메뉴 건너뛰기




Volumn 9, Issue 4, 2013, Pages

All SNPs are not created equal: Genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs

(13)  Schork, Andrew J a,b   Thompson, Wesley K c   Pham, Phillip d,e   Torkamani, Ali d,e   Roddey, J Cooper a   Sullivan, Patrick F f   Kelsoe, John R c   O'Donovan, Michael C g   Furberg, Helena h   Schork, Nicholas J d,e   Andreassen, Ole A c,i,j   Dale, Anders M a,k,l   Levy, Daniel m  


Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BIOINFORMATICS; CROHN DISEASE; GENE CONTROL; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE REPLICATION; GENETIC ASSOCIATION; GENETIC CODE; GENETIC VARIABILITY; GENOMICS; GENOTYPE PHENOTYPE CORRELATION; HUMAN; PHENOTYPIC VARIATION; PREDICTIVE VALUE; SCHIZOPHRENIA; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; GENETIC PREDISPOSITION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; PHENOTYPE;

EID: 84876847154     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003449     Document Type: Article
Times cited : (232)

References (51)
  • 1
    • 0037146578 scopus 로고    scopus 로고
    • Finding genes that underlie complex traits
    • Glazier AM, Nadeau JH, Aitman TJ, (2002) Finding genes that underlie complex traits. Science 298: 2345-2349.
    • (2002) Science , vol.298 , pp. 2345-2349
    • Glazier, A.M.1    Nadeau, J.H.2    Aitman, T.J.3
  • 2
    • 13144306071 scopus 로고    scopus 로고
    • Genome-wide association studies for common diseases and complex traits
    • Hirschhorn JN, Daly MJ, (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6: 95-108.
    • (2005) Nat Rev Genet , vol.6 , pp. 95-108
    • Hirschhorn, J.N.1    Daly, M.J.2
  • 3
    • 67249117049 scopus 로고    scopus 로고
    • Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
    • 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.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 9362-9367
    • Hindorff, L.A.1    Sethupathy, P.2    Junkins, H.A.3    Ramos, E.M.4    Mehta, J.P.5
  • 5
    • 77954140531 scopus 로고    scopus 로고
    • Common SNPs explain a large proportion of the heritability for human height
    • Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, et al. (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42: 565-569.
    • (2010) Nat Genet , vol.42 , pp. 565-569
    • Yang, J.1    Benyamin, B.2    McEvoy, B.P.3    Gordon, S.4    Henders, A.K.5
  • 6
    • 79957588287 scopus 로고    scopus 로고
    • Genome partitioning of genetic variation for complex traits using common SNPs
    • Yang J, Manolio TA, Pasquale LR, Boerwinkle E, Caporaso N, et al. (2011) Genome partitioning of genetic variation for complex traits using common SNPs. Nat Genet 43: 519-525.
    • (2011) Nat Genet , vol.43 , pp. 519-525
    • Yang, J.1    Manolio, T.A.2    Pasquale, L.R.3    Boerwinkle, E.4    Caporaso, N.5
  • 7
    • 84860333083 scopus 로고    scopus 로고
    • Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis
    • Stahl EA, Wegmann D, Trynka G, Gutierrez-Achury J, Do R, et al. (2012) Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis. Nat Genet 44: 483-489.
    • (2012) Nat Genet , vol.44 , pp. 483-489
    • Stahl, E.A.1    Wegmann, D.2    Trynka, G.3    Gutierrez-Achury, J.4    Do, R.5
  • 9
    • 33747595466 scopus 로고    scopus 로고
    • Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies
    • Sun L, Craiu RV, Paterson AD, Bull SB, (2006) Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies. Genet Epidemiol 30: 519-530.
    • (2006) Genet Epidemiol , vol.30 , pp. 519-530
    • Sun, L.1    Craiu, R.V.2    Paterson, A.D.3    Bull, S.B.4
  • 10
    • 71249160225 scopus 로고    scopus 로고
    • Genome-wide association analyses of North American Rheumatoid Arthritis Consortium and Framingham Heart Study data utilizing genome-wide linkage results
    • Yoo YJ, Pinnaduwage D, Waggott D, Bull SB, Sun L, (2009) Genome-wide association analyses of North American Rheumatoid Arthritis Consortium and Framingham Heart Study data utilizing genome-wide linkage results. BMC Proc 3Suppl 7: S103.
    • (2009) BMC Proc , vol.3
    • Yoo, Y.J.1    Pinnaduwage, D.2    Waggott, D.3    Bull, S.B.4    Sun, L.5
  • 11
    • 37149012278 scopus 로고    scopus 로고
    • Prioritized subset analysis: improving power in genome-wide association studies
    • Li C, Li M, Lange EM, Watanabe RM, (2008) Prioritized subset analysis: improving power in genome-wide association studies. Hum Hered 65: 129-141.
    • (2008) Hum Hered , vol.65 , pp. 129-141
    • Li, C.1    Li, M.2    Lange, E.M.3    Watanabe, R.M.4
  • 12
    • 77949907406 scopus 로고    scopus 로고
    • Incorporating prior knowledge to facilitate discoveries in a genome-wide association study on age-related macular degeneration
    • Lin W-Y, Lee W-C, (2010) Incorporating prior knowledge to facilitate discoveries in a genome-wide association study on age-related macular degeneration. BMC Research Notes 3: 1-5.
    • (2010) BMC Research Notes , vol.3 , pp. 1-5
    • Lin, W.-Y.1    Lee, W.-C.2
  • 13
    • 84860350767 scopus 로고    scopus 로고
    • Multiple apical plasma membrane constituents are associated with susceptibility to meconium ileus in individuals with cystic fibrosis
    • Sun L, Rommens JM, Corvol H, Li W, Li X, et al. (2012) Multiple apical plasma membrane constituents are associated with susceptibility to meconium ileus in individuals with cystic fibrosis. Nat Genet 44: 562-569.
    • (2012) Nat Genet , vol.44 , pp. 562-569
    • Sun, L.1    Rommens, J.M.2    Corvol, H.3    Li, W.4    Li, X.5
  • 14
    • 38049000719 scopus 로고    scopus 로고
    • The multiplicity problem in linkage analysis of gene expression data - the power of differentiating cis- and trans-acting regulators
    • Huang B, Rangrej J, Paterson AD, Sun L, (2007) The multiplicity problem in linkage analysis of gene expression data- the power of differentiating cis- and trans-acting regulators. BMC Proc 1 Suppl 1: S142.
    • (2007) BMC Proc , vol.1 , Issue.SUPPL. 1
    • Huang, B.1    Rangrej, J.2    Paterson, A.D.3    Sun, L.4
  • 15
    • 79955683639 scopus 로고    scopus 로고
    • Using functional annotation for the empirical determination of Bayes Factors for genome-wide association study analysis
    • doi:10.1371/journal.pone.0014808
    • Knight J, Barnes MR, Breen G, Weale ME, (2011) Using functional annotation for the empirical determination of Bayes Factors for genome-wide association study analysis. PLoS ONE 6: e14808 doi:10.1371/journal.pone.0014808.
    • (2011) PLoS ONE , vol.6
    • Knight, J.1    Barnes, M.R.2    Breen, G.3    Weale, M.E.4
  • 16
    • 79959813723 scopus 로고    scopus 로고
    • Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes
    • doi:10.1371/journal.pgen.1002134
    • Smith EN, Koller DL, Panganiban C, Szelinger S, Zhang P, et al. (2011) Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes. PLoS Genet 7: e1002134 doi:10.1371/journal.pgen.1002134.
    • (2011) PLoS Genet , vol.7
    • Smith, E.N.1    Koller, D.L.2    Panganiban, C.3    Szelinger, S.4    Zhang, P.5
  • 18
    • 0000992959 scopus 로고
    • Plots of P-Values to Evaluate Many Tests Simultaneously
    • Schweder T, Spjotvoll E, (1982) Plots of P-Values to Evaluate Many Tests Simultaneously. Biometrika 69: 493-502.
    • (1982) Biometrika , vol.69 , pp. 493-502
    • Schweder, T.1    Spjotvoll, E.2
  • 20
    • 0032714352 scopus 로고    scopus 로고
    • Genomic control for association studies
    • Devlin B, Roeder K, (1999) Genomic control for association studies. Biometrics 55: 997-1004.
    • (1999) Biometrics , vol.55 , pp. 997-1004
    • Devlin, B.1    Roeder, K.2
  • 21
    • 85037069846 scopus 로고    scopus 로고
    • Hamshere ML, Walters JT, Smith R, Richards AL, Green E, et al. (2012) Genome-wide significant associations in schizophrenia to ITIH3/4, CACNA1C and SDCCAG8, and extensive replication of associations reported by the Schizophrenia PGC. Mol Psychiatry.
  • 23
    • 55349098276 scopus 로고    scopus 로고
    • Choosing the lesser evil: Trade-off between false discovery rate and non-discovery rate
    • Craiu RV, Sun L, (2008) Choosing the lesser evil: Trade-off between false discovery rate and non-discovery rate. Statistica Sinica 18: 861-879.
    • (2008) Statistica Sinica , vol.18 , pp. 861-879
    • Craiu, R.V.1    Sun, L.2
  • 24
    • 68449086236 scopus 로고    scopus 로고
    • Common polygenic variation contributes to risk of schizophrenia and bipolar disorder
    • Consortium IS, Purcell SM, Wray NR, Stone JL, Visscher PM, et al. (2009) Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 460: 748-752.
    • (2009) Nature , vol.460 , pp. 748-752
    • Consortium, I.S.1    Purcell, S.M.2    Wray, N.R.3    Stone, J.L.4    Visscher, P.M.5
  • 25
    • 0000992959 scopus 로고
    • Plots of P-values to evaluate many tests simultaneously
    • Schweder T, Spjøtvoll E, (1982) Plots of P-values to evaluate many tests simultaneously. Biometrika 69: 493-502.
    • (1982) Biometrika , vol.69 , pp. 493-502
    • Schweder, T.1    Spjøtvoll, E.2
  • 26
    • 66049159816 scopus 로고    scopus 로고
    • Genetic architecture of quantitative traits in mice, flies, and humans
    • Flint J, Mackay TF, (2009) Genetic architecture of quantitative traits in mice, flies, and humans. Genome Res 19: 723-733.
    • (2009) Genome Res , vol.19 , pp. 723-733
    • Flint, J.1    Mackay, T.F.2
  • 27
    • 80052851950 scopus 로고    scopus 로고
    • Mouse genomic variation and its effect on phenotypes and gene regulation
    • Keane TM, Goodstadt L, Danecek P, White MA, Wong K, et al. (2011) Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477: 289-294.
    • (2011) Nature , vol.477 , pp. 289-294
    • Keane, T.M.1    Goodstadt, L.2    Danecek, P.3    White, M.A.4    Wong, K.5
  • 28
    • 79955841697 scopus 로고    scopus 로고
    • Evaluating the heritability explained by known susceptibility variants: a survey of ten complex diseases
    • So HC, Gui AH, Cherny SS, Sham PC, (2011) Evaluating the heritability explained by known susceptibility variants: a survey of ten complex diseases. Genet Epidemiol 35: 310-317.
    • (2011) Genet Epidemiol , vol.35 , pp. 310-317
    • So, H.C.1    Gui, A.H.2    Cherny, S.S.3    Sham, P.C.4
  • 29
    • 78649512740 scopus 로고    scopus 로고
    • Estimating the total number of susceptibility variants underlying complex diseases from genome-wide association studies
    • doi:10.1371/journal.pone.0013898
    • So HC, Yip BH, Sham PC, (2010) Estimating the total number of susceptibility variants underlying complex diseases from genome-wide association studies. PLoS ONE 5: e13898 doi:10.1371/journal.pone.0013898.
    • (2010) PLoS ONE , vol.5
    • So, H.C.1    Yip, B.H.2    Sham, P.C.3
  • 30
    • 77949538156 scopus 로고    scopus 로고
    • How many genetic variants remain to be discovered
    • doi:10.1371/journal.pone.0007969
    • Pawitan Y, Seng KC, Magnusson PK, (2009) How many genetic variants remain to be discovered? PLoS ONE 4: e7969 doi:10.1371/journal.pone.0007969.
    • (2009) PLoS ONE , vol.4
    • Pawitan, Y.1    Seng, K.C.2    Magnusson, P.K.3
  • 32
    • 84860151961 scopus 로고    scopus 로고
    • Evidence-based psychiatric genetics, AKA the false dichotomy between common and rare variant hypotheses
    • Visscher PM, Goddard ME, Derks EM, Wray NR, (2012) Evidence-based psychiatric genetics, AKA the false dichotomy between common and rare variant hypotheses. Mol Psychiatry 17: 474-485.
    • (2012) Mol Psychiatry , vol.17 , pp. 474-485
    • Visscher, P.M.1    Goddard, M.E.2    Derks, E.M.3    Wray, N.R.4
  • 34
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
    • (2005) Genome Res , vol.15 , pp. 1034-1050
    • Siepel, A.1    Bejerano, G.2    Pedersen, J.S.3    Hinrichs, A.S.4    Hou, M.5
  • 35
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • King MC, Wilson AC, (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
    • (1975) Science , vol.188 , pp. 107-116
    • King, M.C.1    Wilson, A.C.2
  • 36
    • 80051968181 scopus 로고    scopus 로고
    • Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data
    • Cooper GM, Shendure J, (2011) Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet 12: 628-640.
    • (2011) Nat Rev Genet , vol.12 , pp. 628-640
    • Cooper, G.M.1    Shendure, J.2
  • 37
    • 78049337953 scopus 로고    scopus 로고
    • Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index
    • Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, et al. (2010) Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet 42: 937-948.
    • (2010) Nat Genet , vol.42 , pp. 937-948
    • Speliotes, E.K.1    Willer, C.J.2    Berndt, S.I.3    Monda, K.L.4    Thorleifsson, G.5
  • 38
    • 78049349396 scopus 로고    scopus 로고
    • Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution
    • Heid IM, Jackson AU, Randall JC, Winkler TW, Qi L, et al. (2010) Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat Genet 42: 949-960.
    • (2010) Nat Genet , vol.42 , pp. 949-960
    • Heid, I.M.1    Jackson, A.U.2    Randall, J.C.3    Winkler, T.W.4    Qi, L.5
  • 39
    • 78649489009 scopus 로고    scopus 로고
    • Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci
    • Franke A, McGovern DP, Barrett JC, Wang K, Radford-Smith GL, et al. (2010) Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet 42: 1118-1125.
    • (2010) Nat Genet , vol.42 , pp. 1118-1125
    • Franke, A.1    McGovern, D.P.2    Barrett, J.C.3    Wang, K.4    Radford-Smith, G.L.5
  • 40
    • 79952195585 scopus 로고    scopus 로고
    • Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47
    • Anderson CA, Boucher G, Lees CW, Franke A, D'Amato M, et al. (2011) Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet 43: 246-252.
    • (2011) Nat Genet , vol.43 , pp. 246-252
    • Anderson, C.A.1    Boucher, G.2    Lees, C.W.3    Franke, A.4    D'Amato, M.5
  • 41
    • 80053384370 scopus 로고    scopus 로고
    • Genome-wide association study identifies five new schizophrenia loci
    • Schizophrenia Psychiatric Genome-Wide Association Study (GWAS) Consortium
    • Schizophrenia Psychiatric Genome-Wide Association Study (GWAS) Consortium (2011) Genome-wide association study identifies five new schizophrenia loci. Nat Genet 43: 969-976.
    • (2011) Nat Genet , vol.43 , pp. 969-976
  • 42
    • 80053385384 scopus 로고    scopus 로고
    • Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4
    • Psychiatric GWAS Consortium Bipolar Disorder Working Group
    • Psychiatric GWAS Consortium Bipolar Disorder Working Group (2011) Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. Nat Genet 43: 977-983.
    • (2011) Nat Genet , vol.43 , pp. 977-983
  • 43
    • 77951711343 scopus 로고    scopus 로고
    • Genome-wide meta-analyses identify multiple loci associated with smoking behavior
    • Tobacco and Genetics Consortium
    • Tobacco and Genetics Consortium (2010) Genome-wide meta-analyses identify multiple loci associated with smoking behavior. Nat Genet 42: 441-447.
    • (2010) Nat Genet , vol.42 , pp. 441-447
  • 44
    • 80053907554 scopus 로고    scopus 로고
    • Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk
    • Ehret GB, Munroe PB, Rice KM, Bochud M, Johnson AD, et al. (2011) Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk. Nature 478: 103-109.
    • (2011) Nature , vol.478 , pp. 103-109
    • Ehret, G.B.1    Munroe, P.B.2    Rice, K.M.3    Bochud, M.4    Johnson, A.D.5
  • 45
  • 46
    • 85037061633 scopus 로고    scopus 로고
    • Purcell S (2009) Plink. 1.07 ed.
  • 47
    • 34548292504 scopus 로고    scopus 로고
    • PLINK: a tool set for whole-genome association and population-based linkage analyses
    • 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.
    • (2007) Am J Hum Genet , vol.81 , pp. 559-575
    • Purcell, S.1    Neale, B.2    Todd-Brown, K.3    Thomas, L.4    Ferreira, M.A.5
  • 49
  • 51
    • 79952159600 scopus 로고    scopus 로고
    • The effect of correlation in false discovery rate estimation
    • Schwartzman A, Lin X, (2011) The effect of correlation in false discovery rate estimation. Biometrika 98: 199-214.
    • (2011) Biometrika , vol.98 , pp. 199-214
    • Schwartzman, A.1    Lin, X.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.