[1] | Haines JL, Hauser MA, Schmidt S, Scott WK, Olson LM, et al. (2005) Complement factor H variant increases the risk of age-related macular degeneration. Science 308: 419–421 doi: 10.1126/science.1110359.
|
[2] | Edwards AO, Ritter R III, Abel KJ, Manning A, Panhuysen C, et al. (2005) Complement factor H polymorphism and age-related macular degeneration. Science 308: 421–424 doi: 10.1126/science.1110189.
|
[3] | Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, et al. (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308: 385–389 doi: 10.1126/science.1109557.
|
[4] | Cooper GM, Johnson JA, Langaee TY, Feng H, Stanaway IB, et al. (2008) A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose. Blood 112: 1022–1027 doi: 10.1182/blood-2008-01-134247.
|
[5] | Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061–1073 doi: 10.1038/nature09534.
|
[6] | Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, et al. (2008) ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res 36: D107–D113 doi: 10.1093/nar/gkm967.
|
[7] | Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467: 52–58 doi: 10.1038/nature09298.
|
[8] | Kerem B, Rommens JM, Buchanan JA, Markiewicz D, et al. (1989) Identification of the cystic fibrosis gene: genetic analysis. Science 245: 1073–1080. doi: 10.1126/science.2570460
|
[9] | MacDonald ME, Novelletto A, Lin C, Tagle D, Barnes G, et al. (1992) The Huntington's disease candidate region exhibits many different haplotypes. Nat Genet 1: 99–103 doi: 10.1038/ng0592-99.
|
[10] | Hirschhorn JN, Daly MJ (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6: 95–108 doi: 10.1038/nrg1521.
|
[11] | Corder EH, Saunders AM, Strittmatter WJ, Schmechel DE, Gaskell PC, et al. (1993) Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families. Science 261: 921–923. doi: 10.1126/science.8346443
|
[12] | Altshuler D, Hirschhorn JN, Klannemark M, Lindgren CM, Vohl MC, et al. (2000) The common PPARgamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes. Nat Genet 26: 76–80 doi: 10.1038/79216.
|
[13] | Reich DE, Lander ES (2001) On the allelic spectrum of human disease. Trends Genet 17: 502–510. doi: 10.1016/s0168-9525(01)02410-6
|
[14] | Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106: 9362–9367 doi: 10.1073/pnas.0903103106.
|
[15] | International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437: 1299–1320 doi: 10.1038/nature04226.
|
[16] | Ritchie MD, Denny JC, Crawford DC, Ramirez AH, Weiner JB, et al. (2010) Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record. Am J Hum Genet 86: 560–572 doi: 10.1016/j.ajhg.2010.03.003.
|
[17] | Devlin B, Risch N (1995) A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29: 311–322 doi: 10.1006/geno.1995.9003.
|
[18] | Fallin D, Schork NJ (2000) Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. Am J Hum Genet 67: 947–959 doi: 10.1086/303069.
|
[19] | Li M, Li C, Guan W (2008) Evaluation of coverage variation of SNP chips for genome-wide association studies. Eur J Hum Genet 16: 635–643 doi: 10.1038/sj.ejhg.5202007.
|
[20] | Distefano JK, Taverna DM (2011) Technological issues and experimental design of gene association studies. Methods Mol Biol 700: 3–16 doi: 10.1007/978-1-61737-954-3_1.
|
[21] | Teslovich TM, Musunuru K, Smith AV, Edmondson AC, Stylianou IM, et al. (2010) Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466: 707–713 doi: 10.1038/nature09270.
|
[22] | Habek M, Brinar VV, Borovecki F (2010) Genes associated with multiple sclerosis: 15 and counting. Expert Rev Mol Diagn 10: 857–861 doi: 10.1586/erm.10.77.
|
[23] | Polman CH, Reingold SC, Edan G, Filippi M, Hartung HP, et al. (2005) Diagnostic criteria for multiple sclerosis: 2005 revisions to the “McDonald Criteria”. Ann Neurol 58: 840–846 doi: 10.1002/ana.20703.
|
[24] | Chew EY, Kim J, Sperduto RD, Datiles MB III, Coleman HR, et al. (2010) Evaluation of the age-related eye disease study clinical lens grading system AREDS report No. 31. Ophthalmology 117: 2112–2119 doi: 10.1016/j.ophtha.2010.02.033.
|
[25] | Denny JC, Ritchie MD, Crawford DC, Schildcrout JS, Ramirez AH, et al. (2010) Identification of genomic predictors of atrioventricular conduction: using electronic medical records as a tool for genome science. Circulation 122: 2016–2021 doi: 10.1161/CIRCULATIONAHA.110.948828.
|
[26] | Wilke RA, Berg RL, Linneman JG, Peissig P, Starren J, et al. (2010) Quantification of the clinical modifiers impacting high-density lipoprotein cholesterol in the community: Personalized Medicine Research Project. Prev Cardiol 13: 63–68 doi: 10.1111/j.1751-7141.2009.00055.x.
|
[27] | Kullo IJ, Fan J, Pathak J, Savova GK, Ali Z, et al. (2010) Leveraging informatics for genetic studies: use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease. J Am Med Inform Assoc 17: 568–574 doi: 10.1136/jamia.2010.004366.
|
[28] | McCarty CA, Wilke RA (2010) Biobanking and pharmacogenomics. Pharmacogenomics 11: 637–641 doi: 10.2217/pgs.10.13.
|
[29] | Lewis CM (2002) Genetic association studies: design, analysis and interpretation. Brief Bioinform 3: 146–153. doi: 10.1093/bib/3.2.146
|
[30] | Lettre G, Lange C, Hirschhorn JN (2007) Genetic model testing and statistical power in population-based association studies of quantitative traits. Genet Epidemiol 31: 358–362 doi: 10.1002/gepi.20217.
|
[31] | Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587.
|
[32] | Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904–909 doi: 10.1038/ng1847.
|
[33] | Hochberg Y, Benjamini Y (1990) More powerful procedures for multiple significance testing. Stat Med 9: 811–818. doi: 10.1002/sim.4780090710
|
[34] | van den Oord EJ (2008) Controlling false discoveries in genetic studies. Am J Med Genet B Neuropsychiatr Genet 147B: 637–644 doi: 10.1002/ajmg.b.30650.
|
[35] | Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559–575 doi: 10.1086/519795.
|
[36] | Browning BL (2008) PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies. BMC Bioinformatics 9: 309 doi: 10.1186/1471-2105-9-309.
|
[37] | Pahl R, Schafer H (2010) PERMORY: an LD-exploiting permutation test algorithm for powerful genome-wide association testing. Bioinformatics 26: 2093–2100 doi: 10.1093/bioinformatics/btq399.
|
[38] | Dudbridge F, Gusnanto A (2008) Estimation of significance thresholds for genomewide association scans. Genet Epidemiol 32: 227–234 doi: 10.1002/gepi.20297.
|
[39] | Moore JH, Ritchie MD (2004) STUDENTJAMA. The challenges of whole-genome approaches to common diseases. JAMA 291: 1642–1643 doi: 10.1001/jama.291.13.1642.
|
[40] | Grady BJ, Torstenson ES, McLaren PJ, de Bakker PI, Haas DW, et al. (2011) Use of biological knowledge to inform the analysis of gene-gene interactions involved in modulating virologic failure with efavirenz-containing treatment regimens in art-naive actg clinical trials participants. Pac Symp Biocomput 253–264. doi: 10.1142/9789814335058_0027
|
[41] | Bush WS, Dudek SM, Ritchie MD (2009) Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies. Pac Symp Biocomput 368–379. doi: 10.1142/9789812836939_0035
|
[42] | Herold C, Steffens M, Brockschmidt FF, Baur MP, Becker T (2009) INTERSNP: genome-wide interaction analysis guided by a priori information. Bioinformatics 25: 3275–3281 doi: 10.1093/bioinformatics/btp596.
|
[43] | Chanock SJ, Manolio T, Boehnke M, Boerwinkle E, Hunter DJ, et al. (2007) Replicating genotype-phenotype associations. Nature 447: 655–660 doi: 10.1038/447655a.
|
[44] | Zollner S, Pritchard JK (2007) Overcoming the winner's curse: estimating penetrance parameters from case-control data. Am J Hum Genet 80: 605–615 doi: 10.1086/512821.
|
[45] | Sanna S, Jackson AU, Nagaraja R, Willer CJ, Chen WM, et al. (2008) Common variants in the GDF5-UQCC region are associated with variation in human height. Nat Genet 40: 198–203 doi: 10.1038/ng.74.
|
[46] | Willer CJ, Sanna S, Jackson AU, Scuteri A, Bonnycastle LL, et al. (2008) Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet 40: 161–169 doi: 10.1038/ng.76.
|
[47] | Zeggini E, Ioannidis JP (2009) Meta-analysis in genome-wide association studies. Pharmacogenomics 10: 191–201 doi: 10.2217/14622416.10.2.191.
|
[48] | Huedo-Medina TB, Sanchez-Meca J, Marin-Martinez F, Botella J (2006) Assessing heterogeneity in meta-analysis: Q statistic or I2 index? Psychol Methods 11: 193–206 doi: 10.1037/1082-989X.11.2.193.
|
[49] | Higgins JP (2008) Commentary: Heterogeneity in meta-analysis should be expected and appropriately quantified. Int J Epidemiol 37: 1158–1160 doi: 10.1093/ije/dyn204.
|
[50] | Li Y, Willer C, Sanna S, Abecasis G (2009) Genotype imputation. Annu Rev Genomics Hum Genet 10: 387–406 doi: 10.1146/annurev.genom.9.081307.164242.
|
[51] | Marchini J, Howie B, Myers S, McVean G, Donnelly P (2007) A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 39: 906–913 doi: 10.1038/ng2088.
|
[52] | Guan Y, Stephens M (2008) Practical issues in imputation-based association mapping. PLoS Genet 4: e1000279 doi: 10.1371/journal.pgen.1000279.
|
[53] | Howie BN, Donnelly P, Marchini J (2009) A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5: e1000529 doi: 10.1371/journal.pgen.1000529.
|
[54] | Biernacka JM, Tang R, Li J, McDonnell SK, Rabe KG, et al. (2009) Assessment of genotype imputation methods. BMC Proc 3 Suppl 7: S5. doi: 10.1186/1753-6561-3-s7-s5
|
[55] | Browning BL, Browning SR (2009) A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 84: 210–223 doi: 10.1016/j.ajhg.2009.01.005.
|