ArticleHuman genetics2004
Does haplotype diversity predict power for association mapping of disease susceptibility?
Article in Human genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Polymorphism of duck MHC class molecules.Immunogenetics · 2019Article
- Genetic variation in SLC7A2 interacts with calcium and magnesium intakes in modulating the risk of colorectal polyps.The Journal of nutritional biochemistry · 2017Article
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- The genetics of breast cancer: risk factors for disease.The application of clinical genetics · 2011Article
- Association of FATP1 gene polymorphisms with chicken carcass traits in Chinese meat-type quality chicken populations.Molecular biology reports · 2010Article
- Polymorphism of chicken myocyte-specific enhancer-binding factor 2A gene and its association with chicken carcass traits.Molecular biology reports · 2010Article
- STrengthening the REporting of Genetic Association studies (STREGA)--an extension of the STROBE statement.European journal of clinical investigation · 2009Article
- Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE Statement.Human genetics · 2009Article
- STrengthening the REporting of Genetic Association Studies (STREGA): an extension of the STROBE statement.PLoS medicine · 2009Article
- Allelic association: linkage disequilibrium structure and gene mapping.Molecular biotechnology · 2009Review
- Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE statement.European journal of epidemiology · 2009Review
- Genome scanning by composite likelihood.American journal of human genetics · 2007Article
- Selection of SNP subsets for association studies in candidate genes: comparison of the power of different strategies to detect single disease susceptibility locus effects.BMC genetics · 2006Article
- Fifty years of genetic epidemiology, with special reference to Japan.Journal of human genetics · 2006Review
- A sparse marker extension tree algorithm for selecting the best set of haplotype tagging single nucleotide polymorphisms.Genetic epidemiology · 2005Article
- Assessing the power of tag SNPs in the mapping of quantitative trait loci (QTL) with extremal and random samples.BMC genetics · 2005Article
- Linkage disequilibrium maps and association mapping.The Journal of clinical investigation · 2005Review
- The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern.Genome research · 2005Article
- Principles in genetic risk assessment.Therapeutics and clinical risk management · 2005Article
- Cosmopolitan linkage disequilibrium maps.Human genomics · 2005Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many recent studies have established that haplotype diversity in a small region may not be greatly diminished when the number of markers is reduced to a smaller set of "haplotype-tagging" single-nucleotide polymorphisms (SNPs) that identify the most common haplotypes. These studies are motivated by the assumption that retention of haplotype diversity assures retention of power for mapping disease susceptibility by allelic association. Using two bodies of real data, three proposed measures of diversity, and regression-based methods for association mapping, we found no scenario for which this assumption was tenable. We compared the chi-square for composite likelihood and the maximum chi-square for single SNPs in diplotypes, excluding the marker designated as causal. All haplotype-tagging methods conserve haplotype diversity by selecting common SNPs. When the causal marker has a range of allele frequencies as in real data, chi-square decreases faster than under random selection as the haplotype-tagging set diminishes. Selecting SNPs by maximizing haplotype diversity is inefficient when their frequency is much different from the unknown frequency of the causal variant. Loss of power is minimized when the difference between minor allele frequencies of the causal SNP and a closely associated marker SNP is small, which is unlikely in ignorance of the frequency of the causal SNP unless dense markers are used. Therefore retention of haplotype diversity in simulations that do not mirror genomic allele frequencies has no relevance to power for association mapping. TagSNPs that are assigned to bins instead of haplotype blocks also lose power compared with random SNPs. This evidence favours a multi-stage design in which both models and density change adaptively.
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