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

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The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection. / Ding, Keyue; Zhou, Kaixin; Zhang, Jing et al.

In: Molecular Biology and Evolution, Vol. 22, No. 1, 01.2005, p. 148-159.

Research output: Contribution to Journal/MagazineJournal articlepeer-review

Harvard

Ding, K, Zhou, K, Zhang, J, Knight, J, Zhang, X & Shen, Y 2005, 'The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection', Molecular Biology and Evolution, vol. 22, no. 1, pp. 148-159. https://doi.org/10.1093/molbev/msh266

APA

Ding, K., Zhou, K., Zhang, J., Knight, J., Zhang, X., & Shen, Y. (2005). The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection. Molecular Biology and Evolution, 22(1), 148-159. https://doi.org/10.1093/molbev/msh266

Vancouver

Ding K, Zhou K, Zhang J, Knight J, Zhang X, Shen Y. The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection. Molecular Biology and Evolution. 2005 Jan;22(1):148-159. Epub 2004 Sep 15. doi: 10.1093/molbev/msh266

Author

Ding, Keyue ; Zhou, Kaixin ; Zhang, Jing et al. / The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection. In: Molecular Biology and Evolution. 2005 ; Vol. 22, No. 1. pp. 148-159.

Bibtex

@article{d8befd6d352e4472ad2de3bb7010d375,
title = "The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection",
abstract = "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.",
keywords = "Algorithms, Chromosome Mapping, Computational Biology, Computer Simulation, Genetic Markers, Genetic Variation, Genetics, Population, Genome, Human, Humans, Models, Genetic, Polymorphism, Single Nucleotide, Recombination, Genetic, Selection, Genetic",
author = "Keyue Ding and Kaixin Zhou and Jing Zhang and Joanne Knight and Xuegong Zhang and Yan Shen",
year = "2005",
month = jan,
doi = "10.1093/molbev/msh266",
language = "English",
volume = "22",
pages = "148--159",
journal = "Molecular Biology and Evolution",
issn = "0737-4038",
publisher = "Oxford University Press",
number = "1",

}

RIS

TY - JOUR

T1 - The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection

AU - Ding, Keyue

AU - Zhou, Kaixin

AU - Zhang, Jing

AU - Knight, Joanne

AU - Zhang, Xuegong

AU - Shen, Yan

PY - 2005/1

Y1 - 2005/1

N2 - 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.

AB - 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.

KW - Algorithms

KW - Chromosome Mapping

KW - Computational Biology

KW - Computer Simulation

KW - Genetic Markers

KW - Genetic Variation

KW - Genetics, Population

KW - Genome, Human

KW - Humans

KW - Models, Genetic

KW - Polymorphism, Single Nucleotide

KW - Recombination, Genetic

KW - Selection, Genetic

U2 - 10.1093/molbev/msh266

DO - 10.1093/molbev/msh266

M3 - Journal article

C2 - 15371531

VL - 22

SP - 148

EP - 159

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

SN - 0737-4038

IS - 1

ER -