메뉴 건너뛰기




Volumn 104, Issue 4, 2010, Pages 401-409

Controlling false positives in the mapping of epistatic QTL

Author keywords

Epistasis; False positive; Multiple testing; Nested test framework; Power; Quantitative trait loci

Indexed keywords

EPISTASIS; GENOME; MAPPING METHOD; NESTING BEHAVIOR;

EID: 77950075619     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2009.129     Document Type: Article
Times cited : (28)

References (50)
  • 1
    • 34250718803 scopus 로고    scopus 로고
    • A unified model for functional and statistical epistasis and its application in quantitative trait Loci analysis
    • Alvarez-Castro JM, Carlborg O (2007). A unified model for functional and statistical epistasis and its application in quantitative trait Loci analysis. Genetics 176: 1151-1167.
    • (2007) Genetics , vol.176 , pp. 1151-1167
    • Alvarez-Castro, J.M.1    Carlborg, O.2
  • 3
    • 41949129310 scopus 로고    scopus 로고
    • From classical genetics to quantitative genetics to systems biology: Modeling epistasis
    • Aylor DL, Zeng Z-B (2008). From classical genetics to quantitative genetics to systems biology: modeling epistasis. PLoS Genet 4: e1000029.
    • (2008) PLoS Genet , vol.4
    • Aylor, D.L.1    Zeng, Z.-B.2
  • 5
    • 33748675883 scopus 로고    scopus 로고
    • Parallel multifactor dimensionality reduction: A tool for the large-scale analysis of gene-gene interactions
    • Bush WS, Dudek SM, Ritchie MD (2006). Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions. Bioinformatics 22: 2173-2174.
    • (2006) Bioinformatics , vol.22 , pp. 2173-2174
    • Bush, W.S.1    Dudek, S.M.2    Ritchie, M.D.3
  • 6
    • 24944555211 scopus 로고    scopus 로고
    • Hox genes specify vertebral types in the presomitic mesoderm
    • Carapuco M, Novoa A, Bobola N, Mallo M (2005). Hox genes specify vertebral types in the presomitic mesoderm. Genes Dev 19: 2116-2121.
    • (2005) Genes Dev , vol.19 , pp. 2116-2121
    • Carapuco, M.1    Novoa, A.2    Bobola, N.3    Mallo, M.4
  • 7
    • 0036251086 scopus 로고    scopus 로고
    • Use of randomization testing to detect multiple epistatic QTLs
    • Carlborg O, Andersson L (2002). Use of randomization testing to detect multiple epistatic QTLs. Genet Res 79: 175-184.
    • (2002) Genet Res , vol.79 , pp. 175-184
    • Carlborg, O.1    Andersson, L.2
  • 8
    • 0033879555 scopus 로고    scopus 로고
    • The use of a genetic algorithm for simultaneous mapping of multiple interacting quantitative trait loci
    • Carlborg O, Andersson L, Kinghorn B (2000). The use of a genetic algorithm for simultaneous mapping of multiple interacting quantitative trait loci. Genetics 155: 2003-2010.
    • (2000) Genetics , vol.155 , pp. 2003-2010
    • Carlborg, O.1    Andersson, L.2    Kinghorn, B.3
  • 9
    • 24644490562 scopus 로고    scopus 로고
    • Simultaneous mapping of epistatic QTL in DU6i x DBA/2 mice
    • Carlborg O, Brockmann GA, Haley CS (2005). Simultaneous mapping of epistatic QTL in DU6i x DBA/2 mice. Mamm Genome 16: 481-494.
    • (2005) Mamm Genome , vol.16 , pp. 481-494
    • Carlborg, O.1    Brockmann, G.A.2    Haley, C.S.3
  • 10
    • 3442894519 scopus 로고    scopus 로고
    • Epistasis: Too often neglected in complex trait studies?
    • Carlborg O, Haley CS (2004). Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5: 618-625.
    • (2004) Nat Rev Genet , vol.5 , pp. 618-625
    • Carlborg, O.1    Haley, C.S.2
  • 11
    • 33645381715 scopus 로고    scopus 로고
    • Epistasis and the release of genetic variation during long-term selection
    • Carlborg O, Jacobsson L, Ahgren P, Siegel P, Andersson L (2006). Epistasis and the release of genetic variation during long-term selection. Nat Genet 38: 418-420.
    • (2006) Nat Genet , vol.38 , pp. 418-420
    • Carlborg, O.1    Jacobsson, L.2    Ahgren, P.3    Siegel, P.4    Andersson, L.5
  • 12
    • 0037350268 scopus 로고    scopus 로고
    • A global search reveals epistatic interaction between QTL for early growth in the chicken
    • Carlborg O, Kerje S, Schutz K, Jacobsson L, Jensen P, Andersson L (2003). A global search reveals epistatic interaction between QTL for early growth in the chicken. Genome Res 13: 413-421.
    • (2003) Genome Res , vol.13 , pp. 413-421
    • Carlborg, O.1    Kerje, S.2    Schutz, K.3    Jacobsson, L.4    Jensen, P.5    Andersson, L.6
  • 13
    • 0028151261 scopus 로고
    • Empirical threshold values for quantitative triat mapping
    • Churchill GA, Doerge RW (1994). Empirical threshold values for quantitative triat mapping. Genetics 138: 963-971.
    • (1994) Genetics , vol.138 , pp. 963-971
    • Churchill, G.A.1    Doerge, R.W.2
  • 14
    • 33846277942 scopus 로고    scopus 로고
    • The evolution of sex: Empirical insights into the roles of epistasis and drift
    • de Visser JAGM, Elena SF (2007). The evolution of sex: empirical insights into the roles of epistasis and drift. Nat Rev Genet 8: 139-149.
    • (2007) Nat Rev Genet , vol.8 , pp. 139-149
    • De Visser Jagm1    Elena, S.F.2
  • 16
    • 0037433052 scopus 로고    scopus 로고
    • Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions
    • Hahn LW, Ritchie MD, Moore JH (2003). Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics 19: 376-382.
    • (2003) Bioinformatics , vol.19 , pp. 376-382
    • Hahn, L.W.1    Ritchie, M.D.2    Moore, J.H.3
  • 17
    • 33646942472 scopus 로고
    • A simple regression method for mapping quantitative trait loci in line crosses using flanking markers
    • Haley CS, Knott SA (1992). A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315-324.
    • (1992) Heredity , vol.69 , pp. 315-324
    • Haley, C.S.1    Knott, S.A.2
  • 18
    • 40149087235 scopus 로고    scopus 로고
    • Data and theory point to mainly additive genetic variance for complex traits
    • Hill WG, Goddard ME, Visscher PM (2008). Data and theory point to mainly additive genetic variance for complex traits. PLoS Genet 4: e1000008.
    • (2008) PLoS Genet , vol.4
    • Hill, W.G.1    Goddard, M.E.2    Visscher, P.M.3
  • 19
    • 0001002693 scopus 로고
    • Simulation of quantitative characters from qualitatively acting genes. I. Nonallelic gene interactions involving two or three loci
    • Jana S (1971). Simulation of quantitative characters from qualitatively acting genes. I. Nonallelic gene interactions involving two or three loci. Theor Appl Genet 41: 216-226.
    • (1971) Theor Appl Genet , vol.41 , pp. 216-226
    • Jana, S.1
  • 20
    • 33846646557 scopus 로고
    • Simulation of quantitative characters from qualitatively acting genes. II. Orthogonal subdivision of hereditary variance in two-locus genetic systems
    • Jana S (1972). Simulation of quantitative characters from qualitatively acting genes. II. Orthogonal subdivision of hereditary variance in two-locus genetic systems. Theor Appl Genet 42: 119-124.
    • (1972) Theor Appl Genet , vol.42 , pp. 119-124
    • Jana, S.1
  • 21
    • 0035148614 scopus 로고    scopus 로고
    • Mapping epistatic quantitative trait loci with one-dimensional genome searches
    • Jannink J-L, Jansen R (2001). Mapping epistatic quantitative trait loci with one-dimensional genome searches. Genetics 157: 445-454.
    • (2001) Genetics , vol.157 , pp. 445-454
    • Jannink, J.-L.1    Jansen, R.2
  • 22
    • 42249099044 scopus 로고    scopus 로고
    • Increasing the power of identifying gene x gene interactions in genome-wide association studies
    • Kooperberg C, Leblanc M (2008). Increasing the power of identifying gene x gene interactions in genome-wide association studies. Genet Epidemiol 32: 255-263.
    • (2008) Genet Epidemiol , vol.32 , pp. 255-263
    • Kooperberg, C.1    Leblanc, M.2
  • 23
    • 53749090751 scopus 로고    scopus 로고
    • Estimation of genetic effects and genotype-phenotype maps
    • Le Rouzic A, Alvarez-Castro JM (2008). Estimation of genetic effects and genotype-phenotype maps. Evol Bioinform 4: 225-235.
    • (2008) Evol Bioinform , vol.4 , pp. 225-235
    • Le Rouzic, A.1    Alvarez-Castro, J.M.2
  • 24
    • 3442879533 scopus 로고    scopus 로고
    • Simultaneous search for multiple QTL using the global optimization algorithm DIRECT
    • Ljungberg K, Holmgren S, Carlborg O (2004). Simultaneous search for multiple QTL using the global optimization algorithm DIRECT. Bioinformatics 20: 1887-1895.
    • (2004) Bioinformatics , vol.20 , pp. 1887-1895
    • Ljungberg, K.1    Holmgren, S.2    Carlborg, O.3
  • 25
    • 69949142078 scopus 로고    scopus 로고
    • Genome-wide identification of quantitative trait loci for carcass composition and meat quality in a large-scale White Duroc x Chinese Erhualian resource population
    • Ma J, Ren J, Guo Y, Duan Y, Ding N, Zhou L et al. (2009). Genome-wide identification of quantitative trait loci for carcass composition and meat quality in a large-scale White Duroc x Chinese Erhualian resource population. Anim Genet 40: 637-647.
    • (2009) Anim Genet , vol.40 , pp. 637-647
    • Ma, J.1    Ren, J.2    Guo, Y.3    Duan, Y.4    Ding, N.5    Zhou, L.6
  • 26
    • 29244456137 scopus 로고    scopus 로고
    • QTL-based evidence for the role of epistasis in evolution
    • Malmberg RL, Mauricio R (2005). QTL-based evidence for the role of epistasis in evolution. Genet Res 86: 89-95.
    • (2005) Genet Res , vol.86 , pp. 89-95
    • Malmberg, R.L.1    Mauricio, R.2
  • 27
    • 42949084703 scopus 로고    scopus 로고
    • Polymorphism interaction analysis (PIA): A method for investigating complex gene-gene interactions
    • Mechanic LE, Luke BT, Goodman JE, Chanock SJ, Harris CC (2008). Polymorphism interaction analysis (PIA): a method for investigating complex gene-gene interactions. BMC Bioinformatics 9: 146.
    • (2008) BMC Bioinformatics , vol.9 , pp. 146
    • Mechanic, L.E.1    Luke, B.T.2    Goodman, J.E.3    Chanock, S.J.4    Harris, C.C.5
  • 29
    • 72249093591 scopus 로고    scopus 로고
    • A computationally efficient hypothesis testing method for epistasis analysis using multifactor dimensionality reduction
    • Pattin KA, White BC, Barney N, Gui J, Nelson HH, Kelsey KT et al. (2008). A computationally efficient hypothesis testing method for epistasis analysis using multifactor dimensionality reduction. Genet Epidemiol 31: 31.
    • (2008) Genet Epidemiol , vol.31 , pp. 31
    • Pattin, K.A.1    White, B.C.2    Barney, N.3    Gui, J.4    Nelson, H.H.5    Kelsey, K.T.6
  • 31
    • 54149088214 scopus 로고    scopus 로고
    • Epistasis-the essential role of gene interactions in the structure and evolution of genetic systems
    • Phillips PC (2008). Epistasis-the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9: 855-867.
    • (2008) Nat Rev Genet , vol.9 , pp. 855-867
    • Phillips, P.C.1
  • 32
    • 40749097651 scopus 로고    scopus 로고
    • Methods for handling multiple testing
    • Rice TK, Schork NJ, Rao DC (2008). Methods for handling multiple testing. Adv Genet 60: 293-308.
    • (2008) Adv Genet , vol.60 , pp. 293-308
    • Rice, T.K.1    Schork, N.J.2    Rao, D.C.3
  • 33
    • 28444434756 scopus 로고    scopus 로고
    • Multifactor dimensionality reduction for detecting gene-gene and gene-environment interactions in pharmacogenomics studies
    • Ritchie MD, Motsinger AA (2005). Multifactor dimensionality reduction for detecting gene-gene and gene-environment interactions in pharmacogenomics studies. Pharmacogenomics 6: 823-834.
    • (2005) Pharmacogenomics , vol.6 , pp. 823-834
    • Ritchie, M.D.1    Motsinger, A.A.2
  • 35
    • 0034817026 scopus 로고    scopus 로고
    • A statistical framework for quantitative trait mapping
    • Sen S, Churchill GA (2001). A statistical framework for quantitative trait mapping. Genetics 159: 371-387.
    • (2001) Genetics , vol.159 , pp. 371-387
    • Sen, S.1    Churchill, G.A.2
  • 36
    • 34548570371 scopus 로고    scopus 로고
    • Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy
    • Stich B, Yu J, Melchinger AE, Piepho HP, Utz HF, Maurer HP et al. (2007). Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy. Genetics 176: 563-570.
    • (2007) Genetics , vol.176 , pp. 563-570
    • Stich, B.1    Yu, J.2    Melchinger, A.E.3    Piepho, H.P.4    Utz, H.F.5    Maurer, H.P.6
  • 37
    • 23644434473 scopus 로고    scopus 로고
    • Multiple locus linkage analysis of genomewide expression in yeast
    • Storey JD, Akey JM, Kruglyak L (2005). Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biol 3: e267.
    • (2005) PLoS Biol , vol.3
    • Storey, J.D.1    Akey, J.M.2    Kruglyak, L.3
  • 38
    • 30744473697 scopus 로고    scopus 로고
    • Quantitative trait locus analysis for obesity reveals multiple networks of interacting loci
    • Stylianou IM, Korstanje R, Li R, Sheehan S, Paigen B, Churchill GA (2006). Quantitative trait locus analysis for obesity reveals multiple networks of interacting loci. Mamm Genome 17: 22-36.
    • (2006) Mamm Genome , vol.17 , pp. 22-36
    • Stylianou, I.M.1    Korstanje, R.2    Li, R.3    Sheehan, S.4    Paigen, B.5    Churchill, G.A.6
  • 39
    • 0035140274 scopus 로고    scopus 로고
    • Concordance of murine quantitative trait loci for salt-induced hypertension with rat and human loci
    • Sugiyama F, Churchill GA, Higgins DC, Johns C, Makaritsis KP, Gavras H et al. (2001). Concordance of murine quantitative trait loci for salt-induced hypertension with rat and human loci. Genomics 71: 70-77.
    • (2001) Genomics , vol.71 , pp. 70-77
    • Sugiyama, F.1    Churchill, G.A.2    Higgins, D.C.3    Johns, C.4    Makaritsis, K.P.5    Gavras, H.6
  • 40
    • 33846407807 scopus 로고    scopus 로고
    • Accounting for epistasis in linkage analysis of general pedigrees
    • Sung YJ, Wijsman EM (2007). Accounting for epistasis in linkage analysis of general pedigrees. Hum Hered 63: 144-152.
    • (2007) Hum Hered , vol.63 , pp. 144-152
    • Sung, Y.J.1    Wijsman, E.M.2
  • 41
    • 33646238044 scopus 로고    scopus 로고
    • Models and partition of variance for quantitative trait loci with epistasis and linkage disequilibrium
    • Wang T, Zeng ZB (2006). Models and partition of variance for quantitative trait loci with epistasis and linkage disequilibrium. BMC Genet 7: 9.
    • (2006) BMC Genet , vol.7 , pp. 9
    • Wang, T.1    Zeng, Z.B.2
  • 43
    • 34249023066 scopus 로고    scopus 로고
    • Genome-wide analysis of epistatic effects for quantitative traits in barley
    • Xu S, Jia Z (2007). Genome-wide analysis of epistatic effects for quantitative traits in barley. Genetics 175: 1955-1963.
    • (2007) Genetics , vol.175 , pp. 1955-1963
    • Xu, S.1    Jia, Z.2
  • 45
    • 34547830821 scopus 로고    scopus 로고
    • Mapping the genetic architecture of complex traits in experimental populations
    • Yang J, Zhu J, Williams RW (2007). Mapping the genetic architecture of complex traits in experimental populations. Bioinformatics 23: 1527-1536.
    • (2007) Bioinformatics , vol.23 , pp. 1527-1536
    • Yang, J.1    Zhu, J.2    Williams, R.W.3
  • 46
    • 39549086997 scopus 로고    scopus 로고
    • Advances in Bayesian multiple quantitative trait loci mapping in experimental crosses
    • Yi N, Shriner D (2008). Advances in Bayesian multiple quantitative trait loci mapping in experimental crosses. Heredity 100: 240-252.
    • (2008) Heredity , vol.100 , pp. 240-252
    • Yi, N.1    Shriner, D.2
  • 47
    • 0036255620 scopus 로고    scopus 로고
    • Mapping quantitative trait loci with epistatic effects
    • Yi N, Xu S (2002). Mapping quantitative trait loci with epistatic effects. Genet Res 79: 185-198.
    • (2002) Genet Res , vol.79 , pp. 185-198
    • Yi, N.1    Xu, S.2
  • 48
    • 0242381258 scopus 로고    scopus 로고
    • Bayesian model choice and search strategies for mapping interacting quantitative trait Loci
    • Yi N, Xu S, Allison DB (2003). Bayesian model choice and search strategies for mapping interacting quantitative trait Loci. Genetics 165: 867-883.
    • (2003) Genetics , vol.165 , pp. 867-883
    • Yi, N.1    Xu, S.2    Allison, D.B.3
  • 49
    • 17444397012 scopus 로고    scopus 로고
    • Modeling quantitative trait Loci and interpretation of models
    • Zeng ZB, Wang T, Zou W (2005). Modeling quantitative trait Loci and interpretation of models. Genetics 169: 1711-1725.
    • (2005) Genetics , vol.169 , pp. 1711-1725
    • Zeng, Z.B.1    Wang, T.2    Zou, W.3
  • 50
    • 34548352849 scopus 로고    scopus 로고
    • Bayesian inference of epistatic interactions in case-control studies
    • Zhang Y, Liu JS (2007). Bayesian inference of epistatic interactions in case-control studies. Nat Genet 39: 1167-1173.
    • (2007) Nat Genet , vol.39 , pp. 1167-1173
    • Zhang, Y.1    Liu, J.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.