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Volumn 97, Issue 1, 2015, Pages 125-138

A Joint Location-Scale Test Improves Power to Detect Associated SNPs, Gene Sets, and Pathways

Author keywords

complex traits; cystic fibrosis; GxE interaction; GxG interaction; HbA1c level; multivariate model; pathway; type 1 diabetes; variance tests

Indexed keywords

HEMOGLOBIN A1C; MULTIPROTEIN COMPLEX; PHOSPHOPROTEIN; SODIUM PROTON EXCHANGE PROTEIN; SODIUM-HYDROGEN EXCHANGER 3; SODIUM-HYDROGEN EXCHANGER REGULATORY FACTOR;

EID: 84937440003     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2015.05.015     Document Type: Article
Times cited : (45)

References (51)
  • 1
    • 67349166946 scopus 로고    scopus 로고
    • Detecting gene-gene interactions that underlie human diseases
    • H.J. Cordell Detecting gene-gene interactions that underlie human diseases Nat. Rev. Genet. 10 2009 392 404
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 392-404
    • Cordell, H.J.1
  • 2
    • 84856155219 scopus 로고    scopus 로고
    • Gene-environment interactions in genome-wide association studies: A comparative study of tests applied to empirical studies of type 2 diabetes
    • M.C. Cornelis, E.J. Tchetgen, L. Liang, L. Qi, N. Chatterjee, F.B. Hu, and P. Kraft Gene-environment interactions in genome-wide association studies: a comparative study of tests applied to empirical studies of type 2 diabetes Am. J. Epidemiol. 175 2012 191 202
    • (2012) Am. J. Epidemiol. , vol.175 , pp. 191-202
    • Cornelis, M.C.1    Tchetgen, E.J.2    Liang, L.3    Qi, L.4    Chatterjee, N.5    Hu, F.B.6    Kraft, P.7
  • 3
    • 84856181067 scopus 로고    scopus 로고
    • Testing gene-environment interaction in large-scale case-control association studies: Possible choices and comparisons
    • B. Mukherjee, J. Ahn, S.B. Gruber, and N. Chatterjee Testing gene-environment interaction in large-scale case-control association studies: possible choices and comparisons Am. J. Epidemiol. 175 2012 177 190
    • (2012) Am. J. Epidemiol. , vol.175 , pp. 177-190
    • Mukherjee, B.1    Ahn, J.2    Gruber, S.B.3    Chatterjee, N.4
  • 4
    • 84904723024 scopus 로고    scopus 로고
    • Gene set analysis methods: Statistical models and methodological differences
    • H. Maciejewski Gene set analysis methods: statistical models and methodological differences Brief. Bioinform. 15 2014 504 518
    • (2014) Brief. Bioinform. , vol.15 , pp. 504-518
    • Maciejewski, H.1
  • 5
    • 84860350767 scopus 로고    scopus 로고
    • Multiple apical plasma membrane constituents are associated with susceptibility to meconium ileus in individuals with cystic fibrosis
    • L. Sun, J.M. Rommens, H. Corvol, W. Li, X. Li, T.A. Chiang, F. Lin, R. Dorfman, P.F. Busson, R.V. Parekh, and et al. Multiple apical plasma membrane constituents are associated with susceptibility to meconium ileus in individuals with cystic fibrosis Nat. Genet. 44 2012 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    Chiang, T.A.6    Lin, F.7    Dorfman, R.8    Busson, P.F.9    Parekh, R.V.10
  • 6
    • 0034973569 scopus 로고    scopus 로고
    • Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer
    • M.D. Ritchie, L.W. Hahn, N. Roodi, L.R. Bailey, W.D. Dupont, F.F. Parl, and J.H. Moore Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer Am. J. Hum. Genet. 69 2001 138 147
    • (2001) Am. J. Hum. Genet. , vol.69 , pp. 138-147
    • Ritchie, M.D.1    Hahn, L.W.2    Roodi, N.3    Bailey, L.R.4    Dupont, W.D.5    Parl, F.F.6    Moore, J.H.7
  • 13
    • 77954157546 scopus 로고    scopus 로고
    • On the use of variance per genotype as a tool to identify quantitative trait interaction effects: A report from the Women's Genome Health Study
    • G. Paré, N.R. Cook, P.M. Ridker, and D.I. Chasman On the use of variance per genotype as a tool to identify quantitative trait interaction effects: a report from the Women's Genome Health Study PLoS Genet. 6 2010 e1000981
    • (2010) PLoS Genet. , vol.6 , pp. e1000981
    • Paré, G.1    Cook, N.R.2    Ridker, P.M.3    Chasman, D.I.4
  • 15
    • 84894356274 scopus 로고    scopus 로고
    • Meta-analysis of SNPs involved in variance heterogeneity using Levene's test for equal variances
    • W.Q. Deng, S. Asma, and G. Pare Meta-analysis of SNPs involved in variance heterogeneity using Levene's test for equal variances Eur. J. Hum. Genet. 22 2014 427 430
    • (2014) Eur. J. Hum. Genet. , vol.22 , pp. 427-430
    • Deng, W.Q.1    Asma, S.2    Pare, G.3
  • 16
    • 84876413661 scopus 로고    scopus 로고
    • A nonparametric test to detect quantitative trait loci where the phenotypic distribution differs by genotypes
    • H. Aschard, N. Zaitlen, R.M. Tamimi, S. Lindström, and P. Kraft A nonparametric test to detect quantitative trait loci where the phenotypic distribution differs by genotypes Genet. Epidemiol. 37 2013 323 333
    • (2013) Genet. Epidemiol. , vol.37 , pp. 323-333
    • Aschard, H.1    Zaitlen, N.2    Tamimi, R.M.3    Lindström, S.4    Kraft, P.5
  • 17
    • 84890198059 scopus 로고    scopus 로고
    • A versatile omnibus test for detecting mean and variance heterogeneity
    • Y. Cao, P. Wei, M. Bailey, J.S. Kauwe, T.J. Maxwell Alzheimer's Disease Neuroimaging Initiative A versatile omnibus test for detecting mean and variance heterogeneity Genet. Epidemiol. 38 2014 51 59
    • (2014) Genet. Epidemiol. , vol.38 , pp. 51-59
    • Cao, Y.1    Wei, P.2    Bailey, M.3    Kauwe, J.S.4    Maxwell, T.J.5
  • 18
    • 77449128370 scopus 로고    scopus 로고
    • A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose
    • Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications Research Group
    • A.D. Paterson, D. Waggott, A.P. Boright, S.M. Hosseini, E. Shen, M.P. Sylvestre, I. Wong, B. Bharaj, P.A. Cleary, J.M. Lachin MAGIC (Meta-Analyses of Glucose and Insulin-related traits Consortium) Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications Research Group A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose Diabetes 59 2010 539 549
    • (2010) Diabetes , vol.59 , pp. 539-549
    • Paterson, A.D.1    Waggott, D.2    Boright, A.P.3    Hosseini, S.M.4    Shen, E.5    Sylvestre, M.P.6    Wong, I.7    Bharaj, B.8    Cleary, P.A.9    Lachin, J.M.10
  • 19
    • 84893158901 scopus 로고    scopus 로고
    • Unraveling the complex genetic model for cystic fibrosis: Pleiotropic effects of modifier genes on early cystic fibrosis-related morbidities
    • W. Li, D. Soave, M.R. Miller, K. Keenan, F. Lin, J. Gong, T. Chiang, A.L. Stephenson, P. Durie, J. Rommens, and et al. Unraveling the complex genetic model for cystic fibrosis: pleiotropic effects of modifier genes on early cystic fibrosis-related morbidities Hum. Genet. 133 2014 151 161
    • (2014) Hum. Genet. , vol.133 , pp. 151-161
    • Li, W.1    Soave, D.2    Miller, M.R.3    Keenan, K.4    Lin, F.5    Gong, J.6    Chiang, T.7    Stephenson, A.L.8    Durie, P.9    Rommens, J.10
  • 20
    • 84871102947 scopus 로고    scopus 로고
    • Robust and powerful tests for rare variants using Fisher's method to combine evidence of association from two or more complementary tests
    • A. Derkach, J.F. Lawless, and L. Sun Robust and powerful tests for rare variants using Fisher's method to combine evidence of association from two or more complementary tests Genet. Epidemiol. 37 2013 110 121
    • (2013) Genet. Epidemiol. , vol.37 , pp. 110-121
    • Derkach, A.1    Lawless, J.F.2    Sun, L.3
  • 21
    • 84907214453 scopus 로고    scopus 로고
    • Pooled association tests for rare genetic variants: A review and some new results
    • A. Derkach, J.F. Lawless, and L. Sun Pooled association tests for rare genetic variants: a review and some new results Stat. Sci. 29 2014 302 321
    • (2014) Stat. Sci. , vol.29 , pp. 302-321
    • Derkach, A.1    Lawless, J.F.2    Sun, L.3
  • 22
    • 73949084229 scopus 로고    scopus 로고
    • Karl Pearson's meta-analysis revisited
    • A.B. Owen Karl Pearson's meta-analysis revisited Ann. Stat. 37 2009 3867 3892
    • (2009) Ann. Stat. , vol.37 , pp. 3867-3892
    • Owen, A.B.1
  • 23
    • 84876122740 scopus 로고    scopus 로고
    • Nonparametric simultaneous tests for location and scale testing: S comparison of several methods
    • M. Marozzi Nonparametric simultaneous tests for location and scale testing: s comparison of several methods Commun. Stat. Simul. Comput. 42 2013 1298 1317
    • (2013) Commun. Stat. Simul. Comput. , vol.42 , pp. 1298-1317
    • Marozzi, M.1
  • 27
    • 78649508578 scopus 로고    scopus 로고
    • Mach: Using sequence and genotype data to estimate haplotypes and unobserved genotypes
    • Y. Li, C.J. Willer, J. Ding, P. Scheet, and G.R. Abecasis MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes Genet. Epidemiol. 34 2010 816 834
    • (2010) Genet. Epidemiol. , vol.34 , pp. 816-834
    • Li, Y.1    Willer, C.J.2    Ding, J.3    Scheet, P.4    Abecasis, G.R.5
  • 28
    • 42249087793 scopus 로고    scopus 로고
    • Estimation of significance thresholds for genomewide association scans
    • F. Dudbridge, and A. Gusnanto Estimation of significance thresholds for genomewide association scans Genet. Epidemiol. 32 2008 227 234
    • (2008) Genet. Epidemiol. , vol.32 , pp. 227-234
    • Dudbridge, F.1    Gusnanto, A.2
  • 29
    • 79952748854 scopus 로고    scopus 로고
    • Modulatory effect of the SLC9A3 gene on susceptibility to infections and pulmonary function in children with cystic fibrosis
    • R. Dorfman, C. Taylor, F. Lin, L. Sun, A. Sandford, P. Paré, Y. Berthiaume, M. Corey, P. Durie, J. Zielenski Members of Canadian Consortium for CF Genetic Studies Modulatory effect of the SLC9A3 gene on susceptibility to infections and pulmonary function in children with cystic fibrosis Pediatr. Pulmonol. 46 2011 385 392
    • (2011) Pediatr. Pulmonol. , vol.46 , pp. 385-392
    • Dorfman, R.1    Taylor, C.2    Lin, F.3    Sun, L.4    Sandford, A.5    Paré, P.6    Berthiaume, Y.7    Corey, M.8    Durie, P.9    Zielenski, J.10
  • 30
    • 34447629085 scopus 로고    scopus 로고
    • Regulatory binding partners and complexes of NHE3
    • M. Donowitz, and X. Li Regulatory binding partners and complexes of NHE3 Physiol. Rev. 87 2007 825 872
    • (2007) Physiol. Rev. , vol.87 , pp. 825-872
    • Donowitz, M.1    Li, X.2
  • 31
    • 0034703069 scopus 로고    scopus 로고
    • E3KARP mediates the association of ezrin and protein kinase A with the cystic fibrosis transmembrane conductance regulator in airway cells
    • F. Sun, M.J. Hug, C.M. Lewarchik, C.H. Yun, N.A. Bradbury, and R.A. Frizzell E3KARP mediates the association of ezrin and protein kinase A with the cystic fibrosis transmembrane conductance regulator in airway cells J. Biol. Chem. 275 2000 29539 29546
    • (2000) J. Biol. Chem. , vol.275 , pp. 29539-29546
    • Sun, F.1    Hug, M.J.2    Lewarchik, C.M.3    Yun, C.H.4    Bradbury, N.A.5    Frizzell, R.A.6
  • 32
    • 79951788578 scopus 로고    scopus 로고
    • Regulation of electroneutral NaCl absorption by the small intestine
    • A. Kato, and M.F. Romero Regulation of electroneutral NaCl absorption by the small intestine Annu. Rev. Physiol. 73 2011 261 281
    • (2011) Annu. Rev. Physiol. , vol.73 , pp. 261-281
    • Kato, A.1    Romero, M.F.2
  • 33
    • 67249153145 scopus 로고    scopus 로고
    • The role of the NHERF family of PDZ scaffolding proteins in the regulation of salt and water transport
    • U. Seidler, A.K. Singh, A. Cinar, M. Chen, J. Hillesheim, B. Hogema, and B. Riederer The role of the NHERF family of PDZ scaffolding proteins in the regulation of salt and water transport Ann. N Y Acad. Sci. 1165 2009 249 260
    • (2009) Ann. N y Acad. Sci. , vol.1165 , pp. 249-260
    • Seidler, U.1    Singh, A.K.2    Cinar, A.3    Chen, M.4    Hillesheim, J.5    Hogema, B.6    Riederer, B.7
  • 34
    • 84881662190 scopus 로고    scopus 로고
    • What is the significance of difference in phenotypic variability across SNP genotypes?
    • X. Sun, R. Elston, N. Morris, and X. Zhu What is the significance of difference in phenotypic variability across SNP genotypes? Am. J. Hum. Genet. 93 2013 390 397
    • (2013) Am. J. Hum. Genet. , vol.93 , pp. 390-397
    • Sun, X.1    Elston, R.2    Morris, N.3    Zhu, X.4
  • 35
    • 77957729947 scopus 로고    scopus 로고
    • Variance heterogeneity analysis for detection of potentially interacting genetic loci: Method and its limitations
    • M.V. Struchalin, A. Dehghan, J.C. Witteman, C. van Duijn, and Y.S. Aulchenko Variance heterogeneity analysis for detection of potentially interacting genetic loci: method and its limitations BMC Genet. 11 2010 92
    • (2010) BMC Genet. , vol.11 , pp. 92
    • Struchalin, M.V.1    Dehghan, A.2    Witteman, J.C.3    Van Duijn, C.4    Aulchenko, Y.S.5
  • 36
    • 84908234268 scopus 로고    scopus 로고
    • Gene-environment dependence creates spurious gene-environment interaction
    • F. Dudbridge, and O. Fletcher Gene-environment dependence creates spurious gene-environment interaction Am. J. Hum. Genet. 95 2014 301 307
    • (2014) Am. J. Hum. Genet. , vol.95 , pp. 301-307
    • Dudbridge, F.1    Fletcher, O.2
  • 38
    • 84885843711 scopus 로고    scopus 로고
    • Gene-environment interactions in cancer epidemiology: A National Cancer Institute Think Tank report
    • C.M. Hutter, L.E. Mechanic, N. Chatterjee, P. Kraft, E.M. Gillanders NCI Gene-Environment Think Tank Gene-environment interactions in cancer epidemiology: a National Cancer Institute Think Tank report Genet. Epidemiol. 37 2013 643 657
    • (2013) Genet. Epidemiol. , vol.37 , pp. 643-657
    • Hutter, C.M.1    Mechanic, L.E.2    Chatterjee, N.3    Kraft, P.4    Gillanders, E.M.5
  • 39
    • 84879603122 scopus 로고    scopus 로고
    • A generalized Kruskal-Wallis test incorporating group uncertainty with application to genetic association studies
    • E.F. Acar, and L. Sun A generalized Kruskal-Wallis test incorporating group uncertainty with application to genetic association studies Biometrics 69 2013 427 435
    • (2013) Biometrics , vol.69 , pp. 427-435
    • Acar, E.F.1    Sun, L.2
  • 43
    • 80053569489 scopus 로고    scopus 로고
    • Approximated distributions of the weighted sum of correlated chi-squared random variables
    • L.-L. Chuang, and Y.-S. Shih Approximated distributions of the weighted sum of correlated chi-squared random variables J. Stat. Plan. Inference 142 2012 457 472
    • (2012) J. Stat. Plan. Inference , vol.142 , pp. 457-472
    • Chuang, L.-L.1    Shih, Y.-S.2
  • 44
    • 20444434361 scopus 로고    scopus 로고
    • A simple approximation for the distribution of the weighted combination of non-independent or independent probabilities
    • C.-D. Hou A simple approximation for the distribution of the weighted combination of non-independent or independent probabilities Stat. Probab. Lett. 73 2005 179 187
    • (2005) Stat. Probab. Lett. , vol.73 , pp. 179-187
    • Hou, C.-D.1
  • 45
    • 77951152163 scopus 로고    scopus 로고
    • ProbABEL package for genome-wide association analysis of imputed data
    • Y.S. Aulchenko, M.V. Struchalin, and C.M. van Duijn ProbABEL package for genome-wide association analysis of imputed data BMC Bioinformatics 11 2010 134
    • (2010) BMC Bioinformatics , vol.11 , pp. 134
    • Aulchenko, Y.S.1    Struchalin, M.V.2    Van Duijn, C.M.3
  • 46
    • 0036155283 scopus 로고    scopus 로고
    • Score tests for association between traits and haplotypes when linkage phase is ambiguous
    • D.J. Schaid, C.M. Rowland, D.E. Tines, R.M. Jacobson, and G.A. Poland 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
  • 47
    • 0035055544 scopus 로고    scopus 로고
    • The family based association test method: Strategies for studying general genotype - Phenotype associations
    • S. Horvath, X. Xu, and N.M. Laird The family based association test method: strategies for studying general genotype - phenotype associations Eur. J. Hum. Genet. 9 2001 301 306
    • (2001) Eur. J. Hum. Genet. , vol.9 , pp. 301-306
    • Horvath, S.1    Xu, X.2    Laird, N.M.3
  • 48
    • 53049102597 scopus 로고    scopus 로고
    • A combinatorial approach to detecting gene-gene and gene-environment interactions in family studies
    • X.Y. Lou, G.B. Chen, L. Yan, J.Z. Ma, J.E. Mangold, J. Zhu, R.C. Elston, and M.D. Li A combinatorial approach to detecting gene-gene and gene-environment interactions in family studies Am. J. Hum. Genet. 83 2008 457 467
    • (2008) Am. J. Hum. Genet. , vol.83 , pp. 457-467
    • Lou, X.Y.1    Chen, G.B.2    Yan, L.3    Ma, J.Z.4    Mangold, J.E.5    Zhu, J.6    Elston, R.C.7    Li, M.D.8
  • 49
    • 84858010549 scopus 로고    scopus 로고
    • Family-based association tests using genotype data with uncertainty
    • Z. Yu Family-based association tests using genotype data with uncertainty Biostatistics 13 2012 228 240
    • (2012) Biostatistics , vol.13 , pp. 228-240
    • Yu, Z.1
  • 51
    • 34147108263 scopus 로고    scopus 로고
    • Snp.plotter: An R-based SNP/haplotype association and linkage disequilibrium plotting package
    • A. Luna, and K.K. Nicodemus snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package Bioinformatics 23 2007 774 776
    • (2007) Bioinformatics , vol.23 , pp. 774-776
    • Luna, A.1    Nicodemus, K.K.2


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