Genetic association studies of complex traits: design and analysis issues
Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis - Tập 573 - Trang 54-69 - 2005
Tài liệu tham khảo
Clarke, 1956, ABO blood groups and secretor character in duodenal ulcer: population and sibship studies, BMJ, 725, 10.1136/bmj.2.4995.725
Harris, 1970, Enzyme and protein diversity in human populations
Redondo, 2001, Genetics of type 1A diabetes, Recent Prog. Horm. Res., 56, 69, 10.1210/rp.56.1.69
Hirschhorn, 2002, A comprehensive review of genetic association studies, Genet. Med., 4, 45, 10.1097/00125817-200203000-00002
Lohmueller, 2003, Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease, Nat. Genet., 33, 177, 10.1038/ng1071
Murray, 1994, A comprehensive human linkage map with centimorgan density: Cooperative Human Linkage Center (CHLC), Science, 265, 2049, 10.1126/science.8091227
Dib, 1996, A comprehensive genetic map of the human genome based on 5264 microsatellites, Nature, 380, 152, 10.1038/380152a0
Broman, 1998, Comprehensive human genetic maps: individual and sex-specific variation in recombination, Am. J. Hum. Genet., 63, 861, 10.1086/302011
Sklar, 2002, Linkage analysis in psychiatric disorders: the emerging picture, Annu. Rev. Genomics Hum. Genet., 3, 371, 10.1146/annurev.genom.3.022502.103141
Florez, 2003, The inherited basis of diabetes mellitus: implications for the genetic analysis of complex traits, Annu. Rev. Genomics Hum. Genet., 4, 257, 10.1146/annurev.genom.4.070802.110436
Altmuller, 2001, Genome-wide scans of complex human diseases: true linkage is hard to find, Am. J. Hum. Genet., 69, 936, 10.1086/324069
Hugot, 2001, Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease, Nature, 411, 599, 10.1038/35079107
Ogura, 2001, A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease, Nature, 411, 603, 10.1038/35079114
Rioux, 2001, Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease, Nat. Genet., 29, 223, 10.1038/ng1001-223
Guo, 2004, A functional variant of SUMO4, a new IkappaBalpha modifier, is associated with type 1 diabetes, Nat. Genet., 36, 837, 10.1038/ng1391
Cox, 2001, Seven regions of the genome show evidence of linkage to type 1 diabetes in a consensus analysis of 767 multiplex families, Am. J. Hum. Genet., 69, 820, 10.1086/323501
Kong, 2002, A high-resolution recombination map of the human genome, Nat. Genet., 31, 241, 10.1038/ng917
Stefansson, 2002, Neuregulin 1 and susceptibility to schizophrenia, Am. J. Hum. Genet., 71, 877, 10.1086/342734
Matise, 2003, A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set, Am. J. Hum. Genet., 73, 271, 10.1086/377137
Middleton, 2004, Genomewide linkage analysis of bipolar disorder by use of a high-density single-nucleotide-polymorphism (SNP) genotyping assay: a comparison with microsatellite marker assays and finding of significant linkage to chromosome 6q22, Am. J. Hum. Genet., 74, 886, 10.1086/420775
Risch, 1996, The future of genetic studies of complex human diseases, Science, 273, 1516, 10.1126/science.273.5281.1516
Collins, 2003, The Human Genome Project: lessons from large-scale biology, Science, 300, 286, 10.1126/science.1084564
Lander, 2001, Initial sequencing and analysis of the human genome, Nature, 409, 860, 10.1038/35057062
Venter, 2001, The sequence of the human genome, Science, 291, 1304, 10.1126/science.1058040
Ardlie, 2002, Patterns of linkage disequilibrium in the human genome, Nat. Rev. Genet., 3, 299, 10.1038/nrg777
Gibbs, 2003, The International HapMap Project, Nature, 426, 789, 10.1038/nature02168
Sham, 2000, Power of linkage versus association analysis of quantitative traits, by use of variance-components models, for sibship data, Am. J. Hum. Genet., 66, 1616, 10.1086/302891
Boomsma, 2002, Classical twin studies and beyond, Nat. Rev. Genet., 3, 872, 10.1038/nrg932
Risch, 1990, Linkage strategies for genetically complex traits. Part II: the power of affected relative pairs, Am. J. Hum. Genet., 46, 229
Harris, 1992, Onset of NIDDM occurs at least 4–7yr before clinical diagnosis, Diabetes Care, 15, 815, 10.2337/diacare.15.7.815
Levy, 2000, Evidence for a gene influencing blood pressure on chromosome 17: genome scan linkage results for longitudinal blood pressure phenotypes in subjects from the framingham heart study, Hypertension, 36, 477, 10.1161/01.HYP.36.4.477
Kruglyak, 2001, Variation is the spice of life, Nat. Genet., 27, 234, 10.1038/85776
Fay, 2001, Positive and negative selection on the human genome, Genetics, 158, 1227, 10.1093/genetics/158.3.1227
Cargill, 1999, Characterization of single-nucleotide polymorphisms in coding regions of human genes, Nat. Genet., 22, 231, 10.1038/10290
Botstein, 2003, Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease, Nat. Genet., 33, 228, 10.1038/ng1090
Pennacchio, 2001, Genomic strategies to identify mammalian regulatory sequences, Nat. Rev. Genet., 2, 100, 10.1038/35052548
Bennett, 1996, Human type 1 diabetes and the insulin gene: principles of mapping polygenes, Annu. Rev. Genet., 30, 343, 10.1146/annurev.genet.30.1.343
Ueda, 2003, Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease, Nature, 423, 506, 10.1038/nature01621
Stefansson, 2003, Association of neuregulin 1 with schizophrenia confirmed in a Scottish population, Am. J. Hum. Genet., 72, 83, 10.1086/345442
Johnson, 2001, Haplotype tagging for the identification of common disease genes, Nat. Genet., 29, 233, 10.1038/ng1001-233
Gabriel, 2002, The structure of haplotype blocks in the human genome, Science, 296, 2225, 10.1126/science.1069424
Patil, 2001, Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21, Science, 294, 1719, 10.1126/science.1065573
Matsuzaki, 2004, Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array, Genome Res., 14, 414, 10.1101/gr.2014904
Altshuler, 2000, An SNP map of the human genome generated by reduced representation shotgun sequencing, Nature, 407, 513, 10.1038/35035083
Hirschhorn, 2002, Once and again-issues surrounding replication in genetic association studies, J. Clin. Endocrinol. Metab., 87, 4438, 10.1210/jc.2002-021329
Spielman, 1993, Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM), Am. J. Hum. Genet., 52, 506
Curtis, 1995, A note on the application of the transmission disequilibrium test when a parent is missing, Am. J. Hum. Genet., 56, 811
Spielman, 1996, The TDT and other family-based tests for linkage disequilibrium and association, Am. J. Hum. Genet., 59, 983
Martin, 2000, A test for linkage and association in general pedigrees: the pedigree disequilibrium test, Am. J. Hum. Genet., 67, 146, 10.1086/302957
Mitchell, 2003, Undetected genotyping errors cause apparent overtransmission of common alleles in the transmission/disequilibrium test, Am. J. Hum. Genet., 72, 598, 10.1086/368203
Spielman, 1998, A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test, Am. J. Hum. Genet., 62, 450, 10.1086/301714
Boehnke, 1998, Genetic association mapping based on discordant sib pairs: the discordant-alleles test, Am. J. Hum. Genet., 62, 950, 10.1086/301787
Allison, 1997, Transmission–disequilibrium tests for quantitative traits, Am. J. Hum. Genet., 60, 676
Chapman, 2003, Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power, Hum. Hered., 56, 18, 10.1159/000073729
Cardon, 2001, Association study designs for complex diseases, Nat. Rev. Genet., 2, 91, 10.1038/35052543
Tabor, 2002, Opinion: candidate-gene approaches for studying complex genetic traits. Practical considerations, Nat. Rev. Genet., 3, 391, 10.1038/nrg796
Ioannidis, 2001, Replication validity of genetic association studies, Nat. Genet., 29, 306, 10.1038/ng749
Doerge, 1996, Permutation tests for multiple loci affecting a quantitative character, Genetics, 142, 285, 10.1093/genetics/142.1.285
Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc., 57, 289
Dudbridge, 2004, Efficient computation of significance levels for multiple associations in large studies of correlated data, including genomewide association studies, Am. J. Hum. Genet., 75, 424, 10.1086/423738
Wacholder, 2004, Assessing the probability that a positive report is false: an approach for molecular epidemiology studies, J. Natl. Cancer Inst., 96, 434, 10.1093/jnci/djh075
Morton, 1998, Tests and estimates of allelic association in complex inheritance, Proc. Natl. Acad. Sci. U.S.A., 95, 11389, 10.1073/pnas.95.19.11389
Ardlie, 2002, Testing for population subdivision and association in four case–control studies, Am. J. Hum. Genet., 71, 304, 10.1086/341719
Freedman, 2004, Assessing the impact of population stratification on genetic association studies, Nat. Genet., 36, 388, 10.1038/ng1333
Marchini, 2004, The effects of human population structure on large genetic association studies, Nat. Genet., 36, 512, 10.1038/ng1337
Devlin, 1999, Genomic control for association studies, Biometrics, 55, 997, 10.1111/j.0006-341X.1999.00997.x
Pritchard, 1999, Use of unlinked genetic markers to detect population stratification in association studies, Am. J. Hum. Genet., 65, 220, 10.1086/302449
Reich, 2001, Detecting association in a case–control study while correcting for population stratification, Genet. Epidemiol., 20, 4, 10.1002/1098-2272(200101)20:1<4::AID-GEPI2>3.0.CO;2-T
Rosenberg, 2003, Informativeness of genetic markers for inference of ancestry, Am. J. Hum. Genet., 73, 1402, 10.1086/380416
Zar, 1999
Rosner, 1999
Ordovas, 2002, Dietary fat intake determines the effect of a common polymorphism in the hepatic lipase gene promoter on high-density lipoprotein metabolism: evidence of a strong dose effect in this gene–nutrient interaction in the Framingham Study, Circulation, 106, 2315, 10.1161/01.CIR.0000036597.52291.C9
Tai, 2003, Dietary fat interacts with the −514C>T polymorphism in the hepatic lipase gene promoter on plasma lipid profiles in a multiethnic Asian population: the 1998 Singapore National Health Survey, J. Nutr., 133, 3399, 10.1093/jn/133.11.3399
Memisoglu, 2003, Interaction between a peroxisome proliferator-activated receptor gamma gene polymorphism and dietary fat intake in relation to body mass, Hum. Mol. Genet., 12, 2923, 10.1093/hmg/ddg318
Robitaille, 2003, The PPAR-gamma P12A polymorphism modulates the relationship between dietary fat intake and components of the metabolic syndrome: results from the Quebec Family Study, Clin. Genet., 63, 109, 10.1034/j.1399-0004.2003.00026.x
Mirza, 2003, Genetic evidence for interaction of the 5q31 cytokine locus and the CARD15 gene in Crohn disease, Am. J. Hum. Genet., 72, 1018, 10.1086/373880
Negoro, 2003, Analysis of the IBD5 locus and potential gene–gene interactions in Crohn's disease, Gut, 52, 541, 10.1136/gut.52.4.541
Giallourakis, 2003, IBD5 is a general risk factor for inflammatory bowel disease: replication of association with Crohn disease and identification of a novel association with ulcerative colitis, Am. J. Hum. Genet., 73, 205, 10.1086/376417
Vermeire, 2002, CARD15 genetic variation in a Quebec population: prevalence, genotype–phenotype relationship, and haplotype structure, Am. J. Hum. Genet., 71, 74, 10.1086/341124
Hampe, 2001, Association between insertion mutation in NOD2 gene and Crohn's disease in German and British populations, Lancet, 357, 1925, 10.1016/S0140-6736(00)05063-7
Cavanaugh, 2003, CARD15/NOD2 risk alleles in the development of Crohn's disease in the Australian population, Ann. Hum. Genet., 67, 35, 10.1046/j.1469-1809.2003.00006.x
Florez, 2004, Haplotype structure and genotype–phenotype correlations of the sulfonylurea receptor and the islet ATP-sensitive potassium channel gene region, Diabetes, 53, 1360, 10.2337/diabetes.53.5.1360
Karolchik, 2003, The UCSC genome browser database, Nucleic Acids Res., 31, 51, 10.1093/nar/gkg129
Kent, 2002, The human genome browser at UCSC, Genome Res., 12, 996, 10.1101/gr.229102. Article published online before print in May 2002