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Volumn 71, Issue 3, 2011, Pages 186-195

On the uses and applications of the most commonly used measures of linkage disequilibrium from the comparative analysis of their statistical properties

Author keywords

2 2 contingency tables; D and r coefficients; Linkage disequilibrium; Measures of disequilibrium; Range of disequilibrium measures; Sampling distributions; Sampling variance and bias

Indexed keywords

ACCURACY; ARTICLE; COEFFICIENT D'; COEFFICIENT R; COMPARATIVE STUDY; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC CORRELATION; SAMPLE SIZE; SIMULATION; STATISTICS;

EID: 79960822415     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000327732     Document Type: Article
Times cited : (7)

References (49)
  • 1
    • 43749105558 scopus 로고    scopus 로고
    • Linkage disequilibrium - Understanding the evolutionary past and mapping the medical future
    • DOI 10.1038/nrg2361, PII NRG2361
    • Slatkin M: Linkage disequilibrium - understanding the evolutionary past and mapping the medical future. Nat Rev Genet 2008; 9: 477-485. (Pubitemid 351693977)
    • (2008) Nature Reviews Genetics , vol.9 , Issue.6 , pp. 477-485
    • Slatkin, M.1
  • 2
    • 35348983887 scopus 로고    scopus 로고
    • The international hapmap consortium: A second generation human haplotype map of over 3.1 million SNPs
    • The International HapMap Consortium: A second generation human haplotype map of over 3.1 million SNPs. Nature 2007; 449: 851-862.
    • (2007) Nature , vol.449 , pp. 851-862
  • 4
    • 0029150074 scopus 로고
    • A comparison of linkage disequilibrium measures for fine-scale mapping
    • Devlin B, Risch N: A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 1995; 29: 311-322.
    • (1995) Genomics , vol.29 , pp. 311-322
    • Devlin, B.1    Risch, N.2
  • 6
    • 0002907949 scopus 로고
    • The interaction of selection and linkage I general considerations: Heterotic models
    • Lewontin RC: The interaction of selection and linkage. I. General considerations: heterotic models. Genetics 1964; 49: 49-67.
    • (1964) Genetics , vol.49 , pp. 49-67
    • Lewontin, R.C.1
  • 7
    • 33646226097 scopus 로고
    • Linkage disequilibrium in finite populations
    • Hill WG, Robertson A: Linkage disequilibrium in finite populations. Theor Appl Genet 1968; 38: 226-231.
    • (1968) Theor. Appl. Genet. , vol.38 , pp. 226-231
    • Hill, W.G.1    Robertson, A.2
  • 8
    • 0023430504 scopus 로고
    • Gametic disequilibrium measures: Proceed with caution
    • Hedrick PW: Gametic disequilibrium measures: proceed with caution. Genetics 1987; 117: 331-341.
    • (1987) Genetics , vol.117 , pp. 331-341
    • Hedrick, P.W.1
  • 10
    • 0034674090 scopus 로고    scopus 로고
    • Questioning evidence for recombination in human mitochondrial DNA
    • Jorde LB, Bamshad M: Questioning evidence for recombination in human mitochondrial DNA. Science 2000; 288: 1931a.
    • (2000) Science , vol.288
    • Jorde, L.B.1    Bamshad, M.2
  • 11
    • 0034674094 scopus 로고    scopus 로고
    • Questioning evidence for recombination in human mitochondrial DNA
    • Kumar S, Hedrick PW, Dowling T, Stoneking M: Questioning evidence for recombination in human mitochondrial DNA. Science 2000; 288: 1931a.
    • (2000) Science , vol.288
    • Kumar, S.1    Hedrick, P.W.2    Dowling, T.3    Stoneking, M.4
  • 13
    • 0036240964 scopus 로고    scopus 로고
    • Homozygosity and linkage disequilibrium
    • Sabatti C, Risch N: Homozygosity and linkage disequilibrium. Genetics 2002; 160: 1707-1719. (Pubitemid 34454391)
    • (2002) Genetics , vol.160 , Issue.4 , pp. 1707-1719
    • Sabatti, C.1    Risch, N.2
  • 14
    • 0036137130 scopus 로고    scopus 로고
    • Linkage disequilibrium and the mapping of complex human traits
    • DOI 10.1016/S0168-9525(01)02550-1, PII S0168952501025501
    • Weiss KM, Clark AG: Linkage disequilibrium and the mapping of complex human traits. Trends Genet 2002; 18: 19-24. (Pubitemid 34031854)
    • (2002) Trends in Genetics , vol.18 , Issue.1 , pp. 19-24
    • Weiss, K.M.1    Clark, A.G.2
  • 15
    • 0030910081 scopus 로고    scopus 로고
    • Testing for homogeneity of gametic disequilibrium among populations
    • Zapata C, Alvarez G: Testing for homogeneity of gametic disequilibrium among populations. Evolution 1997; 51: 606-607. (Pubitemid 27201511)
    • (1997) Evolution , vol.51 , Issue.2 , pp. 606-607
    • Zapata, C.1    Alvarez, G.2
  • 16
    • 0033786787 scopus 로고    scopus 로고
    • Linkage disequilibrium and the search for complex disease genes
    • Jorde LB: Linkage disequilibrium and the search for complex disease genes. Genome Res 2000; 10: 1435-1444.
    • (2000) Genome Res. , vol.10 , pp. 1435-1444
    • Jorde, L.B.1
  • 17
    • 0036208832 scopus 로고    scopus 로고
    • Patterns of linkage disequilibrium in the human genome
    • DOI 10.1038/nrg777
    • Ardlie K, Kruglyak L, Seielstad M: Patterns of linkage disequilibrium in the human genome. Nat Rev Genet 2002; 3: 299-309. (Pubitemid 34279798)
    • (2002) Nature Reviews Genetics , vol.3 , Issue.4 , pp. 299-309
    • Ardlie, K.G.1    Kruglyak, L.2    Seielstad, M.3
  • 19
    • 20544447886 scopus 로고    scopus 로고
    • Linkage disequilibrium for different scales and applications
    • Mueller JC: Linkage disequilibrium for different scales and applications. Brief Bioinform 2004; 5: 355-364.
    • (2004) Brief Bioinform. , vol.5 , pp. 355-364
    • Mueller, J.C.1
  • 20
    • 0023796209 scopus 로고
    • On measures of gametic disequilibrium
    • Lewontin RC: On measures of gametic disequilibrium. Genetics 1988; 120: 849-852. (Pubitemid 18260517)
    • (1988) Genetics , vol.120 , Issue.3 , pp. 849-852
    • Lewontin, R.C.1
  • 23
    • 33645775067 scopus 로고    scopus 로고
    • An utter refutation of the fundamental theorem of the hapmap
    • Terwilliger JD, Hiekkalinna T: An utter refutation of the 'Fundamental Theorem of the HapMap'. Eur J Hum Genet 2006; 14: 426-437.
    • (2006) Eur. J. Hum. Genet. , vol.14 , pp. 426-437
    • Terwilliger, J.D.1    Hiekkalinna, T.2
  • 24
    • 0344585289 scopus 로고    scopus 로고
    • Role of evolutionary history on haplotype block structure in the human genome: Implications for disease mapping
    • DOI 10.1016/j.gde.2003.10.010
    • Tishkoff SA, Verrelli BC: Role of evolutionary history on haplotype block structure in the human genome: implications for disease mapping. Curr Opin Genet Dev 2003; 13: 569-575. (Pubitemid 37456873)
    • (2003) Current Opinion in Genetics and Development , vol.13 , Issue.6 , pp. 569-575
    • Tishkoff, S.A.1    Verrelli, B.C.2
  • 25
    • 0030767229 scopus 로고    scopus 로고
    • Approximate variance of the standardized measure of gametic disequilibrium D' [5]
    • Zapata C, Alvarez G, Carollo C: Approximate variance of the standardized measure of gametic disequilibrium D . Am J Hum Genet 1997; 61: 771-774. (Pubitemid 27418420)
    • (1997) American Journal of Human Genetics , vol.61 , Issue.3 , pp. 771-774
    • Zapata, C.1    Alvarez, G.2    Carollo, C.3
  • 26
    • 0016144327 scopus 로고
    • Linkage disequilibrium in natural populations of drosophila melanogaster
    • Langley CH, Tobari YN, Kojima K: Linkage disequilibrium in natural populations of Drosophila melanogaster . Genetics 1974; 78: 921-936.
    • (1974) Genetics , vol.78 , pp. 921-936
    • Langley, C.H.1    Tobari, Y.N.2    Kojima, K.3
  • 27
    • 0016560436 scopus 로고
    • Sample sizes required to detect linkage disequilibrium between two or three loci
    • Brown AHD: Sample sizes required to detect linkage disequilibrium between two or three loci. Theor Pop Biol 1975; 8: 184-201.
    • (1975) Theor. Pop Biol. , vol.8 , pp. 184-201
    • Brown, A.H.D.1
  • 28
    • 0023915850 scopus 로고
    • The detection of linkage disequilibrium between closely linked markers: RFLPs at the AI-CIII apolipoprotein genes
    • Thompson EA, Deeb S, Walker D, Motulsky AG: The detection of linkage disequilibrium between closely linked markers: RFLPs at the AI-CIII apolipoprotein genes. Am J Hum Genet 1988; 42: 113-124. (Pubitemid 18081288)
    • (1988) American Journal of Human Genetics , vol.42 , Issue.1 , pp. 113-124
    • Thompson, E.A.1    Deeb, S.2    Walker, D.3    Motulsky, A.G.4
  • 29
    • 0027301373 scopus 로고
    • On the detection of nonrandom associations between DNA polymorphisms in natural populations of Drosophila
    • Zapata C, Alvarez G: On the detection of non-random associations between DNA polymorphisms in natural populations of Drosophila . Mol Biol Evol 1993; 10: 823-841. (Pubitemid 23204798)
    • (1993) Molecular Biology and Evolution , vol.10 , Issue.4 , pp. 823-841
    • Zapata, C.1    Alvarez, G.2
  • 30
    • 0035711599 scopus 로고    scopus 로고
    • Mutation and linkage disequilibrium in human mtDNA
    • Hedrick PW, Kumar S: Mutation and linkage disequilibrium in human mtDNA. Eur J Hum Genet 2001; 9: 969-972. (Pubitemid 34145118)
    • (2001) European Journal of Human Genetics , vol.9 , Issue.12 , pp. 969-972
    • Hedrick, P.1    Kumar, S.2
  • 31
    • 46449095087 scopus 로고    scopus 로고
    • Mathematical properties of the r 2 measure of linkage disequilibrium
    • VanLiere JM, Rosenberg NA: Mathematical properties of the r 2 measure of linkage disequilibrium. Theor Pop Biol 2008; 74: 130-137.
    • (2008) Theor. Pop Biol. , vol.74 , pp. 130-137
    • VanLiere, J.M.1    Rosenberg, N.A.2
  • 35
    • 33749394003 scopus 로고    scopus 로고
    • Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome
    • DOI 10.1371/journal.pgen.0020142
    • Eberle MA, Rieder MJ, Kruglyak L, Nickerson DA: Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome. PLoS Genet 2006; 2: 1319-1327. (Pubitemid 44504784)
    • (2006) PLoS Genetics , vol.2 , Issue.9 , pp. 1319-1327
    • Eberle, M.A.1    Rieder, M.J.2    Kruglyak, L.3    Nickerson, D.A.4
  • 36
    • 0030807876 scopus 로고    scopus 로고
    • Linkage disequilibrium measures for fine-scale mapping: A comparison
    • Guo S-W: Linkage disequilibrium measures for fine-scale mapping: a comparison. Hum Hered 1997; 47: 301-314. (Pubitemid 27483056)
    • (1997) Human Heredity , vol.47 , Issue.6 , pp. 301-314
    • Guo, S.-W.1
  • 37
    • 0037234025 scopus 로고    scopus 로고
    • The interval of linkage disequilibrium (LD) detected with microsatellite and SNP markers in chromosomes of Finnish populations with different histories
    • DOI 10.1093/hmg/ddg005
    • Varilo T, Paunio T, Parker A, Perola M, Meyer J, Terwilliger JD, Peltonen L: The interval of linkage disequilibrium (LD) detected with microsatellite and SNP markers in chromosomes of Finnish populations with different histories. Hum Mol Biol 2003; 12: 51-59. (Pubitemid 36097715)
    • (2003) Human Molecular Genetics , vol.12 , Issue.1 , pp. 51-59
    • Varilo, T.1    Paunio, T.2    Parker, A.3    Perola, M.4    Meyer, J.5    Terwilliger, J.D.6    Peltonen, L.7
  • 39
    • 0021709390 scopus 로고
    • Detection of nonrandom association of alleles from the distribution of the number of heterozygous loci in a sample
    • Chakraborty R: Detection of nonrandom association of alleles from the distribution of the number of heterozygous loci in a sample. Genetics 1984; 108: 719-731 (Pubitemid 15208412)
    • (1984) Genetics , vol.108 , Issue.3 , pp. 719-731
    • Chakraborty, R.1
  • 40
    • 84966177118 scopus 로고
    • Inference of recombinational hotspots using gametic disequilibrium values
    • Hedrick PW: Inference of recombinational hotspots using gametic disequilibrium values. Heredity 1988; 60: 435-438.
    • (1988) Heredity , vol.60 , pp. 435-438
    • Hedrick, P.W.1
  • 41
    • 0034916018 scopus 로고    scopus 로고
    • Genome-wide distribution of linkage disequilibrium in the population of Palau and its implications for gene flow in Remote Oceania
    • DOI 10.1007/s004390100511
    • Devlin B, Roeder K, Otto C, Tiobech S, Byerkey W: Genome-wide distribution and linkage disequilibrium in the population of Palau and its implications for gene flow in Remote Oceania. Hum Genet 2001; 108: 521-528. (Pubitemid 32700355)
    • (2001) Human Genetics , vol.108 , Issue.6 , pp. 521-528
    • Devlin, B.1    Roeder, K.2    Otto, C.3    Tiobech, S.4    Byerley, W.5
  • 42
    • 0022574916 scopus 로고
    • A two-locus neutrality test: Applications to humans, E. coli and lodgepole pine
    • Hedrick PW, Thomson G: A two-locus neutrality test: applications to humans, E. coli and lodgepole pine. Genetics 1986; 112: 135-156. (Pubitemid 16160162)
    • (1986) Genetics , vol.112 , Issue.1 , pp. 135-156
    • Hedrick, P.W.1    Thomson, G.2
  • 43
    • 0344091561 scopus 로고    scopus 로고
    • Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans
    • DOI 10.1038/ng1128
    • Carlson CS, Eberle MA., Rieder MJ, Smith JD, Kruglyak L, Nickerson D: Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat Genet 2003; 33: 518-521. (Pubitemid 36390016)
    • (2003) Nature Genetics , vol.33 , Issue.4 , pp. 518-521
    • Carlson, C.S.1    Eberle, M.A.2    Rieder, M.J.3    Smith, J.D.4    Kruglyak, L.5    Nickerson, D.A.6
  • 45
    • 12344333331 scopus 로고    scopus 로고
    • The optimal measure of linkage disequilibrium reduces error in association mapping of affection status
    • Maniatis N, Morton NE, Gibson J, Xu C-F, Hosking LK, Collins A: The optimal measure of linkage disequilibrium reduces error in association mapping of affection status. Hum Mol Genet 2005; 14: 45-153.
    • (2005) Hum. Mol. Genet. , vol.14 , pp. 45-153
    • Maniatis, N.1    Morton, N.E.2    Gibson, J.3    Xu, C.-F.4    Hosking, L.K.5    Collins, A.6
  • 46
    • 0141889553 scopus 로고    scopus 로고
    • A note on the optimal measure of allelic association
    • DOI 10.1046/j.1469-1809.2003.00025.x
    • Shete S: A note on the optimal measure of allelic association. Ann Hum Genet 2003; 67: 189-191. (Pubitemid 38312825)
    • (2003) Annals of Human Genetics , vol.67 , Issue.2 , pp. 189-191
    • Shete, S.1
  • 47
    • 0348143122 scopus 로고    scopus 로고
    • A metric linkage disequilibrium map of a human chromosome
    • DOI 10.1046/j.1469-1809.2003.00050.x
    • Tapper WJ, Maniatis N, Morton NE, Collins A: A metric linkage disequilibrium map of a human chromosome. Ann Hum Genet 2003; 67: 487-494. (Pubitemid 38016709)
    • (2003) Annals of Human Genetics , vol.67 , Issue.6 , pp. 487-494
    • Tapper, W.J.1    Maniatis, N.2    Morton, N.E.3    Collins, A.4
  • 48
    • 46749129459 scopus 로고    scopus 로고
    • The estimator of the optimal measure of allelic association: Mean variance and probability distribution when the sample size tends to infinite
    • Mangin B, Garnier-Géré P, Cierco-Ayrolles C: The estimator of the optimal measure of allelic association: mean, variance and probability distribution when the sample size tends to infinite. Stat Appl Genet Mol Biol 2008; 7: 1-23.
    • (2008) Stat. Appl. Genet. Mol. Biol. , vol.7 , pp. 1-23
    • Mangin, B.1    Garnier-Géré, P.2    Cierco-Ayrolles, C.3
  • 49
    • 0002481078 scopus 로고    scopus 로고
    • Linkage disequilibrium and recombination
    • Bishop BD, Cannings C eds New York, Willey & Sons
    • Hudson RR: Linkage disequilibrium and recombination; in Bishop BD, Cannings C (eds): Handbook of Statistical Genetics. New York, Willey & Sons, 2001, pp 309-324.
    • (2001) Handbook of Statistical Genetics , pp. 309-324
    • Hudson, R.R.1


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