ArticleBMC genetics2005
Assessing the power of tag SNPs in the mapping of quantitative trait loci (QTL) with extremal and random samples.
Article in BMC genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Global and Local Ancestry and its Importance: A Review.Current genomics · 2024Review
- Multilocus association testing of quantitative traits based on partial least-squares analysis.PloS one · 2011Article
- Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array.BMC genomics · 2011Article
- LRRK2 gene G2019S mutation and SNPs [haplotypes] in subtypes of Parkinson's disease.Parkinsonism & related disorders · 2009Article
- Genome-wide association studies: progress and potential for drug discovery and development.Nature reviews. Drug discovery · 2008Review
- Genotype matrix mapping: searching for quantitative trait loci interactions in genetic variation in complex traits.DNA research : an international journal for rapid publication of reports on genes and genomes · 2007Article
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2 authors.
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Abstract
backgroundRecent studies have indicated that the human genome could be divided into regions with low haplotype diversity interspersed with regions of high haplotype diversity. In regions of low haplotype diversity, a small fraction of SNPs (tag SNPs) are sufficient to account for most of the haplotype diversity of the human genome. These tag SNPs can be extremely useful for testing the association of a marker locus with a qualitative or quantitative trait locus in that it may not be necessary to genotype all the SNPs. When tag SNPs are used to reduce the genotyping effort in association studies, it is important to know how much power is lost. It is also important to know how much power is gained when tag SNPs instead of the same number of randomly chosen SNPs are used.
resultsWe design a simulation study to tackle these problems for a variety of quantitative association tests using either case-parent samples or unrelated population samples. First, the samples are generated based on the quantitative trait model with the assumption of either an extremal sampling scheme or a random sampling scheme. Second, a small number of samples are selected to determine the haplotype blocks and the tag SNPs. Third, the statistical power of the tests is evaluated using four kinds of data: (1) all the SNPs and the corresponding haplotypes, (2) the tag SNPs and the corresponding haplotypes, (3) the same number of evenly spaced SNPs with minor allele frequency greater than a threshold and the corresponding haplotypes, (4) the same number of randomly chosen SNPs and their corresponding haplotypes.
conclusionOur results suggest that in most situations genotyping efforts can be significantly reduced by using tag SNPs for mapping the QTL in association studies without much loss of power, which is consistent with previous studies on association mapping of qualitative traits. For all situations considered, two-locus haplotype analysis using tag SNPs are more powerful than those using the same number of randomly selected SNPs, but the degree of such power differences depends upon the sampling scheme and the population history.
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