjoribanks, C., McDonough, D. P., et al. (2001) · Science · doi:10.1126/science.1065573 · Cited by 1,145
Inference of haplotypes from PCR-amplified samples of diploid populations.
(1990) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040591 · Cited by 765
Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots
Phillips, M. S., Lawrence, R., Sachidanandam, R., Morris, A. P., Balding, D. J., Donaldson, M. A., Studebaker, J. F., Ankener, W. M., Alfisi, S. V., Kuo, F.-S., et al. (2003) · Nature Genetics · doi:10.1038/ng1100 · Cited by 278
Finding Haplotype Block Boundaries by Using the Minimum-Description-Length Principle
Anderson, E. C., & Novembre, J. (2003) · The American Journal of Human Genetics · doi:10.1086/377106 · Cited by 90
Cited by
The Future of Association Studies: Gene-Based Analysis and Replication
Neale, B. M., & Sham, P. C. (2004) · The American Journal of Human Genetics · doi:10.1086/423901 · Cited by 606
Definition And Clinical Importance Of Haplotypes.
Crawford, D. C., & Nickerson, D. A. (2005) · Annual Review of Medicine · doi:10.1146/annurev.med.56.082103.104540 · Cited by 344
Optimal selection of SNP markers for disease association studies.
Halldórsson, B. V., Istrail, S., & De La Vega, F. M. (2004) · Human Heredity · doi:10.1159/000083546 · Cited by 65
Metadata
- Authors
- Zhang, K., Qin, Z. S., Liu, J. S., Chen, T., Waterman, M. S., & Sun, F.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2004-04-12
- Volume
- 14
- Issue
- 5
- Pages
- 908-916
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2164628101
- Cited by
- 175
- References
- 9
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Zhang, K., Qin, Z. S., Liu, J. S., Chen, T., Waterman, M. S., & Sun, F. (2004). Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies. Genome Research. https://doi.org/10.1101/gr.1837404
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