ArticleProceedings of the National Academy of Sciences of the United States of America2001
The optimal measure of allelic association.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers, 1 of them a synthesis that pooled it.
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Who cites it
50 citing papers in PubMed, 1 synthesis or guideline pooled it.
- CHROMSCAN: genome-wide association using a linkage disequilibrium map.Journal of human genetics · 2008Pooled it
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- Mathematical Properties of Linkage Disequilibrium Statistics Defined by Normalization of the Coefficient D = pAB - pApB.Human heredity · 2019Article
- Minor alleles are associated with white rust (Horticulture research · 2019Article
- One Hundred Years of Linkage Disequilibrium.Genetics · 2018Article
- Commercial chicken breeds exhibit highly divergent patterns of linkage disequilibrium.Heredity · 2016Article
- Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations.BMC genomics · 2015Article
- A Scale-Corrected Comparison of Linkage Disequilibrium Levels between Genic and Non-Genic Regions.PloS one · 2015Article
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- The utility of low-density genotyping for imputation in the Thoroughbred horse.Genetics, selection, evolution : GSE · 2014Article
- On measures of association among genetic variables.Animal genetics · 2012Article
- Dissecting the genetics of complex inheritance: linkage disequilibrium mapping provides insight into Crohn disease.American journal of human genetics · 2011Article
- Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome.Genome research · 2010Article
- An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population.European journal of human genetics : EJHG · 2009Article
- Allelic association: linkage disequilibrium structure and gene mapping.Molecular biotechnology · 2009Review
- Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies.BMC genomics · 2008Article
- Mathematical properties of the r2 measure of linkage disequilibrium.Theoretical population biology · 2008Article
- Kernel-based association test.Genetics · 2008Article
Corrections and comments
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6 authors.
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Abstract
Allelic association between pairs of loci is derived in terms of the association probability rho as a function of recombination theta, effective population size N, linear systematic pressure v, and time t, predicting both rho(rt), the decrease of association from founders and rho(ct), the increase by genetic drift, with rho(t) = rho(rt) + rho(ct). These results conform to the Malecot equation, with time replaced by distance on the genetic map, or on the physical map if recombination in the region is uniform. Earlier evidence suggested that rho is less sensitive to variations in marker allele frequencies than alternative metrics for which there is no probability theory. This robustness is confirmed for six alternatives in eight samples. In none of these 48 tests was the residual variance as small as for rho. Overall, efficiency was less than 80% for all alternatives, and less than 30% for two of them. Efficiency of alternatives did not increase when information was estimated simultaneously. The swept radius within which substantial values of rho are conserved lies between 385 and 893 kb, but deviation of parameters between measures is enormously significant. The large effort now being devoted to allelic association has little value unless the rho metric with the strongest theoretical basis and least sensitivity to marker allele frequencies is used for mapping of marker association and localization of disease loci.
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