메뉴 건너뛰기




Volumn 73, Issue 2, 2012, Pages 105-122

A unified framework for detecting rare variant quantitative trait associations in pedigree and unrelated individuals via sequence data

Author keywords

Extreme sampling; Next generation sequencing; Pedigree samples; Quantitative trait loci; Rare variants

Indexed keywords

ARTICLE; GENETIC ALGORITHM; GENETIC ASSOCIATION; GENETIC SCREENING; GENETIC VARIABILITY; HUMAN; MAJOR CLINICAL STUDY; MODELING EXTREME TRAIT GENETIC ASSOCIATION; OBESITY; PEDIGREE; POPULATION SIZE; QUANTITATIVE TRAIT LOCUS MAPPING;

EID: 84860581891     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000336293     Document Type: Article
Times cited : (12)

References (56)
  • 1
    • 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: Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 2008;40: 695-701. (Pubitemid 351748875)
    • (2008) Nature Genetics , vol.40 , Issue.6 , pp. 695-701
    • Bodmer, W.1    Bonilla, C.2
  • 3
    • 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, Hobbs HH: Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 2004;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
  • 6
    • 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, Hobbs HH, Cohen JC: Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nat Genet 2007;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
  • 7
    • 61749090233 scopus 로고    scopus 로고
    • Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans
    • ozlitina J, Pennacchio LA, Boerwinkle E, Hobbs HH, Cohen JC: Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans. J Clin Invest 2009;119: 70-79.
    • (2009) J Clin Invest , vol.119 , pp. 70-79
    • Ozlitina, J.1    Pennacchio, L.A.2    Boerwinkle, E.3    Hobbs, H.H.4    Cohen, J.C.5
  • 9
    • 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: Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 2008;83: 311-321.
    • (2008) Am J Hum Genet , vol.83 , pp. 311-321
    • Li, B.1    Leal, S.M.2
  • 12
    • 0004737767 scopus 로고
    • The Framingham study: A prospective study of coronary heart disease
    • Kagan A, Dawber TR, Kannel WB, Revotskie N: The Framingham study: a prospective study of coronary heart disease. Fed Proc 1962;21(Pt 2):52-57.
    • (1962) Fed Proc , vol.21 , Issue.PART 2 , pp. 52-57
    • Kagan, A.1    Dawber, T.R.2    Kannel, W.B.3    Revotskie, N.4
  • 13
    • 77953416140 scopus 로고    scopus 로고
    • Power analysis for case-control association studies of samples with known family histories
    • Peng B, Li B, Han Y, Amos CI: Power analysis for case-control association studies of samples with known family histories. Hum Genet 2010;127: 699-704.
    • (2010) Hum Genet , vol.127 , pp. 699-704
    • Peng, B.1    Li, B.2    Han, Y.3    Amos, C.I.4
  • 14
    • 33646065685 scopus 로고    scopus 로고
    • Efficient study designs for test of genetic association using sibship data and unrelated cases and controls
    • Li M, Boehnke M, Abecasis GR: Efficient study designs for test of genetic association using sibship data and unrelated cases and controls. Am J Hum Genet 2006;78: 778-792.
    • (2006) Am J Hum Genet , vol.78 , pp. 778-792
    • Li, M.1    Boehnke, M.2    Abecasis, G.R.3
  • 15
    • 76649136928 scopus 로고    scopus 로고
    • An evaluation of statistical approaches to rare variant analysis in genetic association studies
    • Morris AP, Zeggini E: An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 2010;34: 188-193.
    • (2010) Genet Epidemiol , vol.34 , pp. 188-193
    • Morris, A.P.1    Zeggini, E.2
  • 16
    • 61449168010 scopus 로고    scopus 로고
    • A groupwise association test for rare mutations using a weighted sum statistic
    • Madsen BE, Browning SR: A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 2009;5:e1000384.
    • (2009) PLoS Genet , vol.5
    • Madsen, B.E.1    Browning, S.R.2
  • 19
    • 78449245227 scopus 로고    scopus 로고
    • A novel adaptive method for the analysis of next-generation sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions
    • Liu DJ, Leal SM: A novel adaptive method for the analysis of next-generation sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions. PLoS Genet 2010;6:e1001156.
    • PLoS Genet 2010 , vol.6
    • Liu, D.J.1    Leal, S.M.2
  • 20
    • 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: A new testing strategy to identify rare variants with either risk or protective effect on disease. PLoS Genet 2010;7:e1001289.
    • (2010) PLoS Genet , vol.7
    • Ionita-Laza, I.1    Buxbaum, J.D.2    Laird, N.M.3    Lange, C.4
  • 22
    • 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, Lin X: Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet 2011;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    Lin, X.6
  • 23
    • 33746570028 scopus 로고    scopus 로고
    • Closing in on complex traits
    • DOI 10.1038/ng0806-861, PII NG0806861
    • Darvasi A: Closing in on complex traits. Nat Genet 2006;38: 861-862. (Pubitemid 44141648)
    • (2006) Nature Genetics , vol.38 , Issue.8 , pp. 861-862
    • Darvasi, A.1
  • 25
    • 76649122154 scopus 로고    scopus 로고
    • Detecting rare variants for complex traits using family and unrelated data
    • Zhu X, Feng T, Li Y, Lu Q, Elston RC: Detecting rare variants for complex traits using family and unrelated data. Genet Epidemiol 2010;34: 171-187.
    • (2010) Genet Epidemiol , vol.34 , pp. 171-187
    • Zhu, X.1    Feng, T.2    Li, Y.3    Lu, Q.4    Elston, R.C.5
  • 26
    • 79958077854 scopus 로고    scopus 로고
    • Detecting rare and common variants for complex traits: Sibpair and odds ratio weighted sum statistics (SPWSS, ORWSS)
    • Feng T, Elston RC, Zhu X: Detecting rare and common variants for complex traits: sibpair and odds ratio weighted sum statistics (SPWSS, ORWSS). Genet Epidemiol 2011;35: 398-409.
    • (2011) Genet Epidemiol , vol.35 , pp. 398-409
    • Feng, T.1    Elston, R.C.2    Zhu, X.3
  • 27
    • 0034987323 scopus 로고    scopus 로고
    • The power to detect linkage disequilibrium with quantitative traits in selected samples
    • DOI 10.1086/320590
    • Abecasis GR, Cookson WO, Cardon LR: The power to detect linkage disequilibrium with quantitative traits in selected samples. Am J Hum Genet 2001;68: 1463-1474. (Pubitemid 32510622)
    • (2001) American Journal of Human Genetics , vol.68 , Issue.6 , pp. 1463-1474
    • Abecasis, G.R.1    Cookson, W.O.C.2    Cardon, L.R.3
  • 28
    • 0033909546 scopus 로고    scopus 로고
    • A general test of association for quantitative traits in nuclear families
    • DOI 10.1086/302698
    • Abecasis GR, Cardon LR, Cookson WO: A general test of association for quantitative traits in nuclear families. Am J Hum Genet 2000;66: 279-292. (Pubitemid 30481489)
    • (2000) American Journal of Human Genetics , vol.66 , Issue.1 , pp. 279-292
    • Abecasis, G.R.1    Cardon, L.R.2    Cookson, W.O.C.3
  • 29
    • 0029979336 scopus 로고    scopus 로고
    • Mapping quantitative trait loci with extreme discordant sib pairs: Sampling considerations
    • Risch NJ, Zhang H: Mapping quantitative trait loci with extreme discordant sib pairs: sampling considerations. Am J Hum Genet 1996;58: 836-843. (Pubitemid 26086675)
    • (1996) American Journal of Human Genetics , vol.58 , Issue.4 , pp. 836-843
    • Risch, N.J.1    Zhang, H.2
  • 30
    • 0029001682 scopus 로고
    • Extreme discordant sib pairs for mapping quantitative trait loci in humans
    • Risch N, Zhang H: Extreme discordant sib pairs for mapping quantitative trait loci in humans. Science 1995;268: 1584-1589.
    • (1995) Science , vol.268 , pp. 1584-1589
    • Risch, N.1    Zhang, H.2
  • 31
    • 0026047218 scopus 로고
    • Linkage analysis of quantitative traits: Increased power by using selected samples
    • Carey G, Williamson J: Linkage analysis of quantitative traits: increased power by using selected samples. Am J Hum Genet 1991;49: 786-796. (Pubitemid 21891725)
    • (1991) American Journal of Human Genetics , vol.49 , Issue.4 , pp. 786-796
    • Carey, G.1    Williamson, J.2
  • 32
    • 0028102233 scopus 로고
    • Locating human quantitative trait loci: Guidelines for the selection of sibling pairs for genotyping
    • DOI 10.1007/BF01076180
    • Eaves L, Meyer J: Locating human quantitative trait loci: guidelines for the selection of sibling pairs for genotyping. Behav Genet 1994;24: 443-455. (Pubitemid 24309453)
    • (1994) Behavior Genetics , vol.24 , Issue.5 , pp. 443-455
    • Eaves, L.1    Meyer, J.2
  • 33
    • 0030843362 scopus 로고    scopus 로고
    • A linkage strategy for detection of human quantitative-trait loci. I. Generalized relative risk ratios and power of sib pairs with extreme trait values
    • Gu C, Rao DC: A linkage strategy for detection of human quantitative-trait loci. I. Generalized relative risk ratios and power of sib pairs with extreme trait values. Am J Hum Genet 1997;61: 200-210. (Pubitemid 27323340)
    • (1997) American Journal of Human Genetics , vol.61 , Issue.1 , pp. 200-210
    • Gu, C.1    Rao, D.C.2
  • 36
    • 84971185409 scopus 로고
    • The correlation between relatives on the supposition of mendelian inheritance
    • Fisher RA: The correlation between relatives on the supposition of mendelian inheritance. Philos Trans R Soc Edinburgh 1918;52: 399-433.
    • (1918) Philos Trans R Soc Edinburgh , vol.52 , pp. 399-433
    • Fisher, R.A.1
  • 37
    • 34547628858 scopus 로고    scopus 로고
    • Family-based association tests for genomewide association scans
    • DOI 10.1086/521580
    • Chen WM, Abecasis GR: Family-based association tests for genomewide association scans. Am J Hum Genet 2007;81: 913-926. (Pubitemid 47580246)
    • (2007) American Journal of Human Genetics , vol.81 , Issue.5 , pp. 913-926
    • Chen, W.-M.1    Abecasis, G.R.2
  • 38
    • 78649717215 scopus 로고    scopus 로고
    • An evolutionary framework for association testing in resequencing studies
    • King CR, Rathouz PJ, Nicolae DL;An evolutionary framework for association testing in resequencing studies. PLoS Genet 2010;6:e1001202.
    • (2010) PLoS Genet , vol.6
    • King, C.R.1    Rathouz, P.J.2    Nicolae, D.L.3
  • 39
    • 0036206445 scopus 로고    scopus 로고
    • Ascertainment-adjusted parameter estimates revisited
    • DOI 10.1086/339517
    • Epstein MP, Lin X, Boehnke M: Ascertainment-adjusted parameter estimates revisited. Am J Hum Genet 2002;70: 886-895. (Pubitemid 34259305)
    • (2002) American Journal of Human Genetics , vol.70 , Issue.4 , pp. 886-895
    • Epstein, M.P.1    Lin, X.2    Boehnke, M.3
  • 41
    • 0029022967 scopus 로고
    • Exact logistic regression: Theory and examples
    • Mehta CR, Patel NR: Exact logistic regression: theory and examples. Stat Med 1995;14: 2143-2160.
    • (1995) Stat Med , vol.14 , pp. 2143-2160
    • Mehta, C.R.1    Patel, N.R.2
  • 43
    • 56649111423 scopus 로고    scopus 로고
    • A flexible forward simulator for populations subject to selection and demography
    • DOI 10.1093/bioinformatics/btn522
    • Hernandez RD: A flexible forward simulator for populations subject to selection and demography. Bioinformatics 2008;24: 2786-2787. (Pubitemid 352722628)
    • (2008) Bioinformatics , vol.24 , Issue.23 , pp. 2786-2787
    • Hernandez, R.D.1
  • 44
    • 0034969437 scopus 로고    scopus 로고
    • Are rare variants responsible for susceptibility to complex diseases?
    • DOI 10.1086/321272
    • Pritchard JK: Are rare variants responsible for susceptibility to complex diseases? Am J Hum Genet 2001;69: 124-137. (Pubitemid 32614025)
    • (2001) American Journal of Human Genetics , vol.69 , Issue.1 , pp. 124-137
    • Pritchard, J.K.1
  • 45
    • 0033611501 scopus 로고    scopus 로고
    • High genomic deleterious mutation rates in hominids
    • Eyre-Walker A, Keightley PD: High genomic deleterious mutation rates in hominids. Nature 1999;397: 344-347.
    • (1999) Nature , vol.397 , pp. 344-347
    • Eyre-Walker, A.1    Keightley, P.D.2
  • 47
    • 69049094840 scopus 로고    scopus 로고
    • Novel sib pair selection strategy increases power in quantitative association analysis
    • Kwan JS, Cherny SS, Kung AW, Sham PC: Novel sib pair selection strategy increases power in quantitative association analysis. Behav Genet 2009;39: 571-579.
    • (2009) Behav Genet , vol.39 , pp. 571-579
    • Kwan, J.S.1    Cherny, S.S.2    Kung, A.W.3    Sham, P.C.4
  • 48
    • 0033912293 scopus 로고    scopus 로고
    • Bias and efficiency in family-based gene-characterization studies: Conditional, prospective, retrospective, and joint likelihoods
    • DOI 10.1086/302808
    • Kraft P, Thomas DC: Bias and efficiency in family-based gene-characterization studies: conditional, prospective, retrospective, and joint likelihoods. Am J Hum Genet 2000;66: 1119-1131. (Pubitemid 30470509)
    • (2000) American Journal of Human Genetics , vol.66 , Issue.3 , pp. 1119-1131
    • Kraft, P.1    Thomas, D.C.2
  • 49
    • 11144348717 scopus 로고    scopus 로고
    • Genetic investigation of quantitative traits related to autism: Use of multivariate polygenic models with ascertainment adjustment
    • DOI 10.1086/426951
    • Sung YJ, Dawson G, Munson J, Estes A, Schellenberg GD, Wijsman EM: Genetic investigation of quantitative traits related to autism: use of multivariate polygenic models with ascertainment adjustment. Am J Hum Genet 2005;76: 68-81. (Pubitemid 40023766)
    • (2005) American Journal of Human Genetics , vol.76 , Issue.1 , pp. 68-81
    • Sung, Y.J.1    Dawson, G.2    Munson, J.3    Estes, A.4    Schellenberg, G.D.5    Wijsman, E.M.6
  • 50
    • 36749077612 scopus 로고    scopus 로고
    • Common single-nucleotide polymorphisms act in concert to affect plasma levels of high-density lipoprotein cholesterol
    • DOI 10.1086/522497
    • Spirin V, Schmidt S, Pertsemlidis A, Cooper RS, Cohen JC, Sunyaev SR: Common singlenucleotide polymorphisms act in concert to affect plasma levels of high-density lipoprotein cholesterol. Am J Hum Genet 2007;81: 1298-1303. (Pubitemid 350211459)
    • (2007) American Journal of Human Genetics , vol.81 , Issue.6 , pp. 1298-1303
    • Spirin, V.1    Schmidt, S.2    Pertsemlidis, A.3    Cooper, R.S.4    Cohen, J.C.5    Sunyaev, S.R.6
  • 51
    • 13944265645 scopus 로고    scopus 로고
    • Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9
    • Cohen J, Pertsemlidis A, Kotowski IK, Graham R, Garcia CK, Hobbs HH: Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9. Nat Genet 2005;37: 161-165.
    • (2005) Nat Genet , vol.37 , pp. 161-165
    • Cohen, J.1    Pertsemlidis, A.2    Kotowski, I.K.3    Graham, R.4    Garcia, C.K.5    Hobbs, H.H.6
  • 52
    • 33645103550 scopus 로고    scopus 로고
    • Sequence variations in PCSK9, low LDL, and protection against coronary heart disease
    • Cohen JC, Boerwinkle E, Mosley TH Jr, Hobbs HH: Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. N Engl J Med 2006;354: 1264-1272.
    • (2006) N Engl J Med , vol.354 , pp. 1264-1272
    • Cohen, J.C.1    Boerwinkle, E.2    Mosley Jr., T.H.3    Hobbs, H.H.4
  • 53
    • 78649775312 scopus 로고    scopus 로고
    • Replication strategies for rare variant complex trait association studies via next-generation sequencing
    • Liu DJ, Leal SM: Replication strategies for rare variant complex trait association studies via next-generation sequencing. Am J Hum Genet 2010;87: 790-801.
    • (2010) Am J Hum Genet , vol.87 , pp. 790-801
    • Liu, D.J.1    Leal, S.M.2
  • 54
    • 0024508964 scopus 로고
    • Mapping mendelian factors underlying quantitative traits using RFLP linkage maps
    • Lander ES, Botstein D: Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 1989;121: 185-199.
    • (1989) Genetics , vol.121 , pp. 185-199
    • Lander, E.S.1    Botstein, D.2
  • 55
    • 0033358579 scopus 로고    scopus 로고
    • Disequilibrium mapping of a quantitative-trait locus in an expanding population
    • Slatkin M: Disequilibrium mapping of a quantitative-trait locus in an expanding population. Am J Hum Genet 1999;64: 1764-1772.
    • (1999) Am J Hum Genet , vol.64 , pp. 1764-1772
    • Slatkin, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.