NDLI: Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies

Content Provider	PubMed Central
Author	Zhang, Kui Qin, Zhaohui S. Liu, Jun S. Chen, Ting Waterman, Michael S. Sun, Fengzhu
Copyright Year	2004
Abstract	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.
Related Links	http://dx.doi.org/10.1101/gr.1837404
Ending Page	916
Page Count	9
Starting Page	908
File Format	PDF
ISSN	10889051
Journal	Genome Research
Issue Number	5
Volume Number	14
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2004-05-01
Access Restriction	Open
Rights Holder	Cold Spring Harbor Laboratory Press
Subject Keyword	Genetics(clinical) Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

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