메뉴 건너뛰기




Volumn 9, Issue 1, 2014, Pages

Rare variant association testing by adaptive combination of P-values

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE COMBINATION OF P VALUES FOR RARE VARIANT ASSOCIATION TESTING; ANALYTIC METHOD; ARTICLE; CONCEPTUAL FRAMEWORK; DATA ANALYSIS; FUNCTIONAL ASSESSMENT; GENE LINKAGE DISEQUILIBRIUM; GENE MUTATION; GENETIC ASSOCIATION; GENETIC VARIABILITY; MATHEMATICAL ANALYSIS; NEXT GENERATION SEQUENCING; SIMULATION;

EID: 84898618563     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0085728     Document Type: Article
Times cited : (27)

References (45)
  • 2
    • 50949095168 scopus 로고    scopus 로고
    • Methods for detecting associations with rare variants for common diseases: Application to analysis of sequence data
    • Li B, Leal SM (2008) Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 83:311-321.
    • (2008) Am J Hum Genet , vol.83 , pp. 311-321
    • Li, B.1    Leal, S.M.2
  • 3
    • 61449168010 scopus 로고    scopus 로고
    • A groupwise association test for rare mutations using a weighted sum statistic
    • Madsen BE, Browning SR (2009) A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5:e1000384.
    • (2009) PLoS Genet , vol.5
    • Madsen, B.E.1    Browning, S.R.2
  • 4
    • 76649136928 scopus 로고    scopus 로고
    • An evaluation of statistical approaches to rare variant analysis in genetic association studies
    • Morris AP, Zeggini E (2010) An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 34:188-193.
    • (2010) Genet Epidemiol , vol.34 , pp. 188-193
    • Morris, A.P.1    Zeggini, E.2
  • 6
    • 77951028197 scopus 로고    scopus 로고
    • A data-adaptive sum test for disease association with multiple common or rare variants
    • Han F, Pan W (2010) A data-adaptive sum test for disease association with multiple common or rare variants. Hum Hered 70:42-54.
    • (2010) Hum Hered , vol.70 , pp. 42-54
    • Han, F.1    Pan, W.2
  • 7
    • 80051499915 scopus 로고    scopus 로고
    • Rare-variant association testing for sequencing data with the sequence kernel association test
    • Wu MC, Lee S, Cai T, Li Y, Boehnke M, et al. (2011) Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet 89:82-93.
    • (2011) Am J Hum Genet , vol.89 , pp. 82-93
    • Wu, M.C.1    Lee, S.2    Cai, T.3    Li, Y.4    Boehnke, M.5
  • 8
    • 84864953892 scopus 로고    scopus 로고
    • Optimal tests for rare variant effects in sequencing association studies
    • Lee S, Wu MC, Lin X (2012) Optimal tests for rare variant effects in sequencing association studies. Biostatistics 13:762-775.
    • (2012) Biostatistics , vol.13 , pp. 762-775
    • Lee, S.1    Wu, M.C.2    Lin, X.3
  • 10
    • 84855295482 scopus 로고    scopus 로고
    • Hierarchical generalized linear models for multiple groups of rare and common variants: Jointly estimating group and individual-variant effects
    • Yi N, Liu N, Zhi D, Li J (2011) Hierarchical generalized linear models for multiple groups of rare and common variants: jointly estimating group and individual-variant effects. PLoS Genet 7:e1002382.
    • (2011) PLoS Genet , vol.7
    • Yi, N.1    Liu, N.2    Zhi, D.3    Li, J.4
  • 11
    • 78650363812 scopus 로고    scopus 로고
    • Bayesian analysis of rare variants in genetic association studies
    • Yi N, Zhi D (2011) Bayesian analysis of rare variants in genetic association studies. Genet Epidemiol 35:57-69.
    • (2011) Genet Epidemiol , vol.35 , pp. 57-69
    • Yi, N.1    Zhi, D.2
  • 12
    • 82455173743 scopus 로고    scopus 로고
    • Evaluation of pooled association tests for rare variant identification
    • Lin WY, Zhang B, Yi N, Gao G, Liu N (2011) Evaluation of pooled association tests for rare variant identification. BMC Proc 5 Suppl 9:S118.
    • (2011) BMC Proc , vol.5 , Issue.SUPPL. 9
    • Lin, W.Y.1    Zhang, B.2    Yi, N.3    Gao, G.4    Liu, N.5
  • 13
    • 80054728031 scopus 로고    scopus 로고
    • Comparison of statistical tests for disease association with rare variants
    • Basu S, Pan W (2011) Comparison of statistical tests for disease association with rare variants. Genet Epidemiol 35:606-619.
    • (2011) Genet Epidemiol , vol.35 , pp. 606-619
    • Basu, S.1    Pan, W.2
  • 14
    • 84867555327 scopus 로고    scopus 로고
    • A fast and noise-resilient approach to detect rare-variant associations with deep sequencing data for complex disorders
    • Cheung YH, Wang G, Leal SM, Wang S (2012) A fast and noise-resilient approach to detect rare-variant associations with deep sequencing data for complex disorders. Genet Epidemiol 36:675-685.
    • (2012) Genet Epidemiol , vol.36 , pp. 675-685
    • Cheung, Y.H.1    Wang, G.2    Leal, S.M.3    Wang, S.4
  • 16
    • 79952253512 scopus 로고    scopus 로고
    • A new testing strategy to identify rare variants with either risk or protective effect on disease
    • Ionita-Laza I, Buxbaum JD, Laird NM, Lange C (2011) A new testing strategy to identify rare variants with either risk or protective effect on disease. PLoS Genet 7:e1001289.
    • (2011) PLoS Genet , vol.7
    • Ionita-Laza, I.1    Buxbaum, J.D.2    Laird, N.M.3    Lange, C.4
  • 17
    • 80052731371 scopus 로고    scopus 로고
    • A general framework for detecting disease associations with rare variants in sequencing studies
    • Lin DY, Tang ZZ (2011) A general framework for detecting disease associations with rare variants in sequencing studies. Am J Hum Genet 89:354-367.
    • (2011) Am J Hum Genet , vol.89 , pp. 354-367
    • Lin, D.Y.1    Tang, Z.Z.2
  • 18
  • 19
    • 82455170532 scopus 로고    scopus 로고
    • Region-based and pathway-based QTL mapping using a p-value combination method
    • Yang HC, Chen CW (2011) Region-based and pathway-based QTL mapping using a p-value combination method. BMC Proc 5 Suppl 9:S43.
    • (2011) BMC Proc , vol.5 , Issue.SUPPL. 9
    • Yang, H.C.1    Chen, C.W.2
  • 20
    • 38749145596 scopus 로고    scopus 로고
    • Shifting paradigm of association studies: Value of rare single-nucleotide polymorphisms
    • DOI 10.1016/j.ajhg.2007.09.006, PII S0002929707000122
    • Gorlov IP, Gorlova OY, Sunyaev SR, Spitz MR, Amos CI (2008) Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. Am J Hum Genet 82:100-112. (Pubitemid 351726083)
    • (2008) American Journal of Human Genetics , vol.82 , Issue.1 , pp. 100-112
    • Gorlov, I.P.1    Gorlova, O.Y.2    Sunyaev, S.R.3    Spitz, M.R.4    Amos, C.I.5
  • 21
    • 55449120805 scopus 로고    scopus 로고
    • Genetic mapping in human disease
    • Altshuler D, Daly MJ, Lander ES (2008) Genetic mapping in human disease. Science 322:881-888.
    • (2008) Science , vol.322 , pp. 881-888
    • Altshuler, D.1    Daly, M.J.2    Lander, E.S.3
  • 22
    • 77958102016 scopus 로고    scopus 로고
    • Statistical analysis strategies for association studies involving rare variants
    • Bansal V, Libiger O, Torkamani A, Schork NJ (2010) Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet 11:773-785.
    • (2010) Nat Rev Genet , vol.11 , pp. 773-785
    • Bansal, V.1    Libiger, O.2    Torkamani, A.3    Schork, N.J.4
  • 24
    • 34047177395 scopus 로고    scopus 로고
    • Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL
    • DOI 10.1038/ng1984, PII NG1984
    • Romeo S, Pennacchio LA, Fu Y, Boerwinkle E, Tybjaerg-Hansen A, et al. (2007) Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nat Genet 39:513-516. (Pubitemid 46514768)
    • (2007) Nature Genetics , vol.39 , Issue.4 , pp. 513-516
    • Romeo, S.1    Pennacchio, L.A.2    Fu, Y.3    Boerwinkle, E.4    Tybjaerg-Hansen, A.5    Hobbs, H.H.6    Cohen, J.C.7
  • 25
    • 61749090233 scopus 로고    scopus 로고
    • Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans
    • Romeo S, Yin W, Kozlitina J, Pennacchio LA, Boerwinkle E, et al. (2009) Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans. J Clin Invest 119:70-79.
    • (2009) J Clin Invest , vol.119 , pp. 70-79
    • Romeo, S.1    Yin, W.2    Kozlitina, J.3    Pennacchio, L.A.4    Boerwinkle, E.5
  • 27
    • 27544497650 scopus 로고    scopus 로고
    • Calibrating a coalescent simulation of human genome sequence variation
    • DOI 10.1101/gr.3709305
    • Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, et al. (2005) Calibrating a coalescent simulation of human genome sequence variation. Genome Res 15:1576-1583. (Pubitemid 41545011)
    • (2005) Genome Research , vol.15 , Issue.11 , pp. 1576-1583
    • Schaffner, S.F.1    Foo, C.2    Gabriel, S.3    Reich, D.4    Daly, M.J.5    Altshuler, D.6
  • 28
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • Hudson RR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18:337-338. (Pubitemid 34183119)
    • (2002) Bioinformatics , vol.18 , Issue.2 , pp. 337-338
    • Hudson, R.R.1
  • 29
    • 78249272314 scopus 로고    scopus 로고
    • To identify associations with rare variants, just WHaIT: Weighted haplotype and imputation-based tests
    • Li Y, Byrnes AE, Li M (2010) To identify associations with rare variants, just WHaIT: Weighted haplotype and imputation-based tests. Am J Hum Genet 87:728-735.
    • (2010) Am J Hum Genet , vol.87 , pp. 728-735
    • Li, Y.1    Byrnes, A.E.2    Li, M.3
  • 30
    • 84881617137 scopus 로고    scopus 로고
    • Haplotype kernel association test as a powerful method to identify chromosomal regions harboring uncommon causal variants
    • Lin WY, Yi N, Lou XY, Zhi D, Zhang K, et al. (2013) Haplotype kernel association test as a powerful method to identify chromosomal regions harboring uncommon causal variants. Genet Epidemiol 37:560-570.
    • (2013) Genet Epidemiol , vol.37 , pp. 560-570
    • Lin, W.Y.1    Yi, N.2    Lou, X.Y.3    Zhi, D.4    Zhang, K.5
  • 31
    • 84865093332 scopus 로고    scopus 로고
    • Haplotype-based methods for detecting uncommon causal variants with common SNPs
    • Lin WY, Yi N, Zhi D, Zhang K, Gao G, et al. (2012) Haplotype-based methods for detecting uncommon causal variants with common SNPs. Genet Epidemiol 36:572-582.
    • (2012) Genet Epidemiol , vol.36 , pp. 572-582
    • Lin, W.Y.1    Yi, N.2    Zhi, D.3    Zhang, K.4    Gao, G.5
  • 32
    • 84898623125 scopus 로고    scopus 로고
    • Accessed Jan 2, 2013
    • Lee S, Miropolsky L, Wu M (2013) Package 'SKAT', http://cran. r-project.org/web/packages/SKAT/index.html. Accessed Jan 2, 2013.
    • (2013)
    • Lee, S.1    Miropolsky, L.2    Wu, M.3
  • 35
    • 34147116715 scopus 로고    scopus 로고
    • Most rare missense alleles are deleterious in humans: Implications for complex disease and association studies
    • DOI 10.1086/513473
    • Kryukov GV, Pennacchio LA, Sunyaev SR (2007) Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet 80:727-739. (Pubitemid 46564409)
    • (2007) American Journal of Human Genetics , vol.80 , Issue.4 , pp. 727-739
    • Kryukov, G.V.1    Pennacchio, L.A.2    Sunyaev, S.R.3
  • 37
    • 78449245227 scopus 로고    scopus 로고
    • A novel adaptive method for the analysis of nextgeneration sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions
    • Liu DJ, Leal SM (2010) A novel adaptive method for the analysis of nextgeneration sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions. PLoS Genet 6:e1001156.
    • (2010) PLoS Genet , vol.6
    • Liu, D.J.1    Leal, S.M.2
  • 38
    • 77952574849 scopus 로고    scopus 로고
    • Uncovering the roles of rare variants in common disease through whole-genome sequencing
    • Cirulli ET, Goldstein DB (2010) Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet 11:415-425.
    • (2010) Nat Rev Genet , vol.11 , pp. 415-425
    • Cirulli, E.T.1    Goldstein, D.B.2
  • 39
    • 84855925920 scopus 로고    scopus 로고
    • Rare and common variants: Twenty arguments
    • Gibson G (2012) Rare and common variants: twenty arguments. Nat Rev Genet 13:135-145.
    • (2012) Nat Rev Genet , vol.13 , pp. 135-145
    • Gibson, G.1
  • 41
    • 3843056691 scopus 로고    scopus 로고
    • Multiple rare alleles contribute to low plasma levels of HDL cholesterol
    • DOI 10.1126/science.1099870
    • Cohen JC, Kiss RS, Pertsemlidis A, Marcel YL, McPherson R, et al. (2004) Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 305:869-872. (Pubitemid 39038422)
    • (2004) Science , vol.305 , Issue.5685 , pp. 869-872
    • Cohen, J.C.1    Kiss, R.S.2    Pertsemlidis, A.3    Marcel, Y.L.4    McPherson, R.5    Hobbs, H.H.6
  • 42
    • 77953023261 scopus 로고    scopus 로고
    • Coding sequence rare variants identified in MYBPC3, MYH6, TPM1, TNNC1, and TNNI3 from 312 patients with familial or idiopathic dilated cardiomyopathy
    • Hershberger RE, Norton N, Morales A, Li D, Siegfried JD, et al. (2010) Coding sequence rare variants identified in MYBPC3, MYH6, TPM1, TNNC1, and TNNI3 from 312 patients with familial or idiopathic dilated cardiomyopathy. Circ Cardiovasc Genet 3:155-161.
    • (2010) Circ Cardiovasc Genet , vol.3 , pp. 155-161
    • Hershberger, R.E.1    Norton, N.2    Morales, A.3    Li, D.4    Siegfried, J.D.5
  • 43
    • 44349132708 scopus 로고    scopus 로고
    • Common and rare variants in multifactorial susceptibility to common diseases
    • DOI 10.1038/ng.f.136, PII NGF136
    • Bodmer W, Bonilla C (2008) Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 40:695-701. (Pubitemid 351748875)
    • (2008) Nature Genetics , vol.40 , Issue.6 , pp. 695-701
    • Bodmer, W.1    Bonilla, C.2
  • 45
    • 0034969437 scopus 로고    scopus 로고
    • Are rare variants responsible for susceptibility to complex diseases?
    • DOI 10.1086/321272
    • Pritchard JK (2001) Are rare variants responsible for susceptibility to complex diseases? Am J Hum Genet 69:124-137. (Pubitemid 32614025)
    • (2001) American Journal of Human Genetics , vol.69 , Issue.1 , pp. 124-137
    • Pritchard, J.K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.