Inbreeding, inversions and gene conversion Other forces create LD as well. Detecting natural selection Strong positive selection quickly increases the frequency of an advantageous allele, with the result that linked loci remain in unusually strong LD with that allele.
Estimating allele age Strong LD with an allele in a relatively large region indicates that not much time has passed since the allele arose by mutation. Box 2 Genotype data and haplotype phase.
Box 3 Four-haplotype test. Box 4 LD mapping. References 1. Lewontin RC, Kojima K. The evolutionary dynamics of complex polymorphisms.
Weir BS. Genetic Data Analysis II. Sinauer Assoc; Sunderland, Massachusetts: Hedrick PW. Genetic disequilibrium measures: proceed with caution.
Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms. Signatures of demographic history and natural selection in the human major histocompatibility complex loci. Weinberg W. Uber vererbungsgesetze beim menschen. Abst V. Jennings HS. The numerical results of diverse systems of breeding, with respect to two pairs of characters, linked and independent, with special relation to the effects of linkage.
Inferences about linkage disequilibrium. Excoffier L, Slatkin M. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.
Kuhner MK. Miyashita N, Langley CH. Molecular and phenotypic variation of the white locus region in Drosophila melanogaster. High-resolution haplotype structure in the human genome. Gabriel SB, et al. The structure of haplotype blocks in the human genome. Haplotype blocks and linkage disequilibrium in the human genome.
Nature Rev. Kruglyak L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genet. Carlson CS, et al. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Phillips MS, et al. Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Anderson EC, Novembre J. Finding haplotype block boundaries by using the minimum-description-length principle.
International HapMap Consortium A haplotype map of the human genome. International HapMap Consortium A second generation human haplotype map of over 3. Guryev V, et al. Haplotype block structure is conserved across mammals. PLoS Genet. Gautier M, et al. Genetic and haplotypic structure in 14 European and African cattle breeds. Lindblad-Toh K, et al.
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Multilocus structure of natural populations of Hordeum spontaneum.
How clonal are bacteria? Natl Acad. Geiringer H. On the probability theory of linkage in Mendelian heredity. Annals of Mathematical Statistics. Constrained disequilibrium values and hitchhiking in a three-locus system. Ohta T. Linkage disequilibrium due to random genetic drift in finite subdivided populations.
Linkage disequilibrium with the island model. Wright S. Breeding structure of populations in relation to speciation. Raymond M, Rousset F. Genepop Version 1. Lewontin RC. On measures of gametic disequilibrium. The optimal measure of linkage disequilibrium reduces error in association mapping of affection status. Hudson RR. Properties of a neutral allele model with intragenic recombination. Statistical properties of the number of recombination events in the history of a sample of DNA sequences.
Maximum likelihood estimation of recombination rates from population data. Two-locus sampling distributions and their applications. A coalescent-based method for detecting and estimating recombination from gene sequences.
A fine-scale map of recombination rates and hotspots across the human genome. Kimura M. Attainment of quasi linkage equilibrium when gene frequencies are changing by natural selection.
Nagylaki T. Quasilinkage equilibrium and the evolution of two-locus systems. The evolution of one and two-locus systems. Fisher RA. The Genetical Theory of Natural Selection. Clarendon; Oxford: Felsenstein J. The effect of linkage on directional selection. Karlin S, Feldman MW. Linkage and selection: two locus symmetric viability model.
Selection in complex genetic systems I. The symmetric equilibria of the three-locus symmetric viability model. Franklin I, Lewontin RC. Is the gene the unit of selection? Slatkin M. On treating the chromosome as the unit of selection. Charlesworth B, Charlesworth D.
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Hamon SC, et al. Hill WG, Robertson A. Linkage disequilibrium in finite populations. Ohta T, Kimura M. Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation. The sampling distribution of linkage disequilibrium under an infinite allele model without selection. Linkage disequilibrium in growing and stable populations. The effect of linkage on limits to artificial selection. The effects of Hill—Robertson interference between weakly selected mutations on patterns of molecular evolution and variation.
The evolutionary advantage of recombination. Interference among deleterious mutations favours sex and recombination in finite populations. Barton NH. A general model for the evolution of recombination. Nei M, Li W. Linkage disequilibrium in subdivided populations. Population genetics of marine pelecypods. Epistasis between functionally related isoenzymes of Mytilus edulis. Li WH. Stable linkage disequilibrium without epistasis in subdivided populations.
Gene flow and selection in a 2-locus system. Noonan JP, et al. Sequencing and analysis of Neanderthal genomic DNA. Genetic variability in a genomic region with long-range linkage disequilibrium reveals traces of a bottleneck in the history of the European population. Zhang WH, et al. Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps. Thornton K, Andolfatto P. Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster.
You are commenting using your Twitter account. You are commenting using your Facebook account. Notify me of new comments via email. Notify me of new posts via email. Enter your rs ID or chr:pos e. After a couple of minutes, you should get the table where you can choose the population and G version.
Good for checking the LD structure of different population or historical analysis of how LD structure definitions changed over the years. Not feasible for repeated applications. Haploview is also another popular software but I am uncertain of how up-to-date their reference data is. Uses the latest Genomes March haplotypes. No visualization and needs a bit more work e. Figure 2. Five letters in red font represent SNPs in the gene, identified by comparing sequence of this gene among a set of diverse genotypes.
Although a large number of genotyping platforms are available, in principle, the marker could be scored on an agarose gel. Falconer, D. Introduction to Quantitative Genetics 4th ed. Lewontin, R. Genetics 49 1 : 49— BMC Bioinformatics. Home LD Tools. Welcome to. Create an interactive heatmap matrix of pairwise linkage disequilibrium statistics. Investigate correlated alleles for a pair of variants in high LD. Investigate allele frequencies and linkage disequilibrium patterns across G populations.
Interactively explore proxy and putatively functional variants for a query variant. Use example GWAS data. Select Region Gene Region Variant. Gene Name. Index RSID optional. Start Coord chr or in GRCh End Coord chr Index RSID. LD measure:. Collapse transcripts:.
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