Selecting a Maximally Informative Set of Single-Nucleotide Polymorphisms for Association Analyses Using Linkage Disequilibrium

Ackerman, 2003, Haplotypic analysis of the TNF locus by association efficiency and entropy, Genome Biol, 4, R24, 10.1186/gb-2003-4-4-r24

Botstein, 2003, Discovering genotypes underlying human phenotypes: past successes for Mendelian disease, future approaches for complex disease, Nat Genet, 228, 10.1038/ng1090

Cambien, 1999, Sequence diversity in 36 candidate genes for cardiovascular disorders, Am J Hum Genet, 65, 183, 10.1086/302448

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

Carlson, 2003, Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans, Nat Genet, 33, 518, 10.1038/ng1128

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

Collins, 1997, Variations on a theme: cataloging human DNA sequence variation, Science, 278, 1580, 10.1126/science.278.5343.1580

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

Ewens, 1979

Ewing, 1998, Base-calling of automated sequencer traces using Phred. II. Error probabilities, Genome Res, 8, 186, 10.1101/gr.8.3.186

Ewing, 1998, Base-calling of automated sequencer traces using Phred. I. Accuracy assessment, Genome Res, 8, 175, 10.1101/gr.8.3.175

Gabriel, 2002, The structure of haplotype blocks in the human genome, Science, 296, 2225, 10.1126/science.1069424

Gordon, 1998, Consed: a graphical tool for sequence finishing, Genome Res, 8, 195, 10.1101/gr.8.3.195

Halushka, 1999, Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis, Nat Genet, 22, 239, 10.1038/10297

Hill, 1974, Estimation of linkage disequilibrium in randomly mating populations, Heredity, 33, 229, 10.1038/hdy.1974.89

Hill, 1968, The effects of inbreeding at loci with heterozygote advantage, Genetics, 60, 615, 10.1093/genetics/60.3.615

Hudson, 2002, Generating samples under a Wright-Fisher neutral model of genetic variation, Bioinformatics, 18, 337, 10.1093/bioinformatics/18.2.337

Jeffreys, 2001, Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex, Nat Genet, 29, 217, 10.1038/ng1001-217

Johnson, 2001, Haplotype tagging for the identification of common disease genes, Nat Genet, 29, 233, 10.1038/ng1001-233

Ke, 2003, Efficient selective screening of haplotype tag SNPs, Bioinformatics, 19, 287, 10.1093/bioinformatics/19.2.287

Kruglyak, 2001, Variation is the spice of life, Nat Genet, 27, 234, 10.1038/85776

Lander, 2001, Initial sequencing and analysis of the human genome, Nature, 409, 860, 10.1038/35057062

Livak, 1999, Allelic discrimination using fluorogenic probes and the 5′ nuclease assay, Genet Anal, 14, 143, 10.1016/S1050-3862(98)00019-9

Meng, 2003, Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes, Am J Hum Genet, 73, 115, 10.1086/376561

Nickerson, 2000, Sequence diversity and large-scale typing of SNPs in the human apolipoprotein E gene, Genome Res, 10, 1532, 10.1101/gr.146900

Nickerson, 1997, PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing, Nucleic Acids Res, 25, 2745, 10.1093/nar/25.14.2745

Patil, 2001, Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21, Science, 294, 1719, 10.1126/science.1065573

Pritchard, 2001, Linkage disequilibrium in humans: models and data, Am J Hum Genet, 69, 1, 10.1086/321275

Rieder, 1999, Sequence variation in the human angiotensin converting enzyme, Nat Genet, 22, 59, 10.1038/8760

Sachidanandam, 2001, A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms, Nature, 409, 928, 10.1038/35057149

Stephens, 2001, Haplotype variation and linkage disequilibrium in 313 human genes, Science, 293, 489, 10.1126/science.1059431

Stephens, 2001, A new statistical method for haplotype reconstruction from population data, Am J Hum Genet, 68, 978, 10.1086/319501

Stram, 2003, Choosing haplotype-tagging SNPs based on unphased genotype data using a preliminary sample of unrelated subjects with an example from the multiethnic cohort study, Hum Hered, 55, 27, 10.1159/000071807

Subrahmanyan, 2001, Sequence variation and linkage disequilibrium in the human T-cell receptor β(TCRB) locus, Am J Hum Genet, 69, 381, 10.1086/321297

Venter, 2001, The sequence of the human genome, Science, 291, 1304, 10.1126/science.1058040

Wang, 1998, Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome, Science, 280, 1077, 10.1126/science.280.5366.1077

Weale, 2003, Selection and evaluation of tagging SNPs in the neuronal-sodium-channel gene SCN1A: implications for linkage-disequilibrium gene mapping, Am J Hum Genet, 73, 551, 10.1086/378098

Wright, 1931, Evolution in Mendelian populations, Genetics, 16, 97, 10.1093/genetics/16.2.97

Zhang, 2002, Haplotype block structure and its applications to association studies: power and study designs, Am J Hum Genet, 71, 1386, 10.1086/344780

Zhang, 2002, A dynamic programming algorithm for haplotype block partitioning, Proc Natl Acad Sci USA, 99, 7335, 10.1073/pnas.102186799

Zhang, 2003, HaploBlockFinder: haplotype block analyses, Bioinformatics, 19, 1300, 10.1093/bioinformatics/btg142