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Journal articles on the topic 'Linkage disequilibrium'

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Published: 4 June 2021

Last updated: 25 July 2025

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1

Tachida, Hidenori. "Decay of linkage disequilibrium in a finite island model." Genetical Research 64, no. 2 (1994): 137–44. http://dx.doi.org/10.1017/s0016672300032742.

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SummaryTime-dependent behaviour of linkage disequilibrium when there was initial linkage disequilibrium is studied in a finite island model assuming neutrality. Explicit expressions for linkage disequilibrium parameters are obtained. From these expressions, the initial and the ultimate decay rates of linkage disequilibrium parameters are found to be increased and decreased, respectively, by finiteness of the population when recombination rate, migration rate and inverse of subpopulation size are of comparable order. Thus, linkage disequilibrium created in the past may persist longerin smaller

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2

Weitzman, Jonathan B. "Linkage disequilibrium." Genome Biology 2 (2001): spotlight—20010514–01. http://dx.doi.org/10.1186/gb-spotlight-20010514-01.

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3

Miyashita, Naohiko T., Montserrat Aguadé, and Charles H. Langley. "Linkage disequilibrium in the white locus region of Drosophila melanogaster." Genetical Research 62, no. 2 (1993): 101–9. http://dx.doi.org/10.1017/s0016672300031694.

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SummaryLinkage disequilibrium between molecular polymorphisms in a 10 kb region in the white locus of Drosophila melanogaster, revealed with a battery of four-cutter restriction enzymes, was investigated in 266 lines sampled from seven natural populations around the world. A total of 73 (35 restriction site, 37 insertion/deletion and 1 inversion) polymorphisms were detected, of which 55 non-unique polymorphisms were analysed for linkage disequilibrium. Clustering of significant linkage disequilibrium was observed in the transcriptional unit of the white locus as in Miyashita & Langley (198

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4

Wu, Rongling, and Zhao-Bang Zeng. "Joint Linkage and Linkage Disequilibrium Mapping in Natural Populations." Genetics 157, no. 2 (2001): 899–909. http://dx.doi.org/10.1093/genetics/157.2.899.

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Abstract A new strategy for studying the genome structure and organization of natural populations is proposed on the basis of a combined analysis of linkage and linkage disequilibrium using known polymorphic markers. This strategy exploits a random sample drawn from a panmictic natural population and the open-pollinated progeny of the sample. It is established on the principle of gene transmission from the parental to progeny generation during which the linkage between different markers is broken down due to meiotic recombination. The strategy has power to simultaneously capture the informatio

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5

Kuno, Shin-ichi. "Division of linkage disequilibrium between absolute linkage disequilibrium and linkage equilibrium." Journal of Human Genetics 50, no. 6 (2005): 315–16. http://dx.doi.org/10.1007/s10038-005-0256-6.

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6

Schaeffer, S. W., and E. L. Miller. "Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura." Genetics 135, no. 2 (1993): 541–52. http://dx.doi.org/10.1093/genetics/135.2.541.

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Abstract The alcohol dehydrogenase (Adh) region of Drosophila pseudoobscura, which includes the two genes Adh and Adh-Dup, was used to examine the pattern and organization of linkage disequilibrium among pairs of segregating nucleotide sites. A collection of 99 strains from the geographic range of D. pseudoobscura were nucleotide-sequenced with polymerase chain reaction-mediated techniques. All pairs of the 359 polymorphic sites in the 3.5-kb Adh region were tested for significant linkage disequilibrium with Fisher's exact test. Of the 74,278 pairwise comparisons of segregating sites, 127 were

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7

Baird, Stuart J. E. "Exploring linkage disequilibrium." Molecular Ecology Resources 15, no. 5 (2015): 1017–19. http://dx.doi.org/10.1111/1755-0998.12424.

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8

Lou, Xiang-Yang, George Casella, Ramon C. Littell, Mark C. K. Yang, Julie A. Johnson, and Rongling Wu. "A Haplotype-Based Algorithm for Multilocus Linkage Disequilibrium Mapping of Quantitative Trait Loci With Epistasis." Genetics 163, no. 4 (2003): 1533–48. http://dx.doi.org/10.1093/genetics/163.4.1533.

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AbstractFor tightly linked loci, cosegregation may lead to nonrandom associations between alleles in a population. Because of its evolutionary relationship with linkage, this phenomenon is called linkage disequilibrium. Today, linkage disequilibrium-based mapping has become a major focus of recent genome research into mapping complex traits. In this article, we present a new statistical method for mapping quantitative trait loci (QTL) of additive, dominant, and epistatic effects in equilibrium natural populations. Our method is based on haplotype analysis of multilocus linkage disequilibrium a

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9

Hsu, Fang-Chi, Kung-Yee Liang, and Terri H. Beaty. "Multipoint linkage disequilibrium mapping approach: Incorporating evidence of linkage and linkage disequilibrium from unlinked region." Genetic Epidemiology 25, no. 1 (2003): 1–13. http://dx.doi.org/10.1002/gepi.10241.

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10

Sabatti, Chiara, and Neil Risch. "Homozygosity and Linkage Disequilibrium." Genetics 160, no. 4 (2002): 1707–19. http://dx.doi.org/10.1093/genetics/160.4.1707.

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Abstract We illustrate how homozygosity of haplotypes can be used to measure the level of disequilibrium between two or more markers. An excess of either homozygosity or heterozygosity signals a departure from the gametic phase equilibrium: We describe the specific form of dependence that is associated with high (low) homozygosity and derive various linkage disequilibrium measures. They feature a clear biological interpretation, can be used to construct tests, and are standardized to allow comparison across loci and populations. They are particularly advantageous to measure linkage disequilibr

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11

Gorelick, Root, and Manfred D. Laubichler. "Decomposing Multilocus Linkage Disequilibrium." Genetics 166, no. 3 (2004): 1581–83. http://dx.doi.org/10.1534/genetics.166.3.1581.

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12

Goldstein, David B. "Islands of linkage disequilibrium." Nature Genetics 29, no. 2 (2001): 109–11. http://dx.doi.org/10.1038/ng1001-109.

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13

Aissani, Brahim. "Confounding by linkage disequilibrium." Journal of Human Genetics 59, no. 2 (2013): 110–15. http://dx.doi.org/10.1038/jhg.2013.130.

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14

SECALL, MIRIAM, and FRITZ H. BACH. "Linkage Disequilibrium or Epistasis?" Tissue Antigens 6, no. 2 (2008): 161–62. http://dx.doi.org/10.1111/j.1399-0039.1975.tb00629.x.

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15

Gibson, Jane, William Tapper, Weihua Zhang, Newton Morton, and Andrew Collins. "Cosmopolitan linkage disequilibrium maps." Human Genomics 2, no. 1 (2005): 20. http://dx.doi.org/10.1186/1479-7364-2-1-20.

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16

Goddard, M. E., and T. H. E. Meuwissen. "The use of linkage disequilibrium to map quantitative trait loci." Australian Journal of Experimental Agriculture 45, no. 8 (2005): 837. http://dx.doi.org/10.1071/ea05066.

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This paper reviews the causes of linkage disequilibrium and its use in mapping quantitative trait loci. The many causes of linkage disequilibrium can be understood as due to similarity in the coalescence tree of different loci. Consideration of the way this comes about allows us to divide linkage disequilibrium into 2 types: linkage disequilibrium between any 2 loci, even if they are unlinked, caused by variation in the relatedness of pairs of animals; and linkage disequilibrium due to the inheritance of chromosome segments that are identical by descent from a common ancestor. The extent of li

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17

Thomson, Glenys, and William Klitz. "Disequilibrium Pattern Analysis. I. Theory." Genetics 116, no. 4 (1987): 623–32. http://dx.doi.org/10.1093/genetics/116.4.623.

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ABSTRACT We have developed a method, disequilibrium pattern analysis, for examining the disequilibrium distribution of the entire array of two locus multiallelic haplotypes in a population. It is shown that a selected haplotype will produce a distinct pattern of linkage disequilibrium values for all generations while the selection is acting. This pattern will also presumably be maintained for many generations after the selection event, until the disequilibrium pattern is eventually broken down by genetic drift and recombination. Related haplotypes, sharing an allele with a selected haplotype,

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18

Smit-McBride, Z., A. Moya, and F. J. Ayala. "Linkage disequilibrium in natural and experimental populations of Drosophila melanogaster." Genetics 120, no. 4 (1988): 1043–51. http://dx.doi.org/10.1093/genetics/120.4.1043.

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Abstract We have studied linkage disequilibrium in Drosophila melanogaster in two samples from a wild population and in four large laboratory populations derived from the wild samples. We have assayed four polymorphic enzyme loci, fairly closely linked in the third chromosome: Sod Est-6, Pgm, and Odh. The assay method used allows us to identify the allele associations separately in each of the two homologous chromosomes from each male sampled. We have detected significant linkage disequilibrium between two loci in 16.7% of the cases in the wild samples and in 27.8% of the cases in the experime

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19

HANSEN, MATS, THOMAS KRAFT, SARA GANESTAM, TORBJÖRN SÄLL, and NILS-OTTO NILSSON. "Linkage disequilibrium mapping of the bolting gene in sea beet using AFLP markers." Genetical Research 77, no. 1 (2001): 61–66. http://dx.doi.org/10.1017/s0016672300004857.

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The possibility of using linkage disequilibrium mapping in natural plant populations was assessed. In studying linkage disequilibrium among 137 mapped AFLP markers in four populations of sea beet (Beta vulgaris ssp. maritima (L.) Arcang.) it was shown that tightly linked loci could be detected by screening for associations. It was hypothesized that the short distances spanned by linkage disequilibrium enable markers that are very tightly linked to a target gene to be identified. The hypothesis was tested by whole-genome screening of AFLP markers for association with the gene for the annual gro

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20

Garris, Amanda J., Susan R. McCouch, and Stephen Kresovich. "Population Structure and Its Effect on Haplotype Diversity and Linkage Disequilibrium Surrounding the xa5 Locus of Rice (Oryza sativa L.)." Genetics 165, no. 2 (2003): 759–69. http://dx.doi.org/10.1093/genetics/165.2.759.

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Abstract To assess the usefulness of linkage disequilibrium mapping in an autogamous, domesticated species, we have characterized linkage disequilibrium in the candidate region for xa5, a recessive gene conferring race-specific resistance to bacterial blight in rice. This trait and locus have good mapping information, a tractable phenotype, and available sequence data, but no cloned gene. We sampled 13 short segments from the 70-kb candidate region in 114 accessions of Oryza sativa. Five additional segments were sequenced from the adjacent 45-kb region in resistant accessions to estimate the d

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21

�idlov�, Veronika, Radovan Kasarda, Nina Moravc�kov�, Anna Trakovick�, Ino Curik, and Maja Ferencakovic. "Extent of genome-wide linkage disequilibrium in Pinzgau cattle." Journal of Central European Agriculture 17, no. 2 (2016): 294–302. http://dx.doi.org/10.5513/jcea01/17.2.1704.

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22

Schaid, Daniel J. "Linkage Disequilibrium Testing When Linkage Phase Is Unknown." Genetics 166, no. 1 (2004): 505–12. http://dx.doi.org/10.1534/genetics.166.1.505.

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23

Aragaki, Corinne, Filemon Quiaoit, Li Hsu, and Lue Ping Zhao. "Mapping alcoholism genes using linkage/linkage disequilibrium analysis." Genetic Epidemiology 17, S1 (1999): S43—S48. http://dx.doi.org/10.1002/gepi.1370170708.

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24

Hedrick, Philip W. "Assortative Mating and Linkage Disequilibrium." G3: Genes|Genomes|Genetics 7, no. 1 (2016): 55–62. http://dx.doi.org/10.1534/g3.116.034967.

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25

McRae, A. F., J. C. McEwan, K. G. Dodds, T. Wilson, A. M. Crawford, and J. Slate. "Linkage Disequilibrium in Domestic Sheep." Genetics 160, no. 3 (2002): 1113–22. http://dx.doi.org/10.1093/genetics/160.3.1113.

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Abstract The last decade has seen a dramatic increase in the number of livestock QTL mapping studies. The next challenge awaiting livestock geneticists is to determine the actual genes responsible for variation of economically important traits. With the advent of high density single nucleotide polymorphism (SNP) maps, it may be possible to fine map genes by exploiting linkage disequilibrium between genes of interest and adjacent markers. However, the extent of linkage disequilibrium (LD) is generally unknown for livestock populations. In this article microsatellite genotype data are used to as

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26

Schaper, E., A. Eriksson, M. Rafajlovic, S. Sagitov, and B. Mehlig. "Linkage Disequilibrium Under Recurrent Bottlenecks." Genetics 190, no. 1 (2011): 217–29. http://dx.doi.org/10.1534/genetics.111.134437.

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27

Huang, Kang, Derek W. Dunn, Wenkai Li, Dan Wang, and Baoguo Li. "Linkage disequilibrium under polysomic inheritance." Heredity 128, no. 1 (2022): 11–20. http://dx.doi.org/10.1038/s41437-021-00482-1.

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28

Agapow, Paul-Michael, and Austin Burt. "Indices of multilocus linkage disequilibrium." Molecular Ecology Notes 1, no. 1-2 (2001): 101–2. http://dx.doi.org/10.1046/j.1471-8278.2000.00014.x.

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29

Laurie, Cathy C., Deborah A. Nickerson, Amy D. Anderson, et al. "Linkage Disequilibrium in Wild Mice." PLoS Genetics 3, no. 8 (2007): e144. http://dx.doi.org/10.1371/journal.pgen.0030144.

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30

Laurie, Cathy C., Deborah A. Nickerson, Amy D. Anderson, et al. "Linkage disequilibrium in wild mice." PLoS Genetics preprint, no. 2007 (2005): e144. http://dx.doi.org/10.1371/journal.pgen.0030144.eor.

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31

Alfred, Jane. "Linkage disequilibrium — a global view." Nature Reviews Genetics 2, no. 6 (2001): 406. http://dx.doi.org/10.1038/35076552.

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32

Lonjou, C., W. Zhang, A. Collins, et al. "Linkage disequilibrium in human populations." Proceedings of the National Academy of Sciences 100, no. 10 (2003): 6069–74. http://dx.doi.org/10.1073/pnas.1031521100.

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33

Maniatis, Nikolas, Andrew Collins, Jane Gibson, Weihua Zhang, William Tapper, and Newton E. Morton. "Positional Cloning by Linkage Disequilibrium." American Journal of Human Genetics 74, no. 5 (2004): 846–55. http://dx.doi.org/10.1086/383589.

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34

Gaut, Brandon S., and Anthony D. Long. "The Lowdown on Linkage Disequilibrium." Plant Cell 15, no. 7 (2003): 1502–6. http://dx.doi.org/10.1105/tpc.150730.

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35

Green, Jack, and J. C. Woodrow. "Linkage disequilibrium involving three loci." Tissue Antigens 29, no. 1 (2008): 18–20. http://dx.doi.org/10.1111/j.1399-0039.1987.tb01544.x.

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36

Siegmund, Kimberly D., Bryan Langholz, Peter Kraft, and Duncan C. Thomas. "Testing Linkage Disequilibrium in Sibships." American Journal of Human Genetics 67, no. 1 (2000): 244–48. http://dx.doi.org/10.1086/302973.

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37

Weir, B. S. "Linkage Disequilibrium and Association Mapping." Annual Review of Genomics and Human Genetics 9, no. 1 (2008): 129–42. http://dx.doi.org/10.1146/annurev.genom.9.081307.164347.

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38

Xiong, Momiao. "Haplotype bolck linkage disequilibrium mapping." Frontiers in Bioscience 8, no. 1 (2003): a85–93. http://dx.doi.org/10.2741/919.

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39

WANG, Rong-Huan. "Linkage disequilibrium in plant genomes." HEREDITAS 29, no. 11 (2007): 1317. http://dx.doi.org/10.1360/yc-007-1317.

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40

Cheung, Vivian G., Jeffrey P. Gregg, Kathryn J. Gogolin-Ewens, et al. "Linkage-disequilibrium mapping without genotyping." Nature Genetics 18, no. 3 (1998): 225–30. http://dx.doi.org/10.1038/ng0398-225.

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41

Boehnke, Michael. "A look at linkage disequilibrium." Nature Genetics 25, no. 3 (2000): 246–47. http://dx.doi.org/10.1038/76980.

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42

Romanov, Dmitriy, and Nikolai Skoblikow. "Linkage Disequilibrium in Targeted Sequencing." Mathematical Biology and Bioinformatics 17, no. 2 (2022): 325–37. http://dx.doi.org/10.17537/2022.17.325.

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We propose an approach for optimizing the development of gene diagnostic panels, which is based on the construction of non-equilibrium linkage maps. In the process of gene selection we essentially use genome-wide association analysis (GWAS). Whole-genome analysis of associations makes it possible to reveal the relationship of genomic variants with the studied phenotype. However, the nucleotide variants that showed the highest degree of association can only be statistically associated with the phenotype, not being the true cause of the phenotype. In this case, they may be in the block of linked

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43

Rinaldo, Alessandro, Silviu-Alin Bacanu, B. Devlin, Vibhor Sonpar, Larry Wasserman, and Kathryn Roeder. "Characterization of multilocus linkage disequilibrium." Genetic Epidemiology 28, no. 3 (2005): 193–206. http://dx.doi.org/10.1002/gepi.20056.

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44

Hudson, Richard R. "THE SAMPLING DISTRIBUTION OF LINKAGE DISEQUILIBRIUM UNDER AN INFINITE ALLELE MODEL WITHOUT SELECTION." Genetics 109, no. 3 (1985): 611–31. http://dx.doi.org/10.1093/genetics/109.3.611.

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ABSTRACT The sampling distributions of several statistics that measure the association of alleles on gametes (linkage disequilibrium) are estimated under a two-locus neutral infinite allele model using an efficient Monte Carlo method. An often used approximation for the mean squared linkage disequilibrium is shown to be inaccurate unless the proper statistical conditioning is used. The joint distribution of linkage disequilibrium and the allele frequencies in the sample is studied. This estimated joint distribution is sufficient for obtaining an approximate maximum likelihood estimate of C = 4

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45

Jelić, Mihailo, José A. Castro, Zorana Kurbalija Novičić, et al. "Absence of linkage disequilibria between chromosomal arrangements and mtDNA haplotypes in natural populations of Drosophila subobscura from the Balkan Peninsula." Genome 55, no. 3 (2012): 214–21. http://dx.doi.org/10.1139/g2012-004.

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The genetic structure of Drosophila subobscura from the Balkan Peninsula was studied with respect to restriction site polymorphism of mitochondrial DNA in populations from the Derventa River Gorge and Sicevo Gorge (Serbia). To investigate the role of cytonuclear interactions in shaping mitochondrial DNA variability in natural populations of this species, the study was complemented with the analysis of linkage disequilibria between mitochondrial haplotypes and chromosomal inversion arrangements. Similar to other populations of D. subobscura, two main haplotypes (I and II) were found, as well as

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46

Lewontin, R. C. "The detection of linkage disequilibrium in molecular sequence data." Genetics 140, no. 1 (1995): 377–88. http://dx.doi.org/10.1093/genetics/140.1.377.

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Abstract Studies of genetic variation in natural populations at the sequence level usually show that most polymorphic sites are very asymmetrical in allele frequencies, with the rarer allele at a site near fixation. When the rarer allele at a site is present only a few times in the sample, say below five representatives, it becomes very difficult to detect linkage disequilibrium between sites from tests of association. This is a consequence of the numerical properties of even the most powerful test of association, Fisher's exact test. Sites with fewer than five representatives in the sample sh

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47

CHESSA, Stefania, Andrea CRISCIONE, Riccardo MORETTI, Salvatore BORDONARO, Donata MARLETTA, and Bianca CASTIGLIONI. "Estimation of linkage disequilibrium in the Nero Siciliano Italian autochtonous breed using the Illumina 60K SNP array." Acta agriculturae Slovenica. Suplement, no. 4 (September 25, 2013): 37–40. http://dx.doi.org/10.14720/aas-s.2013.4.18988.

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Local breeds represent an important component of the overall farm animal diversity to be maintained and exploited. The new high-throughput molecular technologies allow a wide range of massive, simultaneous genomic analysis. Commercial SNP genotyping platforms are a suitable tool for the genetic characterization and the study of inter-breeds diversity. Linkage disequilibrium, the nonrandom association of alleles at different loci, has received increasing attention in recent years as a result of the availability of genome sequences and large numbers of identified SNP. This study aims to assess t

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48

Hernández-Sánchez, Jules, Peter Visscher, Graham Plastow, and Chris Haley. "Candidate Gene Analysis for Quantitative Traits Using the Transmission Disequilibrium Test: The Example of the Melanocortin 4-Receptor in Pigs." Genetics 164, no. 2 (2003): 637–44. http://dx.doi.org/10.1093/genetics/164.2.637.

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Abstract Population-wide associations between loci due to linkage disequilibrium can be used to map quantitative trait loci (QTL) with high resolution. However, spurious associations between markers and QTL can also arise as a consequence of population stratification. Statistical methods that cannot differentiate between loci associations due to linkage disequilibria from those caused in other ways can render false-positive results. The transmission-disequilibrium test (TDT) is a robust test for detecting QTL. The TDT exploits within-family associations that are not affected by population stra

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49

Kumar, Arun, and J. P. Gupta. "Linkage disequilibrium, natural selection, and epistatic gene interaction in Drosophila nasuta." Genome 30, no. 4 (1988): 495–98. http://dx.doi.org/10.1139/g88-082.

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The data of linkage disequilibrium between III-2 and 111-35 gene arrangements in natural populations of Drosophila nasuta is presented. The results demonstrated that there was significant linkage disequilibrium between the above gene arrangements in natural populations. Among all nine possible karyotypic combinations, only four combinations were seen. The absence of some combinations might be because of sublethal combinations of genes that reduced the viabilities of their carriers. The frequency of double inversion heterozygotes was always in excess and only 1.29% single hetrozygotes were obse

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50

YANG, Wenjie, Jianfeng HUANG, Cailiang YAO, et al. "Linkage and linkage disequilibrium analysis of the lipoprotein lipase gene with lipid profiles in Chinese hypertensive families." Clinical Science 108, no. 2 (2005): 137–42. http://dx.doi.org/10.1042/cs20040101.

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Elevated TG [triacylglycerol (triglyceride)] is a significant independent risk factor for cardiovascular disease. LPL (lipoprotein lipase) is one of the key enzymes in the metabolism of the TG-rich lipoproteins which hydrolyses TG from the chylomicrons and very-LDL (low-density lipoprotein). To investigate the relationship between the LPL gene and lipid profiles, especially TG, in 148 hypertensive families, we have chosen seven flanking microsatellite markers and four internal markers of the LPL gene and conducted linkage analysis by SOLAR and S.A.G.E. (statistical analysis for genetic epidemi

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