The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection

It has been recently suggested that the human genome is organized as a series of haplotype blocks, and efforts to create a genome-wide haplotype map are already underway. Several computational algorithms have been proposed to partition the genome. However, little is known about their behaviors in re...

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Bibliographic Details
Published in:Molecular biology and evolution 2005-01, Vol.22 (1), p.148-159
Main Authors: Ding, Keyue, Zhou, Kaixin, Zhang, Jing, Knight, Joanne, Zhang, Xuegong, Shen, Yan
Format: Article
Language:English
Subjects:
Algorithms
Chromosome Mapping
Computational Biology
Computer Simulation
Genetic Markers
Genetic Variation
Genetics, Population
Genome, Human
Humans
Models, Genetic
Polymorphism, Single Nucleotide - genetics
Recombination, Genetic - genetics
Selection, Genetic
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Summary:It has been recently suggested that the human genome is organized as a series of haplotype blocks, and efforts to create a genome-wide haplotype map are already underway. Several computational algorithms have been proposed to partition the genome. However, little is known about their behaviors in relation to the haplotype-block partitioning and haplotype-tagging SNPs selection. Here, we present a systematic comparison of three classes of haplotype-block partition definitions, a diversity-based method, a linkage-disequilibrium (LD)-based method, and a recombination-based method. The data used were derived from a coalescent simulation under both a uniform recombination model and one that assumes recombination hotspots. There were considerable differences in haplotype information loss in the measure of entropy when the partition methods were compared under different population-genetics scenarios. Under both recombination models, the results from the LD-based definition and the recombination-based definition were more similar to each other than were the results from the diversity-based definition. This work demonstrates that when undertaking haplotype-based association mapping, the choice of haplotype-block definition and SNP selection requires careful consideration.
ISSN:0737-4038
1537-1719
DOI:10.1093/molbev/msh266