Bibliography:
Linkage Disequilibrium Analysis
(2000)
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+ 2000

  1. quantitative-trait
    TDT
    GR Abecasis, LR Cardon, WO Cookson (2000), "A general test of association for quantitative traits in nuclear families ", American Journal of Human Genetics, 66:279-292.
    [PDF] [QTDT program]

  2. GR Abecasis, WO Cookson (2000), "GOLD - graphic overview of linkage disequilibrium", Bioinformatics, 16(2):182-183.
    [GOLD program]

  3. TDT
    GR Abecasis, WOC Cookson, LR Cardon (2000), "Pedigree tests of transmission disequilibrium", European Journal of Human Genetics, 8(7):545-551.

  4. Silviu-Alin Bacanu, B Devlin, Kathryn Roeder (2000), "The power of genomic control", American Journal of Human Genetics , 66:1933-1944.
    [PDF]

  5. NH Barton (2000), "Genetic hitchhiking", Philosophical Transactions of Royal Society of London: B. Biological Sciences, 355:1553-1562.

  6. TDT
    RA Betensky, D Rabinowitz (2000), "Simple approximations for the maximal transmission/disequilibrium test with a multi-allelic marker", Annals of Human Genetics, 64:567-574.

  7. Michael Boehnke (2000), "A look at linkage disequilibrium" (news & views), Nature Genetics, 25:246-247.

  8. population-structure
    C Bourgain, E Genin, H Quesneville, F Clerget-Darpoux (2000), "Search for multifactorial disease susceptibility genes in founder populations", Annals of Human Genetics, 64:255-265.
    [PDF]

  9. quantitative-trait
    LR Cardon (2000), "A sib-pair regression model of linkage disequilibrium for quantitative traits", Human Heredity, 50:350-358.

  10. quantitative-trait
    LR Cardon, GR Abecasis (2000), "Tests of linkage disequilibrium for quantitative traits", GeneScreen, 1:55-57.

  11. ACL Cervino, AVS Hill (2000), "Comparison of tests for association and linkage in incomplete families", American Journal of Human Genetics ,67:120-132.
    [PDF]

  12. CH Chang, WC Lee (2000), "Estimating genotype relative risks in case-parental control studies: a Mantel-Haenszel approach", Chinese Journal of Public Health, 19:485-490.

  13. KH Cheung, PL Miller, JR Kidd, KK Kidd, MV Osier, AJ Pakstis (2000), "ALFRED: A web-accessible allele frequency database", Pacific Symposium on Biocomputing, 5:636-647.
    [ALFRED database]

  14. V Choulakian, S Mahdi (2000), "A new statistic for the analysis of association between trait and polymorphic marker loci", Mathematical Biosciences , 164(2):139-145.

  15. D Clayton (2000), "Linkage disequilibrium mapping of disease susceptibility genes in human populations", International Statistical Review, 68:23-43.

  16. A Collins (2000), "Linkage disequilibrium mapping: using single nucleotide polymorphisms -- which population?" Pacific Symposium on Biocomputing, 5:648-659.

  17. HE Collins, H Li, SE Inda, J Anderson, K Laiho, J Tuomilehto, MF Seldin (2000), "A simple and accurate method for determination of microsatellite total allele content differences between DNA pools", Human Genetics, 106:218-226.

  18. quantitative-trait
    HW Deng, WM Chen, RR Recker (2000), "QTL fine mapping by measuring and testing for Hardy-Weinberg and linkage disequilibrium at a series of linked marker loci in extreme samples of populations". American Journal of Human Genetics , 66:1027-1045.
    [PDF]

  19. B Devlin, K Roeder, L Wasserman (2005), "Genomic control for association studies: a semiparametric test to detect excess-haplotype sharing", Biostatistics, 1(4):369-387.

  20. TDT
    F Dudbridge, BPC Koeleman, JA Todd, DG Clayton (2000), "Unbiased application of the transmission/disequilibrium test to multilocus haplotypes", (report) American Journal of Human Genetics , 66:2009-2012.
    [PDF]

  21. population-structure
    I A Eaves, T R Merriman, R A Barber, S Nutland, E Tuomilehto-Wolf, J Tuomilehto, F Cucca, J A Todd (2000), "The genetically isolated populations of Finland and Sardinia may not be a panacea for linkage disequilibrium mapping of common disease genes", Nature Genetics, 25:320-323.

  22. F Farnir, W Coppieters, JJ Arranz, P Berzi, N Cambisano, B Grisart, L Karim, F Marcq, L Moreau, M Mni, C Nezer, P Simon, P Vanmanshoven, D Wagenaar, M Georges (2000), "Extensive genome-wide linkage disequilibrium in cattle", Genome Research, 10(2):220-227.

  23. Daniele Fallin, Nicholas J Schork (2000), "Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data", American Journal of Human Genetics, 67:947-959.

  24. M Fullerton, AG Clark, KM Weiss, DA Nickerson, SL Taylor, JH Stengard, V Salomaa, E Vartiainen, M Perola, E Boerwinkle, CF Sing (2000), "Apolipoprotein E variation at the sequence haplotype level: implications for the origin and maintenance of a major human polymorphism", American Journal of Human Genetics, 67:881-900.
    [PDF]

  25. population-structure
    KAB Goddard, PJ Hopkins, JM Hall, JS Witte (2000), "Linkage disequilibrium and allele-frequency distributions for 114 single-nucleotide polymorphisms in five populations", American Journal of Human Genetics, 66:216-234.
    [PDF]

  26. population-structure
    R Gonser, P Donnelly, G Nicholson, A Di Rienzo (2000), "Microsatellite mutations and inferences about human evolution", Genetics, 154:1793-1807.

  27. D Gordon, SM Leal, SC Heath, J Ott (2000), "An analytic solution to single nucleotide polymorphism error-detection rates in nuclear families: implications for study design", Pacific Symposium on Biocomputing, 5:660-671.

  28. HHH Goring, JD Terwilliger (2000), "Linkage analysis in the presence of errors III: marker loci and their map as nuisance parameters", American Journal of Human Genetics ,66:1298-1309.
    [PDF]

  29. TDT
    HHH Goring, JD Terwilliger (2000), "Linkage analysis in the presence of errors IV: joint pseudomarker analysis of linkage and/or linkage disequilibrium on a mixture of pedigrees and singletons when the mode of inheritance cannot be accurately specified", American Journal of Human Genetics , 66:1310-1327.
    [PDF]

  30. J Graham, EA Thompson (2000), "A coalescent model of ancestry for a rare allele", Genetics, 156:375-384.

  31. IC Gray, DA Campbell, NK Spurr (2000), "Single nucleotide polymorphisms as tools in human genetics", Human Molecular Genetics, 9:2403-2408.
    [PDF]

  32. D Gusfield (2000), "Inference of haplotypes from samples of diploid populations", Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, ?:?-?.

  33. B Haubold, RR Hudson (2000), "LIAN 3.0: detecting linkage disequilibrium in multilocus data", Bioinformatics, 16(9):847-848.
    [ abstract]

  34. TDT
    GYF Ho, JE Bailey-Wilson (2000), "The transmission/disequilibrium test for linkage on the X chromosome", American Journal of Human Genetics , 66:1158-1160.
    [PDF]

  35. J Hoh, SE Hodge (2000), "A measure of phase ambiguity in pairs of SNPs in the presence of linkage disequilibrium", Human Heredity, 50(6):359-364.

  36. TDT
    S Horvath, NM Laird, M Knapp (2000), "The transmission/disequilibrium test and parental-genotype reconstruction for X-chromosomal markers", American Journal of Human Genetics , 66:1161-1167.
    [PDF]

  37. TDT
    L Hsu, LP Zhao, C Aragaki (2000), "A note on a conditional-likelihood approach for family-based association studies of candidate genes", Human Heredity, 50(3):194-200.

  38. LB Jorde (2000), "Linkage disequilibrium and the search for complex disease genes", Genome Research, 10(10):1435-1444.

  39. population-structure
    LB Jorde, WS Watkins, J Kere, D Nyman, AW Eriksson (2000), "Gene mapping in isolated populations: new roles for old friends?", Human Heredity, 50:57-65.

  40. MJ Khoury, J Little (2001), "Human genome epidemiologic reviews: the beginning of something HuGE", American Journal of Epidemiology, 151:2-3.
    [ HuGE net]

  41. G Kirov, N Williams, P Sham, N Craddock, MJ Owen (2000), "Pooled genotyping of microsatellite markers in parent-offspring trios", Genome Research, 10:105-115.

  42. HG Koch, J McClay, EW Loh, S Higuchi1, JH Zhao, P Sham, D Ball, IW Craig (2000), "Allele association studies with SSR and SNP markers at known physical distances within a 1 Mb region embracing the ALDH2 locus in the Japanese, demonstrates linkage disequilibrium extending up to 400 kb", Human Molecular Genetics, 9:2993-2999.
    [PDF]

  43. TDT
    BPC Koeleman, F Dudbridge, HJ Cordell, JA Todd (2000), "Adaptation of the extended transmission/disequilibrium test to distinguish disease association of multiple loci: the conditional extended transmission/disequilibrium test", Annals of Human Genetics, 64:207-213.
    [PDF ]

  44. TDT
    Nan M Laird, Steve Horvath, Xin Xu (2000), "Implementing a unified approach to family-based tests of association", Genetic Epidemiology, 19:S36-S42.

  45. JC Lam, K Roeder, B Devlin (2000), "Haplotype fine mapping by evolutionary trees", American Journal of Human Genetics, 66(2):659-673.
    [PDF] [FINEMAP program]

  46. TDT
    WC Lee, CH Chang (2000), "Estimating genotype relative risks in case-parental control studies: an optimal weighting approach", American Journal of Epidemiology, 152:487-492.

  47. Hongzhe Li, Juanjuan Fan (2000), "A general test of association for complex diseases with variable age of onset", Genetic Epidemiology, 19:S43-S49.

  48. TDT
    H Li, L Hsu (2000), "Effects of age at onset on the power of the affected sib pair and transmission/disequilibrium tests", Annals of Human Genetics, 64:239-254.

  49. applications
    T Li, D ball, J Zhao, RM Murray, X Liu, PC Sham, DA Collier (2000), "Family-based linkage disequilibrium mapping using SNP marker haplotypes: application to a potential locus for schizophrenia at chromosome 22q11", Molecular Psychiatry, 5(1):77-84.

  50. TDT
    KL Lunetta, SV Faraone, J Biederman, NM Laird (2000), "Family-based tests of association and linkage that use unaffected sibs, covariates, and interactions", American Journal of Human Genetics, 66(2):605-614.
    [PDF]

  51. CJ MacLean, RB Martin, PC Sham, RE Straub, KS Kendler (2000), "The trimmed-haplotype test for linkage disequilibrium", American Journal of Human Genetics, 66:1062-1075.
    [PDF]

  52. TDT
    ER Martin, SA Monks, LL Warren, NL Kaplan (2000), "A test for linkage and association in general pedigrees: the pedigree disequilibrium test", American Journal of Human Genetics, 67:146-154.
    [PDF]

  53. TDT
    Palph McGinnis (2000), "General equations for Pt, Ps, and the power of the TDT and the affected-sib-pair Test", American Journal of Human Genetics, 67(5):1340-1347.
    [PDF]

  54. LM McIntyre, ER Martin, KL Simonsen, NL Kaplan (2000), "Circumventing multiple testing: a multilocus Monte Carlo approach to testing for association", Genetic Epidemiology, 19(1):18-29.

  55. PM McKeigue (2000), "Multipoint admixture mapping", Genetic Epidemiology, 19(4):464-467.

  56. PM McKeigue (2000), "Efficiency of estimation of haplotype frequencies: use of marker phenotypes of unrelated individuals versus counting of phase-known gametes", American Journal of Human Genetics, 67(6):1626-1627.
    [PDF]

  57. PM McKeigue, JR Carpenter, EJ Parra, MD Shriver (2000), "Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations", Annals of Human Genetics, 64:171-186.
    [PDF]

  58. Kalim U Mirand, Edwin M Southern (2000), "Sequence variation in genes and genomic DNA: methods for large-scale analysis", Annual Review of Genomics and Human Genetics, 1:329-360.

  59. Laura E Mitchell (2000), "Relationship between case-control studies and the transmission/disequilibrium test", Genetic Epidemiology, 19:193-201.

  60. quantitative-trait
    TDT
    SA Monks, NL Kaplan (2000), "Removing the sampling restrictions from family-based tests of association for a quantitative-trait locus", American Journal of Human Genetics, 66(2):576-592.
    [PDF]

  61. TDT
    AP Morris, JC Whittaker (2000), "Fine scale association mapping of disease loci using simplex families", Annals of Human Genetics, 64:223-237.
    [PDF]

  62. AP Morris, JC Whittaker, DJ Balding (2000), "Bayesian fine-scale mapping of disease loci, by hidden Markov models", American Journal of Human Genetics,67(1):155-169.
    [html]

  63. Michael W Nachman, Susan L. Crowell (2000), "Estimate of the mutation rate per nucleotide in humans", Genetics, 156:297-304.

  64. M Nordborg (2000), "Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization", Genetics, 154(2):923-929.

  65. Stephen J. O'Brien, George W. Nelson, Cheryl A. Winkler, Michael W. Smith (2000), "Polygenic and multifactorial disease gene association in man: lessons from AIDS", Annual Review of Genetics, 34:563-591.

  66. J Ott (2000), "Predicting the range of linkage disequilibrium", Proceedings of National Academy of Sciences, 97(1):2-3.

  67. applications
    LJ Palmer, WOCM Cookson (2000), "Genomic approaches to understanding Asthma", Genome Research, 10:1280-1287.

  68. BA Payseur, MW Nachman (2000), "Microsatellite variation and recombination rate in the human genome", Genetics, 156:1285-1298.
    [abstract]

  69. population-structure
    Leena Peltonen (2000), "Positional cloning of disease genes: advantages of genetic isolates", Human Heredity, 50:66-75.

  70. population-structure
    L Peltonen, A Palotie, K Lange (2000), "Use of population isolates for mapping complex traits", Nature Reviews Genetics, 1:182-190.
    [PDF]

  71. population-structure
    JK Pritchard, M Stephens, P Donnelly (2000), "Inference of population structure using multilocus genotype data", Genetics, 155:945-959.

  72. JK Pritchard, M Stephens, NA Rosenberg, P Donnelly (2000), "Association mapping in structured populations", American Journal of Human Genetics,67:170-181.
    [PDF]

  73. D Rabinowitz, N Laird (2000), "A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information", Human Heredity, 50(4):227-233.

  74. Bruce Rannala, Montgomery Slatkin (2000), "Methods for multipoint disease mapping using linkage disequilibrium", Genetic Epidemiology, 19:S71-S77.

  75. N Risch (2000), "Searching for genetic determinants in the new millennium", Nature, 405:847-856.

  76. TDT
    Daniel J Schaid, Charles M Rowland (2000), "Robust transmission regression models for linkage and association", Genetic Epidemiology, 19:S78-S84.

  77. Nicholas J Schork, Swapan K Nath, Daniele Fallin, Aravinda Chakravarti (2000), "Linkage disequilibrium analysis of biallelic DNA markers, human quantitative trait loci, and threshold-defined case and control subjects", American Journal of Human Genetics,67(5):1208-1218.
    [PDF]

  78. TDT
    Laura Scott, John J Rogus (2000), "Using unaffected child trios to test for transmission distortion", Genetic Epidemiology, 19:381-394.

  79. quantitative-trait
    PC Sham, SS Cherny, S Purcell, JK Hewitt (2000), "Power of linkage versus association analysis of quantitative traits, by use of variance-components models, for sibship data", American Journal of Human Genetics , 66:1616-1630.
    [PDF]

  80. PC Sham, JH Zhao, D Curtis (2000), "The effect of marker characteristics on the power to detect linkage disequilibrium due to single or multiple ancestral mutations", Annals of Human Genetics, 64:161-169.
    [PDF]

  81. TDT
    PC Sham, JH Zhao, I Waldman, D Curtis (2000), "Should ambiguous trios for the TDT be discarded?", Annals of Human Genetics, 64:575-576.

  82. KD Siegmund, B Langholz, P Kraft, DC Thoms (2000), "Testing linkage disequilibrium in sibships", American Journal of Human Genetics , 67:244-248.
    [PDF]

  83. EK Silverman, LJ Palmer (2000), "Case-control association studies for the genetic of complex respiratory diseases", American Journal of Respiratory Cell Molecular and Biology, 22:645-648.

  84. JS Sinsheimer, J Blangero, K Lange (2000), "Gamete-competition models", American Journal of Human Genetics , 66:1168-1172.
    [PDF]

  85. TDT
    SL Slager, J Huang, VJ Vieland (2000), "Effect of allelic heterogeneity on the power of the transmission disequilibrium test", Genetic Epidemiology, 18(2):143-156.

  86. Montgomery Slatkin, Bruce Rannala (2000), "Estimating allele age", Annual Review of Genomics and Human Genetics, 1:225-249.
    [ abstract]

  87. quantitative-trait
    TDT
    FZ Sun, WD Flanders, QH Yang, HY Zhao (2000), "Transmission/disequilibrium tests for quantitative traits", Annals of Human Genetics, 64:555-565.

  88. haplotype-block
    P Taillon-Miller, I Bauer-Sardiņa, N L Saccone, J Putzel, T Laitinen, A Cao, J Kere, G Pilia, J P Rice & P -Y Kwok (2000), "Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28", Nature Genetics, 25:324-328.

  89. JD Terwilliger (2000), "Inflated false-positive rates in Hardy-Weinberg and linkage-equilibrium tests are due to sampling on the basis of rate familial phenotypes in finite populations" (letter to the editor), American Journal of Human Genetics, 67(1):258-259.
    [PDF]

  90. JD Terwilliger, HH Goring (2000), "Gene mapping in the 20th and 21st centuries: statistical methods, data analysis, and experimental design", Human Biology, 72(1):63-132.

  91. SA Tishkoff, AJ Pakstis, G Ruano, KK Kidd (2000), "The accuracy of statistical methods for estimation of haplotype frequencies: an example from the CD4 locus", American Journal of Human Genetics , 67(2):518-522.

  92. HTT Toivonen, P Onkamo, K Vasko, V Ollikainen, P Sevon, H Mannila, M Herr, J Kere (2000), "Data mining applied to linkage disequilibrium mapping", American Journal of Human Genetics , 67:133-145.
    [PDF] [ supplement material from the authors' site]

  93. TDT
    IP Tu, RR Balise, AS Whittemore (2000), "Detection of disease genes by use of family data. II. application to nuclear families", American Journal of Human Genetics , 66:1341-1350.
    [PDF]

  94. quantitative-trait
    Edwin JCG van den Oord (2000), "Framework for identifying quantitative trait loci in association studies using structural equation modeling", Genetic Epidemiology, 18:341-359.

  95. TDT
    EJCG van den Oord, JK Vermunt (2000), "Testing for linkage disequilibrium, maternal effects, and imprinting with (in)complete case-parent triads, by use of the computer program LEM ", American Journal of Human Genetics, 66:335-338.
    [PDF]

  96. T Varilo, M Laan, I Hovatta, V Wiebe, JD Terwilliger, L Peltonen (2000), "Linkage disequilibrium in isolated populations: Finland and a young sub-population of Kuusamo", European Journal of Human Genetics, 8(8):604-612.

  97. S Wacholder, N Rothman, N Caporaso (2000), "Population stratification in epidemiologic studies of common genetic variants and cancer: quantification of bias", Journal of National Cancer Institute, 92:1151-1158.

  98. TDT
    D Wang, FZ Sun (2000), "Sample sizes for the transmission/disequilibrium tests: the TDT, S-TDT and 1-TDT", Communications in Statistics - Theory and Methods, 29:1129-1142.

  99. KM Weiss, JD Terwilliger (2000), "How many diseases does it take to map a gene with SNPs?" Nature Genetics, 26(2):151-157.
    [PDF]

  100. TDT
    JC Whittaker, MC Denham, AP Morris (2000), "The problems of using the transmission/disequilibrium test to infer tight linkage" (report), American Journal of Human Genetics ,67:523-526.
    [PDF]

  101. TDT
    AS Whittemore, IP Tu (2000), "Detection of disease genes by use of family data. I. likelihood-based theory", American Journal of Human Genetics , 66:1328-1340.
    [PDF]

  102. TDT
    J Wicks (2000), "Exploiting excess sharing: a more powerful test of linkage for affected sib pairs than the transmission/disequilibrium test" (report), American Journal of Human Genetics , 66:2005-2008.
    [PDF]

  103. TDT
    J Wicks, SR Wilson (2000), "Evaluating linkage and linkage disequilibrium: use of excess sharing and transmission disequilibrium methods in affected sib pairs", Annals of Human Genetics, 64:419-432.
    [PDF]

  104. haplotype-block
    Thomas Wiehe, Joanna Mountain, Peter Parham, Montgomery Slatkin (2000), "Distinguishing recombination and intragenic gene conversion by linkage disequilibrium patterns", Genetical Research, 75:61-73.

  105. M Xiong, J Akey, L Jin (2000), "The haplotype linkage disequilibrium test for genome-wide screens: its power and study", Pacific Symposium on Biocomputing, 5:672-681.

  106. Momiao Xiong, Li Jin (2000), "Combined linkage and linkage disequilibrium mapping for genome screens", Genetic Epidemiology, 19:211-234.

  107. quantitative-trait
    Momiao Xiong, Sunwei Guo (2000), "Multiple regression approach to mapping of quantitative trait loci (QTL) based on sib-pair data: a theoretical analysis", Annals of Statistics, 28:1245-1278.

  108. Heping Zhang, George Bonney (2000), "Use of classification trees for association studies", Genetic Epidemiology , 19:323-332.

  109. Shuanglin Zhang, Hongyu Zhao (2000), "Linkage disequilibrium mapping in populations of variable size using the decay of haplotype sharing and a stepwise-mutation model", Genetic Epidemiology, 19:S99-S105.

  110. TDT
    H Zhao (2000), "Family-based association studies", Statistical Methods in Medical Research, 9:563-587.

  111. JH Zhao, D Curtis, PC Sham (2000), "Model-free analysis and permutation tests for allelic association", Human Heredity, 50:133-139.
    [EH+ program]

  112. TDT
    H Zhao, S Zhang, KR Merikangas, M Trixler, DB Wildenauer, F Sun, KK Kidd (2000), "Transmission/disequilibrium tests using multiple-tightly linked markers", American Journal of Human Genetics, 67:936-946.
    [PDF]

  113. S Zollner, A von Haeseler (2000), "A coalescent approach to study linkage disequilibrium between single-nucleotide polymorphisms", American Journal of Human Genetics, 66(2):615-628.
    [PDF]

  114. quantitative-trait
    X Zhu, RC Elston (2000), "Power comparison of regression methods to test quantitative traits for association and linkage", Genetic Epidemiology,18:322-330.

  115. ME Zwick, DJ Cutler, A Chakravarti (2000), "Patterns of genetic variation in Mendelian and complex traits", Annual Review of Genomics and Human Genetics, 1:387-407