ArticleProceedings of the National Academy of Sciences of the United States of America2004
Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Genetic diversity and population structure of temperate maize (Zea mays L.) inbred lines from a public breeding program in Argentina.BMC plant biology · 2026Article
- Variability and forensic efficiency of 12 X-STR markers in Namibian populations.International journal of legal medicine · 2024Article
- Assessing the causes and consequences of gut mycobiome variation in a wild population of the Seychelles warbler.Microbiome · 2022Article
- The western redcedar genome reveals low genetic diversity in a self-compatible conifer.Genome research · 2022Article
- A linkage disequilibrium-based statistical test for Genome-Wide Epistatic Selection Scans in structured populations.Heredity · 2021Article
- Distinct subtypes of polycystic ovary syndrome with novel genetic associations: An unsupervised, phenotypic clustering analysis.PLoS medicine · 2020Article
- Article
- Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker.BMC plant biology · 2019Article
- Genomic data reveal a loss of diversity in two species of tuco-tucos (genus Ctenomys) following a volcanic eruption.Scientific reports · 2017Article
- Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations.BMC genomics · 2015Article
- Genome-wide linkage disequilibrium in nine-spined stickleback populations.G3 (Bethesda, Md.) · 2014Article
- Modeling associations between genetic markers using Bayesian networks.Bioinformatics (Oxford, England) · 2010Article
- LD-spline: mapping SNPs on genotyping platforms to genomic regions using patterns of linkage disequilibrium.BioData mining · 2009Article
- Linkage disequilibrium--understanding the evolutionary past and mapping the medical future.Nature reviews. Genetics · 2008Review
- Review and evaluation of methods correcting for population stratification with a focus on underlying statistical principles.Human heredity · 2008Review
- Recent human effective population size estimated from linkage disequilibrium.Genome research · 2007Article
- Prospects and pitfalls in whole genome association studies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2005Review
- A map of the human genome in linkage disequilibrium units.Proceedings of the National Academy of Sciences of the United States of America · 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
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Population structure, whether created by pooling samples from divergent populations or by the mating pattern in a mixed population, is accurately bioassayed from genotype frequencies. The effective bottleneck time for Eurasians is substantially less than for migration out of Africa, reflecting later bottlenecks. The classical dependence of allele frequency on mutation age does not hold for the generally shorter time span of inbreeding and LD. Limitation of the classical theory to mutation age justifies the assumption of constant time in a LD map, except for alleles that were rare at the effective bottleneck time or have arisen since. This assumption is derived from the Malecot model and verified in all samples. Tested measures of relative efficiency, support intervals, and localization error determine the operating characteristics of LD maps that are applicable to every sexually reproducing species, with implications for association mapping, high-resolution linkage maps, evolutionary inference, and identification of recombinogenic sequences.
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