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Volumn 86, Issue 6, 2010, Pages 929-942

Powerful SNP-Set Analysis for Case-Control Genome-wide Association Studies

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREAST CANCER; CANCER SUSCEPTIBILITY; CONTROLLED STUDY; GENETIC ASSOCIATION; GENETIC MARKER; GENOMICS; HAPLOTYPE; HUMAN; KERNEL METHOD; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 77953121307     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ajhg.2010.05.002     Document Type: Article
Times cited : (484)

References (49)
  • 8
    • 34249888775 scopus 로고    scopus 로고
    • Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels
    • Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University, and Novartis Institutes of BioMedical Research
    • Saxena R., Voight B.F., Lyssenko V., Burtt N.P., de Bakker P.I., Chen H., Roix J.J., Kathiresan S., Hirschhorn J.N., Daly M.J., et al., Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University, and Novartis Institutes of BioMedical Research. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 316 (2007) 1331-1336
    • (2007) Science , vol.316 , pp. 1331-1336
    • Saxena, R.1    Voight, B.F.2    Lyssenko, V.3    Burtt, N.P.4    de Bakker, P.I.5    Chen, H.6    Roix, J.J.7    Kathiresan, S.8    Hirschhorn, J.N.9    Daly, M.J.10
  • 9
    • 40749098064 scopus 로고    scopus 로고
    • Study designs for genome-wide association studies
    • Kraft P., and Cox D.G. Study designs for genome-wide association studies. Adv. Genet. 60 (2008) 465-504
    • (2008) Adv. Genet. , vol.60 , pp. 465-504
    • Kraft, P.1    Cox, D.G.2
  • 10
    • 0036155283 scopus 로고    scopus 로고
    • Score tests for association between traits and haplotypes when linkage phase is ambiguous
    • Schaid D.J., Rowland C.M., Tines D.E., Jacobson R.M., and Poland G.A. Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am. J. Hum. Genet. 70 (2002) 425-434
    • (2002) Am. J. Hum. Genet. , vol.70 , pp. 425-434
    • Schaid, D.J.1    Rowland, C.M.2    Tines, D.E.3    Jacobson, R.M.4    Poland, G.A.5
  • 11
    • 34547618083 scopus 로고    scopus 로고
    • Drinking from the fire hose-statistical issues in genomewide association studies
    • Hunter D.J., and Kraft P. Drinking from the fire hose-statistical issues in genomewide association studies. N. Engl. J. Med. 357 (2007) 436-439
    • (2007) N. Engl. J. Med. , vol.357 , pp. 436-439
    • Hunter, D.J.1    Kraft, P.2
  • 12
    • 48249142391 scopus 로고    scopus 로고
    • Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models
    • Liu D., Ghosh D., and Lin X. Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. BMC Bioinformatics 9 (2008) 292
    • (2008) BMC Bioinformatics , vol.9 , pp. 292
    • Liu, D.1    Ghosh, D.2    Lin, X.3
  • 13
    • 40749104728 scopus 로고    scopus 로고
    • A powerful and flexible multilocus association test for quantitative traits
    • Kwee L.C., Liu D., Lin X., Ghosh D., and Epstein M.P. A powerful and flexible multilocus association test for quantitative traits. Am. J. Hum. Genet. 82 (2008) 386-397
    • (2008) Am. J. Hum. Genet. , vol.82 , pp. 386-397
    • Kwee, L.C.1    Liu, D.2    Lin, X.3    Ghosh, D.4    Epstein, M.P.5
  • 15
    • 33751114975 scopus 로고    scopus 로고
    • Generalized genomic distance-based regression methodology for multilocus association analysis
    • Wessel J., and Schork N.J. Generalized genomic distance-based regression methodology for multilocus association analysis. Am. J. Hum. Genet. 79 (2006) 792-806
    • (2006) Am. J. Hum. Genet. , vol.79 , pp. 792-806
    • Wessel, J.1    Schork, N.J.2
  • 16
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa M., and Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28 (2000) 27-30
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 18
    • 4444311171 scopus 로고    scopus 로고
    • Multiple-sequence functional annotation and the generalized hidden Markov phylogeny
    • McAuliffe J.D., Pachter L., and Jordan M.I. Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics 20 (2004) 1850-1860
    • (2004) Bioinformatics , vol.20 , pp. 1850-1860
    • McAuliffe, J.D.1    Pachter, L.2    Jordan, M.I.3
  • 19
    • 13444269543 scopus 로고    scopus 로고
    • Haploview: analysis and visualization of LD and haplotype maps
    • Barrett J.C., Fry B., Maller J., and Daly M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21 (2005) 263-265
    • (2005) Bioinformatics , vol.21 , pp. 263-265
    • Barrett, J.C.1    Fry, B.2    Maller, J.3    Daly, M.J.4
  • 22
    • 0015000439 scopus 로고
    • Some results on Tchebycheffian spline functions
    • Kimeldorf G.S., and Wahba G. Some results on Tchebycheffian spline functions. J. Math. Anal. Appl. 33 (1971) 82-95
    • (1971) J. Math. Anal. Appl. , vol.33 , pp. 82-95
    • Kimeldorf, G.S.1    Wahba, G.2
  • 23
    • 66249144684 scopus 로고    scopus 로고
    • Power comparisons between similarity-based multilocus association methods, logistic regression, and score tests for haplotypes
    • Lin W.Y., and Schaid D.J. Power comparisons between similarity-based multilocus association methods, logistic regression, and score tests for haplotypes. Genet. Epidemiol. 33 (2009) 183-197
    • (2009) Genet. Epidemiol. , vol.33 , pp. 183-197
    • Lin, W.Y.1    Schaid, D.J.2
  • 24
    • 77949776227 scopus 로고    scopus 로고
    • Association tests using kernel-based measures of multi-locus genotype similarity between individuals
    • Mukhopadhyay I., Feingold E., Weeks D., and Thalamuthu A. Association tests using kernel-based measures of multi-locus genotype similarity between individuals. Genet. Epidemiol. 34 (2010) 213-221
    • (2010) Genet. Epidemiol. , vol.34 , pp. 213-221
    • Mukhopadhyay, I.1    Feingold, E.2    Weeks, D.3    Thalamuthu, A.4
  • 25
    • 0141767032 scopus 로고    scopus 로고
    • Hypothesis testing in semiparametric additive mixed models
    • Zhang D., and Lin X. Hypothesis testing in semiparametric additive mixed models. Biostatistics 4 (2003) 57-74
    • (2003) Biostatistics , vol.4 , pp. 57-74
    • Zhang, D.1    Lin, X.2
  • 26
    • 15944388957 scopus 로고    scopus 로고
    • An efficient Monte Carlo approach to assessing statistical significance in genomic studies
    • Lin D.Y. An efficient Monte Carlo approach to assessing statistical significance in genomic studies. Bioinformatics 21 (2005) 781-787
    • (2005) Bioinformatics , vol.21 , pp. 781-787
    • Lin, D.Y.1
  • 27
    • 0034781050 scopus 로고    scopus 로고
    • A simple correction for multiple comparisons in interval mapping genome scans
    • Cheverud J.M. A simple correction for multiple comparisons in interval mapping genome scans. Heredity 87 (2001) 52-58
    • (2001) Heredity , vol.87 , pp. 52-58
    • Cheverud, J.M.1
  • 28
    • 1842539516 scopus 로고    scopus 로고
    • A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other
    • Nyholt D.R. A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other. Am. J. Hum. Genet. 74 (2004) 765-769
    • (2004) Am. J. Hum. Genet. , vol.74 , pp. 765-769
    • Nyholt, D.R.1
  • 29
    • 50249187303 scopus 로고    scopus 로고
    • On multiple-testing correction in genome-wide association studies
    • Moskvina V., and Schmidt K.M. On multiple-testing correction in genome-wide association studies. Genet. Epidemiol. 32 (2008) 567-573
    • (2008) Genet. Epidemiol. , vol.32 , pp. 567-573
    • Moskvina, V.1    Schmidt, K.M.2
  • 30
    • 0042881041 scopus 로고    scopus 로고
    • Mathematical multi-locus approaches to localizing complex human trait genes
    • Hoh J., and Ott J. Mathematical multi-locus approaches to localizing complex human trait genes. Nat. Rev. Genet. 4 (2003) 701-709
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 701-709
    • Hoh, J.1    Ott, J.2
  • 31
    • 0036284203 scopus 로고    scopus 로고
    • Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals
    • Zaykin D.V., Westfall P.H., Young S.S., Karnoub M.A., Wagner M.J., Ehm M.G., and Inc G. Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum. Hered. 53 (2002) 79-91
    • (2002) Hum. Hered. , vol.53 , pp. 79-91
    • Zaykin, D.V.1    Westfall, P.H.2    Young, S.S.3    Karnoub, M.A.4    Wagner, M.J.5    Ehm, M.G.6    Inc, G.7
  • 32
    • 0344033602 scopus 로고    scopus 로고
    • Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power
    • Chapman J.M., Cooper J.D., Todd J.A., and Clayton D.G. Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power. Hum. Hered. 56 (2003) 18-31
    • (2003) Hum. Hered. , vol.56 , pp. 18-31
    • Chapman, J.M.1    Cooper, J.D.2    Todd, J.A.3    Clayton, D.G.4
  • 33
    • 15544379620 scopus 로고    scopus 로고
    • Analysis of single-locus tests to detect gene/disease associations
    • Roeder K., Bacanu S.A., Sonpar V., Zhang X., and Devlin B. Analysis of single-locus tests to detect gene/disease associations. Genet. Epidemiol. 28 (2005) 207-219
    • (2005) Genet. Epidemiol. , vol.28 , pp. 207-219
    • Roeder, K.1    Bacanu, S.A.2    Sonpar, V.3    Zhang, X.4    Devlin, B.5
  • 34
    • 35348887757 scopus 로고    scopus 로고
    • Haplotype-based association analysis via variance-components score test
    • Tzeng J.Y., and Zhang D. Haplotype-based association analysis via variance-components score test. Am. J. Hum. Genet. 81 (2007) 927-938
    • (2007) Am. J. Hum. Genet. , vol.81 , pp. 927-938
    • Tzeng, J.Y.1    Zhang, D.2
  • 35
    • 33751112507 scopus 로고    scopus 로고
    • Mapping trait loci by use of inferred ancestral recombination graphs
    • Minichiello M.J., and Durbin R. Mapping trait loci by use of inferred ancestral recombination graphs. Am. J. Hum. Genet. 79 (2006) 910-922
    • (2006) Am. J. Hum. Genet. , vol.79 , pp. 910-922
    • Minichiello, M.J.1    Durbin, R.2
  • 36
    • 34547638844 scopus 로고    scopus 로고
    • Genetic association mapping via evolution-based clustering of haplotypes
    • Tachmazidou I., Verzilli C.J., and De Iorio M. Genetic association mapping via evolution-based clustering of haplotypes. PLoS Genet. 3 (2007) e111
    • (2007) PLoS Genet. , vol.3
    • Tachmazidou, I.1    Verzilli, C.J.2    De Iorio, M.3
  • 39
    • 67149095078 scopus 로고    scopus 로고
    • Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip
    • Spencer C., Su Z., Donnelly P., and Marchini J. Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PLoS Genet. 5 (2009) e1000477
    • (2009) PLoS Genet. , vol.5
    • Spencer, C.1    Su, Z.2    Donnelly, P.3    Marchini, J.4
  • 41
    • 34347344976 scopus 로고    scopus 로고
    • A new multipoint method for genome-wide association studies by imputation of genotypes
    • Marchini J., Howie B., Myers S., McVean G., and Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39 (2007) 906-913
    • (2007) Nat. Genet. , vol.39 , pp. 906-913
    • Marchini, J.1    Howie, B.2    Myers, S.3    McVean, G.4    Donnelly, P.5
  • 42
    • 43249090541 scopus 로고    scopus 로고
    • A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms
    • Gao X., Starmer J., and Martin E.R. A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms. Genet. Epidemiol. 32 (2008) 361-369
    • (2008) Genet. Epidemiol. , vol.32 , pp. 361-369
    • Gao, X.1    Starmer, J.2    Martin, E.R.3
  • 43
    • 33746512512 scopus 로고    scopus 로고
    • Principal components analysis corrects for stratification in genome-wide association studies
    • Price A.L., Patterson N.J., Plenge R.M., Weinblatt M.E., Shadick N.A., and Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38 (2006) 904-909
    • (2006) Nat. Genet. , vol.38 , pp. 904-909
    • Price, A.L.1    Patterson, N.J.2    Plenge, R.M.3    Weinblatt, M.E.4    Shadick, N.A.5    Reich, D.6
  • 44
    • 0001287271 scopus 로고    scopus 로고
    • Regression shrinkage and selection via the lasso
    • Tibshirani R. Regression shrinkage and selection via the lasso. J. Roy. Statist. Soc., B 58 (1996) 267-288
    • (1996) J. Roy. Statist. Soc., B , vol.58 , pp. 267-288
    • Tibshirani, R.1
  • 45
    • 0038449175 scopus 로고    scopus 로고
    • Analysis of multilocus models of association
    • Devlin B., Roeder K., and Wasserman L. Analysis of multilocus models of association. Genet. Epidemiol. 25 (2003) 36-47
    • (2003) Genet. Epidemiol. , vol.25 , pp. 36-47
    • Devlin, B.1    Roeder, K.2    Wasserman, L.3
  • 46
    • 71249154139 scopus 로고    scopus 로고
    • Analysis of North American Rheumatoid Arthritis Consortium data using a penalized logistic regression approach
    • BioMed Central Ltd
    • Croiseau, P., and Cordell, H. (2009). Analysis of North American Rheumatoid Arthritis Consortium data using a penalized logistic regression approach. BMC Proceedings (BioMed Central Ltd) 3, S61.
    • (2009) BMC Proceedings , vol.3
    • Croiseau, P.1    Cordell, H.2
  • 48
    • 0000072057 scopus 로고    scopus 로고
    • Variance component testing in generalised linear models with random effects
    • Lin X. Variance component testing in generalised linear models with random effects. Biometrika 84 (1997) 309-326
    • (1997) Biometrika , vol.84 , pp. 309-326
    • Lin, X.1
  • 49
    • 84872636119 scopus 로고
    • An approximate distribution of estimates of variance components
    • Satterthwaite F. An approximate distribution of estimates of variance components. Biom. Bull. 2 (1946) 110-114
    • (1946) Biom. Bull. , vol.2 , pp. 110-114
    • Satterthwaite, F.1


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