Linkage Disequilibrium in Humans: Models and Data

Abecasis, 2001, Extent and distribution of linkage disequilibrium in three genomic regions, Am J Hum Genet, 68, 191, 10.1086/316944

Andolfatto, 2001, Inversion polymorphisms and nucleotide variability in Drosophila, Genet Res, 77, 1, 10.1017/S0016672301004955

Andolfatto, 1998, The effect of gene conversion on intralocus associations, Genetics, 148, 1397, 10.1093/genetics/148.3.1397

Awadalla, 1999, Linkage disequilibrium and recombination in hominid mitochondrial DNA, Science, 286, 2524, 10.1126/science.286.5449.2524

Broman, 1999, Long homozygous chromosomal segments in reference families from the Centre d’Etude du Polymorphisme Humain, Am J Hum Genet, 65, 1493, 10.1086/302661

Cargill, 1999, Characterization of single-nucleotide polymorphisms in coding regions of human genes, Nat Genet, 22, 231, 10.1038/10290

Chakraborty, 1988, Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci, Proc Natl Acad Sci USA, 85, 9119, 10.1073/pnas.85.23.9119

Chakravarti, 1984, Nonuniform recombination within the human β-globin gene cluster, Am J Hum Genet, 36, 1239

Clark, 1999, The size distribution of homozygous segments in the human genome, Am J Hum Genet, 65, 1489, 10.1086/302668

Clark, 1998, Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase, Am J Hum Genet, 63, 595, 10.1086/301977

Devlin, 1995, A comparison of linkage disequilibrium measures for fine-scale mapping, Genomics, 29, 311, 10.1006/geno.1995.9003

Dunning, 2000, The extent of linkage disequilibrium in four populations with distinct demographic histories, Am J Hum Genet, 67, 1544, 10.1086/316906

Eaves, 2000, The genetically isolated populations of Finland and Sardinia may not be a panacea for linkage disequilibrium mapping of common disease genes, Nat Genet, 25, 320, 10.1038/77091

Eisenbarth, 2000, An isochore transition in the NF1 gene region coincides with a switch in the extent of linkage disequilibrium, Am J Hum Genet, 67, 873, 10.1086/303085

Giglio, 2001, Olfactory receptor-gene clusters, genomic-inversion polymorphisms, and common chromosome rearrangements, Am J Hum Genet, 68, 874, 10.1086/319506

Gordon, 2000, Significant evidence for linage disequilibrium over a 5-cM region among Afrikaners, Genomics, 66, 87, 10.1006/geno.2000.6190

Griffiths, 1996, Ancestral inference from samples of DNA sequences with recombination, J Comput Biol, 3, 479, 10.1089/cmb.1996.3.479

Harding, 1997, Archaic African and Asian lineages in the genetic ancestry of modern humans, Am J Hum Genet, 60, 772

Hartl, 1997

Hey, 1999, The neutralist, the fly, and the selectionist, Trends Ecol Evol, 14, 35, 10.1016/S0169-5347(98)01497-9

Horikawa, 2000, Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus, Nat Genet, 26, 163, 10.1038/79876

Hudson, 1993, The how and why of generating gene genealogies, 23

Hudson, 2001, Linkage disequilibrium and recombination, 309

Huttley, 1999, A scan for linkage disequilibrium across the human genome, Genetics, 152, 1711, 10.1093/genetics/152.4.1711

International SNP Map Working Group, 2001, A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms, Nature, 409, 928, 10.1038/35057149

Jorde, 2000, Linkage disequilibrium and the search for complex disease genes, Genome Res, 10, 1435, 10.1101/gr.144500

Kaplan, 1989, The “hitchhiking effect” revisited, Genetics, 123, 887, 10.1093/genetics/123.4.887

Kelly, 2000, Molecular evolution near a two-locus balanced polymorphism, J Theor Biol, 204, 83, 10.1006/jtbi.2000.2003

Kidd, 1998, A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus, Hum Genet, 103, 211, 10.1007/s004390050809

Kruglyak, 1999, Prospects for whole-genome linkage disequilibrium mapping of common disease genes, Nat Genet, 22, 139, 10.1038/9642

Kuhner, 2000, Maximum likelihood estimation of recombination rates from population data, Genetics, 156, 1393, 10.1093/genetics/156.3.1393

Laan, 1997, Demographic history and linkage disequilibrium in human populations, Nat Genet, 17, 435, 10.1038/ng1297-435

Lewontin, 1964, The interaction of selection and linkage. I. General considerations: heterotic models, Genetics, 49, 49, 10.1093/genetics/49.1.49

Li, 1991, Low nucleotide diversity in man, Genetics, 129, 513, 10.1093/genetics/129.2.513

Lien, 2000, Evidence for heterogeneity in recombination in the human pseudoautosomal region: high resolution analysis by sperm typing and radiation-hybrid mapping, Am J Hum Genet, 66, 557, 10.1086/302754

Long, 1999, The power of association studies to detect the contribution of candidate gene loci to variation in complex traits, Genome Res, 9, 720, 10.1101/gr.9.8.720

Martin, 1999, Sperm chromosome analysis in a man heterozygous for a paracentric inversion of chromosome 14 (q24.1q32.1), Am J Hum Genet, 64, 1480, 10.1086/302363

McKeigue, 1997, Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admixed populations, Am J Hum Genet, 60, 188

McPeek, 1999, Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping, Am J Hum Genet, 65, 858, 10.1086/302537

Morris, 2000, Bayesian fine-scale mapping of disease loci, by hidden Markov models, Am J Hum Genet, 67, 155, 10.1086/302956

Nachman, 2000, Estimate of the mutation rate per nucleotide in humans, Genetics, 156, 297, 10.1093/genetics/156.1.297

Nicolas, 1998, Relationship between transcription and initiation of meiotic recombination: towards chromatin accessibility, Proc Natl Acad Sci USA, 6, 87, 10.1073/pnas.95.1.87

Nielsen, 2000, Estimation of population parameters and recombination rates from single nucleotide polymorphisms, Genetics, 154, 931, 10.1093/genetics/154.2.931

Nordborg, 2000, Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization, Genetics, 154, 923, 10.1093/genetics/154.2.923

Nordborg, 2001, Coalescent theory, 179

Payseur, 2000, Microsatellite variation and recombination rate in the human genome, Genetics, 156, 1285, 10.1093/genetics/156.3.1285

Peterson, 1995, The distribution of linkage disequilibrium over anonymous genome regions, Hum Mol Genet, 4, 887, 10.1093/hmg/4.5.887

Pfaff, 2001, Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium, Am J Hum Genet, 68, 198, 10.1086/316935

Pritchard, 2001, Are rare variants responsible for susceptibility to common diseases?, Am J Hum Genet, 69, 124, 10.1086/321272

Pritchard, 1999, Use of unlinked genetic markers to detect population stratification in association studies, Am J Hum Genet, 65, 220, 10.1086/302449

Pritchard, 1999, Population growth of human Y chromosomes: a study of Y chromosome microsatellites, Mol Biol Evol, 16, 1791, 10.1093/oxfordjournals.molbev.a026091

Przeworski, 2000, Adjusting the focus on human variation, Trends Genet, 16, 296, 10.1016/S0168-9525(00)02030-8

Przeworski, 2001, Why is there so little intragenic linkage disequilibrium in humans?, Genet Res, 77, 143, 10.1017/S0016672301004967

Reich, 2001, Linkage disequilibrium in the human genome, Nature, 411, 199, 10.1038/35075590

Risch, 1996, The future of genetic studies of complex human diseases, Science, 273, 1516, 10.1126/science.273.5281.1516

Roberts, 1976, The genetics of chromosome aberration, 67

Saunier, 2000, Characterization of the NPHP1 locus: mutational mechanisms involved in deletions in familial juvenile nephronophthisis, Am J Hum Genet, 66, 778, 10.1086/302819

Service, 2001, The genome-wide distribution of background linkage disequilibrium in a population isolate, Hum Mol Genet, 10, 545, 10.1093/hmg/10.5.545

Slatkin, 1994, Linkage disequilibrium in growing and stable populations, Genetics, 137, 331, 10.1093/genetics/137.1.331

Small, 1997, Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats, Nat Genet, 16, 96, 10.1038/ng0597-96

Stephens M (2001) Inference under the coalescent. In: Balding D, Bishop M, Cannings C (eds) Handbook of statistical genetics.

Taillon-Miller, 2000, Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28, Nat Genet, 25, 324, 10.1038/77100

Tajima, 1989, The effect of change in population size on DNA polymorphism, Genetics, 123, 597, 10.1093/genetics/123.3.597

Tilford, 2001, A physical map of the Y chromosome, Nature, 409, 943, 10.1038/35057170

Tishkoff, 1996, Global patterns of linkage disequilibrium at the CD4 locus and modern human origins, Science, 271, 1380, 10.1126/science.271.5254.1380

Wall, 2000, A comparison of estimators of the population recombination rate, Mol Biol Evol, 17, 156, 10.1093/oxfordjournals.molbev.a026228

Wall, 2000, When did the human population start increasing?, Genetics, 155, 1865, 10.1093/genetics/155.4.1865

Weir, 1996

Wilson, 2000, Consistent long-range linkage disequilibrium generated by admixture in a Bantu-Semitic hybrid population, Am J Hum Genet, 67, 926, 10.1086/303083

Wright, 1951, The genetical structure of populations, Ann Eugenics, 15, 323, 10.1111/j.1469-1809.1949.tb02451.x

Yu, 2001, Comparisons of human genetic and sequence-based physical maps, Nature, 409, 951, 10.1038/35057185

Zavattari, 2000, Major factors influencing linkage disequilibrium by analysis of different chromosome regions in distinct populations: demography, chromosome recombination frequency and selection, Hum Mol Genet, 9, 2947, 10.1093/hmg/9.20.2947