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Volumn 38, Issue 6, 2014, Pages 560-571

A General Efficient and Flexible Approach for Genome-Wide Association Analyses of Imputed Genotypes in Family-Based Designs

Author keywords

Family based association test; Genetic imputation; Genome wide association studies; Leprosy

Indexed keywords

INTERLEUKIN 23 RECEPTOR; IL23R PROTEIN, HUMAN; INTERLEUKIN RECEPTOR; RAB PROTEIN; RAB32 PROTEIN, HUMAN;

EID: 84907811699     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21842     Document Type: Article
Times cited : (22)

References (50)
  • 2
    • 79954600411 scopus 로고    scopus 로고
    • Human leukocyte antigen class I region single-nucleotide polymorphisms are associated with leprosy susceptibility in Vietnam and India
    • Alter A, Huong NT, Singh M, Orlova M, Van Thuc N, Katoch K, Gao X, Thai VH, Ba NN, Carrington M and others. 2011. Human leukocyte antigen class I region single-nucleotide polymorphisms are associated with leprosy susceptibility in Vietnam and India. J Infect Dis 203(9):1274-1281.
    • (2011) J Infect Dis , vol.203 , Issue.9 , pp. 1274-1281
    • Alter, A.1    Huong, N.T.2    Singh, M.3    Orlova, M.4    Van Thuc, N.5    Katoch, K.6    Gao, X.7    Thai, V.H.8    Ba, N.N.9    Carrington, M.10
  • 3
    • 34447324105 scopus 로고    scopus 로고
    • GenABEL: an R library for genome-wide association analysis
    • Aulchenko YS, Ripke S, Isaacs A, van Duijn CM. 2007. GenABEL: an R library for genome-wide association analysis. Bioinformatics 23(10):1294-1296.
    • (2007) Bioinformatics , vol.23 , Issue.10 , pp. 1294-1296
    • Aulchenko, Y.S.1    Ripke, S.2    Isaacs, A.3    van Duijn, C.M.4
  • 4
  • 5
    • 0037228604 scopus 로고    scopus 로고
    • Correcting for nonrandom ascertainment in generalized linear mixed models (GLMMs), fitted using Gibbs sampling
    • Burton PR. 2003. Correcting for nonrandom ascertainment in generalized linear mixed models (GLMMs), fitted using Gibbs sampling. Genet Epidemiol 24(1):24-35.
    • (2003) Genet Epidemiol , vol.24 , Issue.1 , pp. 24-35
    • Burton, P.R.1
  • 6
    • 34547628858 scopus 로고    scopus 로고
    • Family-based association tests for genomewide association scans
    • Chen WM, Abecasis GR. 2007. Family-based association tests for genomewide association scans. Am J Hum Genet 81(5):913-926.
    • (2007) Am J Hum Genet , vol.81 , Issue.5 , pp. 913-926
    • Chen, W.M.1    Abecasis, G.R.2
  • 7
    • 84856478855 scopus 로고    scopus 로고
    • A linear complexity phasing method for thousands of genomes
    • Delaneau O, Marchini J, Zagury JF. 2012. A linear complexity phasing method for thousands of genomes. Nat Methods 9(2):179-181.
    • (2012) Nat Methods , vol.9 , Issue.2 , pp. 179-181
    • Delaneau, O.1    Marchini, J.2    Zagury, J.F.3
  • 8
    • 84871952176 scopus 로고    scopus 로고
    • Improved whole-chromosome phasing for disease and population genetic studies
    • Delaneau O, Zagury JF, Marchini J. 2013. Improved whole-chromosome phasing for disease and population genetic studies. Nat Methods 10(1):5-6.
    • (2013) Nat Methods , vol.10 , Issue.1 , pp. 5-6
    • Delaneau, O.1    Zagury, J.F.2    Marchini, J.3
  • 10
    • 0033366671 scopus 로고    scopus 로고
    • Combined linkage and association sib-pair analysis for quantitative traits
    • Fulker DW, Cherny SS, Sham PC, Hewitt JK. 1999. Combined linkage and association sib-pair analysis for quantitative traits. Am J Hum Genet 64(1):259-267.
    • (1999) Am J Hum Genet , vol.64 , Issue.1 , pp. 259-267
    • Fulker, D.W.1    Cherny, S.S.2    Sham, P.C.3    Hewitt, J.K.4
  • 12
    • 58149175796 scopus 로고    scopus 로고
    • Practical issues in imputation-based association mapping
    • Guan Y, Stephens M. 2008. Practical issues in imputation-based association mapping. PLoS Genet 4(12):e1000279.
    • (2008) PLoS Genet , vol.4 , Issue.12
    • Guan, Y.1    Stephens, M.2
  • 13
    • 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(2):95-108.
    • (2005) Nat Rev Genet , vol.6 , Issue.2 , pp. 95-108
    • Hirschhorn, J.N.1    Daly, M.J.2
  • 14
    • 84863845193 scopus 로고    scopus 로고
    • Genotype imputation with thousands of genomes
    • Howie B, Marchini J, Stephens M. 2011. Genotype imputation with thousands of genomes. G3 (Bethesda) 1(6):457-470.
    • (2011) G3 (Bethesda) , vol.1 , Issue.6 , pp. 457-470
    • Howie, B.1    Marchini, J.2    Stephens, M.3
  • 15
    • 84864417548 scopus 로고    scopus 로고
    • Fast and accurate genotype imputation in genome-wide association studies through pre-phasing
    • Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR. 2012. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet 44(8):955-959.
    • (2012) Nat Genet , vol.44 , Issue.8 , pp. 955-959
    • Howie, B.1    Fuchsberger, C.2    Stephens, M.3    Marchini, J.4    Abecasis, G.R.5
  • 16
    • 67651222400 scopus 로고    scopus 로고
    • A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    • Howie BN, Donnelly P, Marchini J. 2009. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5(6):e1000529.
    • (2009) PLoS Genet , vol.5 , Issue.6
    • Howie, B.N.1    Donnelly, P.2    Marchini, J.3
  • 17
    • 84859064895 scopus 로고    scopus 로고
    • Regulation of C/EBPbeta and resulting functions in cells of the monocytic lineage
    • Huber R, Pietsch D, Panterodt T, Brand K. 2012. Regulation of C/EBPbeta and resulting functions in cells of the monocytic lineage. Cell Signal 24(6):1287-1296.
    • (2012) Cell Signal , vol.24 , Issue.6 , pp. 1287-1296
    • Huber, R.1    Pietsch, D.2    Panterodt, T.3    Brand, K.4
  • 18
    • 34548261853 scopus 로고    scopus 로고
    • Genomewide weighted hypothesis testing in family-based association studies, with an application to a 100K scan
    • Ionita-Laza I, McQueen MB, Laird NM, Lange C. 2007. Genomewide weighted hypothesis testing in family-based association studies, with an application to a 100K scan. Am J Hum Genet 81(3):607-614.
    • (2007) Am J Hum Genet , vol.81 , Issue.3 , pp. 607-614
    • Ionita-Laza, I.1    McQueen, M.B.2    Laird, N.M.3    Lange, C.4
  • 19
    • 42249103276 scopus 로고    scopus 로고
    • On the analysis of copy-number variations in genome-wide association studies: a translation of the family-based association test
    • Ionita-Laza I, Perry GH, Raby BA, Klanderman B, Lee C, Laird NM, Weiss ST, Lange C. 2008. On the analysis of copy-number variations in genome-wide association studies: a translation of the family-based association test. Genet Epidemiol 32(3):273-284.
    • (2008) Genet Epidemiol , vol.32 , Issue.3 , pp. 273-284
    • Ionita-Laza, I.1    Perry, G.H.2    Raby, B.A.3    Klanderman, B.4    Lee, C.5    Laird, N.M.6    Weiss, S.T.7    Lange, C.8
  • 21
    • 0033814928 scopus 로고    scopus 로고
    • Implementing a unified approach to family-based tests of association
    • Laird NM, Horvath S, Xu X. 2000. Implementing a unified approach to family-based tests of association. Genet Epidemiol 19(Suppl 1):S36-S42.
    • (2000) Genet Epidemiol , vol.19 , pp. S36-S42
    • Laird, N.M.1    Horvath, S.2    Xu, X.3
  • 22
    • 33646188852 scopus 로고    scopus 로고
    • Family-based designs in the age of large-scale gene-association studies
    • Laird NM, Lange C. 2006. Family-based designs in the age of large-scale gene-association studies. Nat Rev Genet 7(5):385-394.
    • (2006) Nat Rev Genet , vol.7 , Issue.5 , pp. 385-394
    • Laird, N.M.1    Lange, C.2
  • 23
    • 0033652887 scopus 로고    scopus 로고
    • Family-based tests of association in the presence of linkage
    • Lake SL, Blacker D, Laird NM. 2000. Family-based tests of association in the presence of linkage. Am J Hum Genet 67(6):1515-1525.
    • (2000) Am J Hum Genet , vol.67 , Issue.6 , pp. 1515-1525
    • Lake, S.L.1    Blacker, D.2    Laird, N.M.3
  • 24
    • 77950460630 scopus 로고    scopus 로고
    • On genome-wide association studies for family-based designs: an integrative analysis approach combining ascertained family samples with unselected controls
    • Lasky-Su J, Won S, Mick E, Anney RJ, Franke B, Neale B, Biederman J, Smalley SL, Loo SK, Todorov A and others. 2010. On genome-wide association studies for family-based designs: an integrative analysis approach combining ascertained family samples with unselected controls. Am J Hum Genet 86(4):573-580.
    • (2010) Am J Hum Genet , vol.86 , Issue.4 , pp. 573-580
    • Lasky-Su, J.1    Won, S.2    Mick, E.3    Anney, R.J.4    Franke, B.5    Neale, B.6    Biederman, J.7    Smalley, S.L.8    Loo, S.K.9    Todorov, A.10
  • 25
    • 78649508578 scopus 로고    scopus 로고
    • MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
    • Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. 2010. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 34(8):816-834.
    • (2010) Genet Epidemiol , vol.34 , Issue.8 , pp. 816-834
    • Li, Y.1    Willer, C.J.2    Ding, J.3    Scheet, P.4    Abecasis, G.R.5
  • 27
    • 77953808087 scopus 로고    scopus 로고
    • Genotype imputation for genome-wide association studies
    • Marchini J, Howie B. 2010. Genotype imputation for genome-wide association studies. Nat Rev Genet 11(7):499-511.
    • (2010) Nat Rev Genet , vol.11 , Issue.7 , pp. 499-511
    • Marchini, J.1    Howie, B.2
  • 28
    • 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, Donnelly P. 2007. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 39(7):906-913.
    • (2007) Nat Genet , vol.39 , Issue.7 , pp. 906-913
    • Marchini, J.1    Howie, B.2    Myers, S.3    McVean, G.4    Donnelly, P.5
  • 30
    • 0016192958 scopus 로고
    • Analysis of family resemblance. 3. Complex segregation of quantitative traits
    • Morton NE, MacLean CJ. 1974. Analysis of family resemblance. 3. Complex segregation of quantitative traits. Am J Hum Genet 26(4):489-503.
    • (1974) Am J Hum Genet , vol.26 , Issue.4 , pp. 489-503
    • Morton, N.E.1    MacLean, C.J.2
  • 31
    • 79959378465 scopus 로고    scopus 로고
    • Family-based designs for genome-wide association studies
    • Ott J, Kamatani Y, Lathrop M. 2011. Family-based designs for genome-wide association studies. Nat Rev Genet 12(7):465-474.
    • (2011) Nat Rev Genet , vol.12 , Issue.7 , pp. 465-474
    • Ott, J.1    Kamatani, Y.2    Lathrop, M.3
  • 33
    • 0034054165 scopus 로고    scopus 로고
    • A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information
    • Rabinowitz D, Laird N. 2000. A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information. Hum Hered 50(4):211-223.
    • (2000) Hum Hered , vol.50 , Issue.4 , pp. 211-223
    • Rabinowitz, D.1    Laird, N.2
  • 35
    • 74049118029 scopus 로고    scopus 로고
    • A common genetic fingerprint in leprosy and Crohn's disease?
    • Schurr E, Gros P. 2009. A common genetic fingerprint in leprosy and Crohn's disease? N Engl J Med 361(27):2666-2668.
    • (2009) N Engl J Med , vol.361 , Issue.27 , pp. 2666-2668
    • Schurr, E.1    Gros, P.2
  • 36
    • 34547622688 scopus 로고    scopus 로고
    • Imputation-based analysis of association studies: candidate regions and quantitative traits
    • Servin B, Stephens M. 2007. Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet 3(7):e114.
    • (2007) PLoS Genet , vol.3 , Issue.7 , pp. e114
    • Servin, B.1    Stephens, M.2
  • 37
    • 0027377799 scopus 로고
    • Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM)
    • Spielman RS, McGinnis RE, Ewens WJ. 1993. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 52(3):506-516.
    • (1993) Am J Hum Genet , vol.52 , Issue.3 , pp. 506-516
    • Spielman, R.S.1    McGinnis, R.E.2    Ewens, W.J.3
  • 38
    • 84867606311 scopus 로고    scopus 로고
    • Incorporating genotype uncertainties into the genotypic TDT for main effects and gene-environment interactions
    • Taub MA, Schwender H, Beaty TH, Louis TA, Ruczinski I. 2012. Incorporating genotype uncertainties into the genotypic TDT for main effects and gene-environment interactions. Genet Epidemiol 36(3):225-234.
    • (2012) Genet Epidemiol , vol.36 , Issue.3 , pp. 225-234
    • Taub, M.A.1    Schwender, H.2    Beaty, T.H.3    Louis, T.A.4    Ruczinski, I.5
  • 40
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • The 1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-1073.
    • (2010) Nature , vol.467 , Issue.7319 , pp. 1061-1073
  • 41
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • The 1000 Genomes Project Consortium. 2012. An integrated map of genetic variation from 1, 092 human genomes. Nature 491(7422):56-65.
    • (2012) Nature , vol.491 , Issue.7422 , pp. 56-65
  • 42
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57-74.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
  • 43
    • 79959503826 scopus 로고    scopus 로고
    • The International HapMap Project
    • The International HapMap Consortium. 2003. The International HapMap Project. Nature 426(6968):789-796.
    • (2003) Nature , vol.426 , Issue.6968 , pp. 789-796
  • 44
    • 77956331627 scopus 로고    scopus 로고
    • Integrating common and rare genetic variation in diverse human populations
    • The International HapMap Consortium. 2010. Integrating common and rare genetic variation in diverse human populations. Nature 467(7311):52-58.
    • (2010) Nature , vol.467 , Issue.7311 , pp. 52-58
  • 45
    • 79960260455 scopus 로고    scopus 로고
    • Perspectives on genome-wide multi-stage family-based association studies
    • Van Steen K. 2011. Perspectives on genome-wide multi-stage family-based association studies. Stat Med 30(18):2201-2221.
    • (2011) Stat Med , vol.30 , Issue.18 , pp. 2201-2221
    • Van Steen, K.1
  • 47
    • 73649129188 scopus 로고    scopus 로고
    • On the analysis of genome-wide association studies in family-based designs: a universal, robust analysis approach and an application to four genome-wide association studies
    • Won S, Wilk JB, Mathias RA, O'Donnell CJ, Silverman EK, Barnes K, O'Connor GT, Weiss ST, Lange C. 2009. On the analysis of genome-wide association studies in family-based designs: a universal, robust analysis approach and an application to four genome-wide association studies. PLoS Genet 5(11):e1000741.
    • (2009) PLoS Genet , vol.5 , Issue.11
    • Won, S.1    Wilk, J.B.2    Mathias, R.A.3    O'Donnell, C.J.4    Silverman, E.K.5    Barnes, K.6    O'Connor, G.T.7    Weiss, S.T.8    Lange, C.9
  • 48
    • 84858010549 scopus 로고    scopus 로고
    • Family-based association tests using genotype data with uncertainty
    • Yu Z. 2012. Family-based association tests using genotype data with uncertainty. Biostatistics 13(2):228-240.
    • (2012) Biostatistics , vol.13 , Issue.2 , pp. 228-240
    • Yu, Z.1
  • 49
    • 82255179222 scopus 로고    scopus 로고
    • Identification of two new loci at IL23R and RAB32 that influence susceptibility to leprosy
    • Zhang F, Liu H, Chen S, Low H, Sun L, Cui Y, Chu T, Li Y, Fu X, Yu Y and others. 2011. Identification of two new loci at IL23R and RAB32 that influence susceptibility to leprosy. Nat Genet 43(12):1247-1251.
    • (2011) Nat Genet , vol.43 , Issue.12 , pp. 1247-1251
    • Zhang, F.1    Liu, H.2    Chen, S.3    Low, H.4    Sun, L.5    Cui, Y.6    Chu, T.7    Li, Y.8    Fu, X.9    Yu, Y.10
  • 50
    • 78751490178 scopus 로고    scopus 로고
    • A comparison of approaches to account for uncertainty in analysis of imputed genotypes
    • Zheng J, Li Y, Abecasis GR, Scheet P. 2011. A comparison of approaches to account for uncertainty in analysis of imputed genotypes. Genet Epidemiol 35(2):102-110.
    • (2011) Genet Epidemiol , vol.35 , Issue.2 , pp. 102-110
    • Zheng, J.1    Li, Y.2    Abecasis, G.R.3    Scheet, P.4


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