Linkage disequilibrium of single-nucleotide polymorphism data: how sampling methods affect estimates of linkage disequilibrium

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Linkage disequilibrium of single-nucleotide polymorphism data: how sampling methods affect estimates of linkage disequilibrium

UNLABELLED Linkage disequilibrium (LD) is an important measure used in the analysis of single-nucleotide polymorphism (SNP) data. We used the Genetic Analysis Workshop 16 (GAW16) Framingham Heart Study 500 k SNP data to explore the effect of sampling methods on estimating of LD for SNP data. METHOD AND DATA We found 332 trios in the GAW16 Framingham SNP data. Repeated random samples without r...

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Parent-offspring trios are widely collected for disease gene-mapping studies and are being extensively genotyped as part of the International HapMap Project. With dense maps of markers on trios, the effects of LD and linkage can be separated, allowing estimation of recombination rates in a model-free setting. Here we define a model-free multipoint method on the basis of dense sequence polymorph...

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Linkage disequilibrium (LD) is bases of genomic selection, genomic marker imputation, marker assisted selection (MAS), quantitative trait loci (QTL) mapping, parentage testing and whole genome association studies. The Particular alleles at closed loci have a tendency to be co-inherited. In linked loci this pattern leads to association between alleles in population which is known as LD. Two metr...

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The Textile Plot: A New Linkage Disequilibrium Display of Multiple-Single Nucleotide Polymorphism Genotype Data

Linkage disequilibrium (LD) is a major concern in many genetic studies because of the markedly increased density of SNP (Single Nucleotide Polymorphism) genotype markers. This dramatic increase in the number of SNPs may cause problems in statistical analyses, such as by introducing multiple comparisons in hypothesis testing and colinearity in logistic regression models, because of the presence ...

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ژورنال

عنوان ژورنال: BMC Proceedings

سال: 2009

ISSN: 1753-6561

DOI: 10.1186/1753-6561-3-s7-s105