메뉴 건너뛰기




Volumn , Issue SUPPL.73, 2012, Pages

Methods for detecting and correcting for population stratification

Author keywords

Admixture; Association confounding; Global ancestry; Local ancestry; Population stratification

Indexed keywords

ARTICLE; GENE FREQUENCY; GENE MAPPING; GENETIC ASSOCIATION; GENETIC MODEL; GENETIC TRAIT; GENETIC VARIABILITY; HIDDEN MARKOV MODEL; HUMAN; MULTIDIMENSIONAL SCALING; POPULATION GENETIC STRUCTURE; POPULATION GENETICS; POPULATION STRATIFICATION; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; STATISTICAL PARAMETERS; STRATIFICATION SCORE; BIOLOGICAL MODEL; ETHNIC AND RACIAL GROUPS; GENETICS; MOLECULAR EVOLUTION; POPULATION DYNAMICS; STATISTICAL MODEL;

EID: 84863813784     PISSN: 19348266     EISSN: 19348258     Source Type: Journal    
DOI: 10.1002/0471142905.hg0122s73     Document Type: Article
Times cited : (12)

References (75)
  • 1
    • 79958863696 scopus 로고    scopus 로고
    • Enhancements to the ADMIXTURE algorithm for individual ancestry estimation
    • Alexander, D.H. and Lange, K. 2011 Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics 12:246.
    • (2011) BMC Bioinformatics , vol.12 , pp. 246
    • Alexander, D.H.1    Lange, K.2
  • 2
    • 69749099417 scopus 로고    scopus 로고
    • Fast model-based estimation of ancestry in unrelated individuals
    • Alexander, D.H., Novembre, J., and Lange, K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19:1655-1664.
    • (2009) Genome Res , vol.19 , pp. 1655-1664
    • Alexander, D.H.1    Novembre, J.2    Lange, K.3
  • 3
    • 77954209603 scopus 로고    scopus 로고
    • Score-based adjustment for confounding by population stratification in genetic association studies
    • Allen, A., Epstein, M.P., and Satten, G.A. 2010. Score-based adjustment for confounding by population stratification in genetic association studies. Genet. Epidemiol. 34:383-385.
    • (2010) Genet. Epidemiol. , vol.34 , pp. 383-385
    • Allen, A.1    Epstein, M.P.2    Satten, G.A.3
  • 4
    • 77955166399 scopus 로고    scopus 로고
    • Population structure and cryptic relatedness in genetic association studies
    • Astle, W. and Balding, D.J. 2009. Population structure and cryptic relatedness in genetic association studies. Statistical Science 24:451-471.
    • (2009) Statistical Science , vol.24 , pp. 451-471
    • Astle, W.1    Balding, D.J.2
  • 5
    • 0036137032 scopus 로고    scopus 로고
    • Association studies for quantitative traits in structured populations
    • Bacanu, S.A., Devlin, B., and Roeder, K. 2002. Association studies for quantitative traits in structured populations. Genet. Epidemiol. 22:78-93.
    • (2002) Genet. Epidemiol. , vol.22 , pp. 78-93
    • Bacanu, S.A.1    Devlin, B.2    Roeder, K.3
  • 7
    • 77950380766 scopus 로고    scopus 로고
    • Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana
    • Bomblies, K., Yant, L., Laitinen, R.A., Kim, S.T., Hollister, J.D., Warthmann, N., Fitz, J., and Weigel, D. 2010. Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana. PLoS Genet. 6:e1000890.
    • (2010) PLoS Genet , vol.6
    • Bomblies, K.1    Yant, L.2    Laitinen, R.A.3    Kim, S.T.4    Hollister, J.D.5    Warthmann, N.6    Fitz, J.7    Weigel, D.8
  • 12
    • 0037442092 scopus 로고    scopus 로고
    • Population stratification and spurious allelic association
    • Cardon, L.R. and Palmer, L.J. 2003. Population stratification and spurious allelic association. Lancet 361:598-604.
    • (2003) Lancet , vol.361 , pp. 598-604
    • Cardon, L.R.1    Palmer, L.J.2
  • 13
    • 77958598598 scopus 로고    scopus 로고
    • CAPL: A novel association test using case-control and family data and accounting for population stratification
    • Chung, R.H., Schmidt, M.A., Morris, R.W., and Martin, E.R. 2010. CAPL: A novel association test using case-control and family data and accounting for population stratification. Genet. Epidemiol. 34:747-755.
    • (2010) Genet. Epidemiol. , vol.34 , pp. 747-755
    • Chung, R.H.1    Schmidt, M.A.2    Morris, R.W.3    Martin, E.R.4
  • 14
    • 0014297593 scopus 로고
    • The effectiveness of adjustment by subclassification in removing bias in observational studies
    • Cochran, W.G. 1968. The effectiveness of adjustment by subclassification in removing bias in observational studies. Biometrics 24:295-313.
    • (1968) Biometrics , vol.24 , pp. 295-313
    • Cochran, W.G.1
  • 15
    • 66249135302 scopus 로고    scopus 로고
    • A critical evaluation of genomic control methods for genetic association studies
    • Dadd, T., Weale, M.E., and Lewis, C.M. 2009. A critical evaluation of genomic control methods for genetic association studies. Genet. Epidemiol. 33:290-298.
    • (2009) Genet. Epidemiol. , vol.33 , pp. 290-298
    • Dadd, T.1    Weale, M.E.2    Lewis, C.M.3
  • 16
    • 0032714352 scopus 로고    scopus 로고
    • Genomic control for association studies
    • Devlin, B. and Roeder, K. 1999. Genomic control for association studies. Biometrics 55:997-1004.
    • (1999) Biometrics , vol.55 , pp. 997-1004
    • Devlin, B.1    Roeder, K.2
  • 17
    • 0035528921 scopus 로고    scopus 로고
    • Genomic control, a new approach to genetic-based association studies
    • Devlin, B., Roeder, K., and Wasserman, L. 2001. Genomic control, a new approach to genetic-based association studies. Theor. Popul. Biol. 60:155-166.
    • (2001) Theor. Popul. Biol. , vol.60 , pp. 155-166
    • Devlin, B.1    Roeder, K.2    Wasserman, L.3
  • 18
    • 16544380910 scopus 로고    scopus 로고
    • Genomic control to the extreme
    • Devlin, B., Bacanu, S.A., and Roeder, K. 2004. Genomic control to the extreme. Nat. Genet. 36:1129-1130.
    • (2004) Nat. Genet. , vol.36 , pp. 1129-1130
    • Devlin, B.1    Bacanu, S.A.2    Roeder, K.3
  • 20
    • 34247585477 scopus 로고    scopus 로고
    • A simple and improved correction for population stratification in case-control studies
    • Epstein, M.P., Allen, A.S., and Satten, G.A. 2007. A simple and improved correction for population stratification in case-control studies. Am. J. Hum. Genet. 80:921-930.
    • (2007) Am. J. Hum. Genet. , vol.80 , pp. 921-930
    • Epstein, M.P.1    Allen, A.S.2    Satten, G.A.3
  • 21
    • 0041817568 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies
    • Falush, D., Stephens, M.,Pritchard, J.K. 2003. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164:1567-1587.
    • (2003) Genetics , vol.164 , pp. 1567-1587
    • Falush, D.1    Stephens, M.2    Pritchard, J.K.3
  • 25
    • 66749139020 scopus 로고    scopus 로고
    • Using allele sharing distance for detecting human population stratification
    • Gao, X. and Martin, E.R. 2009. Using allele sharing distance for detecting human population stratification. Hum. Hered. 68:182-191.
    • (2009) Hum. Hered. , vol.68 , pp. 182-191
    • Gao, X.1    Martin, E.R.2
  • 26
    • 34547684591 scopus 로고    scopus 로고
    • Human population structure detection via multilocus genotype clustering
    • Gao, X. and Starmer, J. 2007. Human population structure detection via multilocus genotype clustering. BMC Genet. 8:34.
    • (2007) BMC Genet , vol.8 , pp. 34
    • Gao, X.1    Starmer, J.2
  • 31
    • 67349176068 scopus 로고    scopus 로고
    • Genetics in geographically structured populations: defining, estimating and interpreting F(ST)
    • Holsinger, K.E. and Weir, B.S. 2009. Genetics in geographically structured populations: defining, estimating and interpreting F(ST). Nat. Rev. Genet. 10:639-650.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 639-650
    • Holsinger, K.E.1    Weir, B.S.2
  • 32
    • 33644824316 scopus 로고    scopus 로고
    • Case-control association tests correcting for population stratification
    • Kohler, K. and Bickeboller, H. 2006. Case-control association tests correcting for population stratification. Ann. Hum. Genet. 70:98-115.
    • (2006) Ann. Hum. Genet. , vol.70 , pp. 98-115
    • Kohler, K.1    Bickeboller, H.2
  • 33
    • 40749116962 scopus 로고    scopus 로고
    • Comment on a simple and improved correction for population stratification
    • Lee, S., Sullivan, P.F., Zou, F., and Wright, F.A. 2008. Comment on a simple and improved correction for population stratification.Am. J. Hum. Genet. 82:524-526.
    • (2008) Am. J. Hum. Genet. , vol.82 , pp. 524-526
    • Lee, S.1    Sullivan, P.F.2    Zou, F.3    Wright, F.A.4
  • 34
    • 0347361674 scopus 로고    scopus 로고
    • Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data
    • Li, N. and Stephens, M. 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165:2213-2233.
    • (2003) Genetics , vol.165 , pp. 2213-2233
    • Li, N.1    Stephens, M.2
  • 35
    • 42149109325 scopus 로고    scopus 로고
    • Improved correction for population stratification in genome-wide association studies by identifying hidden population structures
    • Li, Q. and Yu, K. 2008. Improved correction for population stratification in genome-wide association studies by identifying hidden population structures. LI2008. Genet. Epidemiol. 32:215-226.
    • (2008) LI2008. Genet. Epidemiol. , vol.32 , pp. 215-226
    • Li, Q.1    Yu, K.2
  • 36
    • 2442585696 scopus 로고    scopus 로고
    • The effects of human population structure on large genetic association studies
    • Marchini, J., Cardon, L.R., Phillips, M.S., and Donnelly, P. 2004. The effects of human population structure on large genetic association studies. Nat. Genet. 36:512-517.
    • (2004) Nat. Genet. , vol.36 , pp. 512-517
    • Marchini, J.1    Cardon, L.R.2    Phillips, M.S.3    Donnelly, P.4
  • 37
    • 0242718698 scopus 로고    scopus 로고
    • Iteratively reweighted partial least squares estimation for generalized linear regression
    • Marx,B.D. 1996. Iteratively reweighted partial least squares estimation for generalized linear regression. Technometrics 38:374-381.
    • (1996) Technometrics , vol.38 , pp. 374-381
    • Marx, B.D.1
  • 38
    • 0018080152 scopus 로고
    • Synthetic maps of human gene frequencies in Europeans
    • Menozzi, P., Piazza, A., and Cavalli-Sforza, L. 1978. Synthetic maps of human gene frequencies in Europeans. Science 201:786-792.
    • (1978) Science , vol.201 , pp. 786-792
    • Menozzi, P.1    Piazza, A.2    Cavalli-Sforza, L.3
  • 39
    • 69949160789 scopus 로고    scopus 로고
    • SNP selection and multidimensional scaling to quantify population structure
    • Miclaus, K., Wolfinger, R., and Czika, W. 2009. SNP selection and multidimensional scaling to quantify population structure. Genet. Epidemiol. 33:488-496.
    • (2009) Genet. Epidemiol. , vol.33 , pp. 488-496
    • Miclaus, K.1    Wolfinger, R.2    Czika, W.3
  • 40
    • 6344244729 scopus 로고    scopus 로고
    • Statistical tests for admixture mapping with case-control and cases-only data
    • Montana, G. and Pritchard, J.K. 2004. Statistical tests for admixture mapping with case-control and cases-only data. Am. J.Hum. Genet. 75:771-789.
    • (2004) Am. J. Hum. Genet. , vol.75 , pp. 771-789
    • Montana, G.1    Pritchard, J.K.2
  • 41
    • 0030776801 scopus 로고    scopus 로고
    • Multilocus genotypes, a tree of individuals, and human evolutionary history
    • Mountain, J.L. and Cavalli-Sforza, L.L. 1997. Multilocus genotypes, a tree of individuals, and human evolutionary history. Am. J. Hum. Genet. 61:705-718.
    • (1997) Am. J. Hum. Genet. , vol.61 , pp. 705-718
    • Mountain, J.L.1    Cavalli-Sforza, L.L.2
  • 43
    • 66349088624 scopus 로고    scopus 로고
    • Inference of locus-specific ancestry in closely related populations
    • Pasaniuc, B., Sankararaman, S., Kimmel, G., and Halperin, E. 2009. Inference of locus-specific ancestry in closely related populations. Bioinformatics 25:i213-i221.
    • (2009) Bioinformatics , vol.25
    • Pasaniuc, B.1    Sankararaman, S.2    Kimmel, G.3    Halperin, E.4
  • 46
    • 33746512512 scopus 로고    scopus 로고
    • Principal components analysis corrects for stratification in genome-wide association studies
    • Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A., and Reich, D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38:904-909.
    • (2006) Nat. Genet. , vol.38 , pp. 904-909
    • Price, A.L.1    Patterson, N.J.2    Plenge, R.M.3    Weinblatt, M.E.4    Shadick, N.A.5    Reich, D.6
  • 48
    • 77953811255 scopus 로고    scopus 로고
    • New approaches to population stratification in genome-wide association studies
    • Price, A.L., Zaitlen, N.A., Reich, D., and Patterson, N. 2010. New approaches to population stratification in genome-wide association studies. Nat. Rev. Genet. 11:459-463.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 459-463
    • Price, A.L.1    Zaitlen, N.A.2    Reich, D.3    Patterson, N.4
  • 49
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • Pritchard, J.K., Stephens, M., and Donnelly, P. 2000a. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
    • (2000) Genetics , vol.155 , pp. 945-959
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.3
  • 53
    • 41649121004 scopus 로고    scopus 로고
    • On the inference of ancestries in admixed populations
    • Sankararaman, S., Kimmel, G., Halperin, E., and Jordan, M.I. 2008a. On the inference of ancestries in admixed populations. Genome Res. 18:668-675.
    • (2008) Genome Res , vol.18 , pp. 668-675
    • Sankararaman, S.1    Kimmel, G.2    Halperin, E.3    Jordan, M.I.4
  • 55
    • 79960566302 scopus 로고    scopus 로고
    • New approaches to disease mapping in admixed populations
    • Seldin, M.F., Pasaniuc, B., and Price, A.L. 2011. New approaches to disease mapping in admixed populations. Nat. Rev. Genet. 12:523-528.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 523-528
    • Seldin, M.F.1    Pasaniuc, B.2    Price, A.L.3
  • 56
    • 32044443597 scopus 로고    scopus 로고
    • Logistic regression protects against population structure in genetic association studies
    • Setakis, E., Stirnadel, H., and Balding, D.J. 2006. Logistic regression protects against population structure in genetic association studies. Genome Res. 16:290-296.
    • (2006) Genome Res , vol.16 , pp. 290-296
    • Setakis, E.1    Stirnadel, H.2    Balding, D.J.3
  • 57
    • 41649089607 scopus 로고    scopus 로고
    • Effect of genetic divergence in identifying ancestral origin using HAPAA
    • Sundquist,A., Fratkin, E.,Do, C.B., and Batzoglou, S. 2008. Effect of genetic divergence in identifying ancestral origin using HAPAA. Genome Res. 18:676-682.
    • (2008) Genome Res , vol.18 , pp. 676-682
    • Sundquist, A.1    Fratkin, E.2    Do, C.B.3    Batzoglou, S.4
  • 58
    • 33745228973 scopus 로고    scopus 로고
    • Reconstructing genetic ancestry blocks in admixed individuals
    • Tang, H., Coram,M.,Wang, P., Zhu, X., and Risch, N. 2006. Reconstructing genetic ancestry blocks in admixed individuals. Am. J. Hum. Genet. 79:1-12.
    • (2006) Am. J. Hum. Genet. , vol.79 , pp. 1-12
    • Tang, H.1    Coram, M.2    Wang, P.3    Zhu, X.4    Risch, N.5
  • 59
    • 76049108917 scopus 로고    scopus 로고
    • ROADTRIPS: Case-control association testing with partially or completely unknown population and pedigree structure
    • Thornton, T. and McPeek, M.S. 2010. ROADTRIPS: Case-control association testing with partially or completely unknown population and pedigree structure.Am. J. Hum. Genet. 86:172-184.
    • (2010) Am. J. Hum. Genet. , vol.86 , pp. 172-184
    • Thornton, T.1    McPeek, M.S.2
  • 62
    • 53749084482 scopus 로고    scopus 로고
    • Preterm birth in Caucasians is associated with coagulation and inflammation pathway gene variants
    • Velez, D.R., Fortunato, S.J., Thorsen, P., Lombardi, S.J.,Williams, S.M., andMenon, R. 2008. Preterm birth in Caucasians is associated with coagulation and inflammation pathway gene variants. PLoS One 3:e3283.
    • (2008) PLoS One , vol.3
    • Velez, D.R.1    Fortunato, S.J.2    Thorsen, P.3    Lombardi, S.J.4    Williams, S.M.5    Menon, R.6
  • 63
    • 84982339813 scopus 로고
    • Composition of populations from the perspective of the theory of heredity
    • Wahlund, S. 1928. Composition of populations from the perspective of the theory of heredity. Hereditas 11:65-105.
    • (1928) Hereditas , vol.11 , pp. 65-105
    • Wahlund, S.1
  • 64
    • 79951997040 scopus 로고    scopus 로고
    • Adjustment for local ancestry in genetic association analysis of admixed populations
    • Wang, X., Zhu, X., Qin, H., Cooper, R.S., Ewens, W.J., Li, C., and Li, M. 2011. Adjustment for local ancestry in genetic association analysis of admixed populations. Bioinformatics 27:670-677.
    • (2011) Bioinformatics , vol.27 , pp. 670-677
    • Wang, X.1    Zhu, X.2    Qin, H.3    Cooper, R.S.4    Ewens, W.J.5    Li, C.6    Li, M.7
  • 65
    • 0012145281 scopus 로고    scopus 로고
    • Genetic Data Analysis II 2nd ed. Sinauer Associates, Inc., Sunderland, Massachusetts
    • Weir,B.S. 1996. Population Structure. Genetic Data Analysis II, 2nd ed., pp 161-201. Sinauer Associates, Inc., Sunderland, Massachusetts.
    • (1996) Population Structure , pp. 161-201
    • Weir, B.S.1
  • 66
    • 0021566877 scopus 로고
    • Estimating F-statistics for the analysis of populationstructure
    • Weir, B.S. and Cockerham, C.C. 1984. Estimating F-statistics for the analysis of populationstructure. Evolution 38:1358-1370.
    • (1984) Evolution , vol.38 , pp. 1358-1370
    • Weir, B.S.1    Cockerham, C.C.2
  • 68
    • 79960026939 scopus 로고    scopus 로고
    • Genome-wide local ancestry approach identifies genes and variants associated with chemotherapeutic susceptibility in African Americans
    • Wheeler, H.E., Gorsic, L.K., Welsh, M., Stark, A.L., Gamazon, E.R., Cox, N.J., and Dolan, M.E. 2011. Genome-wide local ancestry approach identifies genes and variants associated with chemotherapeutic susceptibility in African Americans. PLoS One 6:e21920.
    • (2011) PLoS One , vol.6
    • Wheeler, H.E.1    Gorsic, L.K.2    Welsh, M.3    Stark, A.L.4    Gamazon, E.R.5    Cox, N.J.6    Dolan, M.E.7
  • 70
    • 0000929750 scopus 로고
    • Systems of mating
    • Wright, S. 1921. Systems of mating. Genetics 6:111-178.
    • (1921) Genetics , vol.6 , pp. 111-178
    • Wright, S.1
  • 71
    • 0001771498 scopus 로고
    • Evolution in Mendelian populations
    • Wright, S. 1931. Evolution in Mendelian populations. Genetics 16:97-159.
    • (1931) Genetics , vol.16 , pp. 97-159
    • Wright, S.1
  • 72
    • 17644416423 scopus 로고    scopus 로고
    • Practical population group assignment with selected informative markers: Characteristics and properties of Bayesian clustering via STRUCTURE
    • Yang, B.Z., Zhao, H.,Kranzler, H.R., and Gelernter, J. 2005. Practical population group assignment with selected informative markers: Characteristics and properties of Bayesian clustering via STRUCTURE. Genet. Epidemiol. 28:302-312.
    • (2005) Genet. Epidemiol. , vol.28 , pp. 302-312
    • Yang, B.Z.1    Zhao, H.2    Kranzler, H.R.3    Gelernter, J.4
  • 73
    • 54449089328 scopus 로고    scopus 로고
    • Comparison of population-based association study methods correcting for population stratification
    • Zhang, F., Wang, Y., and Deng, H.W. 2008. Comparison of population-based association study methods correcting for population stratification. PLoS One 3:e3392.
    • (2008) PLoS One , vol.3
    • Zhang, F.1    Wang, Y.2    Deng, H.W.3
  • 74
    • 2442688965 scopus 로고    scopus 로고
    • Linkage analysis of a complex disease through use of admixed populations
    • Zhu, X., Cooper, R.S., and Elston, R.C. 2004. Linkage analysis of a complex disease through use of admixed populations. Am. J. Hum. Genet. 74:1136-1153.
    • (2004) Am. J. Hum. Genet. , vol.74 , pp. 1136-1153
    • Zhu, X.1    Cooper, R.S.2    Elston, R.C.3
  • 75
    • 40749128980 scopus 로고    scopus 로고
    • A unified association analysis approach for family and unrelated samples correcting for stratification
    • Zhu, X., Li, S., Cooper, R.S., and Elston, R.C. 2008. A unified association analysis approach for family and unrelated samples correcting for stratification. Am. J. Hum. Genet. 82:352-365.
    • (2008) Am. J. Hum. Genet. , vol.82 , pp. 352-365
    • Zhu, X.1    Li, S.2    Cooper, R.S.3    Elston, R.C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.