메뉴 건너뛰기




Volumn 10, Issue 1, 2017, Pages

Genome-wide methylation data mirror ancestry information

(20)  Rahmani, Elior a   Shenhav, Liat a   Schweiger, Regev a   Yousefi, Paul b   Huen, Karen b   Eskenazi, Brenda b   Eng, Celeste c   Huntsman, Scott c   Hu, Donglei c   Galanter, Joshua c,d   Oh, Sam S c   Waldenberger, Melanie e   Strauch, Konstantin e,f   Grallert, Harald e,g   Meitinger, Thomas e,h   Gieger, Christian e,g   Holland, Nina b   Burchard, Esteban G c,d   Zaitlen, Noah c   Halperin, Eran i,j  


Author keywords

Ancestry; DNA methylation; Epigenetics; Epigenome wide association study (EWAS); Illumina 450K; Population structure

Indexed keywords

ARTICLE; CHILD; CONSANGUINITY; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; EPIGENETICS; GENOTYPE; HUMAN; INFORMATION PROCESSING; POPULATION STRUCTURE; SCHOOL CHILD; SINGLE NUCLEOTIDE POLYMORPHISM; ALGORITHM; COMPUTER INTERFACE; GENETIC DATABASE; GENOME-WIDE ASSOCIATION STUDY; HUMAN GENOME; INTERNET; PRINCIPAL COMPONENT ANALYSIS; PROCEDURES;

EID: 85010825671     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/s13072-016-0108-y     Document Type: Article
Times cited : (75)

References (67)
  • 3
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • 1:STN:280:DC%2BD3cvislKrtA%3D%3D 10835412 1461096
    • Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155(2):945-59.
    • (2000) Genetics. , vol.155 , Issue.2 , pp. 945-959
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.3
  • 4
    • 33746512512 scopus 로고    scopus 로고
    • Principal components analysis corrects for stratification in genome-wide association studies
    • 1:CAS:528:DC%2BD28XnsVCgsrg%3D 16862161
    • Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 2006;38(8):904-9.
    • (2006) Nat. Genet. , vol.38 , Issue.8 , 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
  • 5
    • 69749099417 scopus 로고    scopus 로고
    • Fast model-based estimation of ancestry in unrelated individuals
    • 1:CAS:528:DC%2BD1MXhtFCjsLvL 19648217 2752134
    • Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19(9):1655-64.
    • (2009) Genome Res. , vol.19 , Issue.9 , pp. 1655-1664
    • Alexander, D.H.1    Novembre, J.2    Lange, K.3
  • 6
    • 84861597739 scopus 로고    scopus 로고
    • A model-based approach for analysis of spatial structure in genetic data
    • 1:CAS:528:DC%2BC38XntF2iu7k%3D 22610118 3592563
    • Yang W-Y, Novembre J, Eskin E, Halperin E. A model-based approach for analysis of spatial structure in genetic data. Nat. Genet. 2012;44(6):725-31.
    • (2012) Nat. Genet. , vol.44 , Issue.6 , pp. 725-731
    • Yang, W.-Y.1    Novembre, J.2    Eskin, E.3    Halperin, E.4
  • 8
    • 79955578094 scopus 로고    scopus 로고
    • Enhanced statistical tests for GWAS in admixed populations: Assessment using African Americans from care and a Breast Cancer Consortium
    • Pasaniuc B, Zaitlen N, Lettre G, Chen GK, Tandon A, Kao WL, Ruczinski I, Fornage M, Siscovick DS, Zhu X, et al. Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from care and a Breast Cancer Consortium. PLoS Genet. 2011;7(4):1001371.
    • (2011) PLoS Genet. , vol.7 , Issue.4 , pp. 1001371
    • Pasaniuc, B.1    Zaitlen, N.2    Lettre, G.3    Chen, G.K.4    Tandon, A.5    Kao, W.L.6    Ruczinski, I.7    Fornage, M.8    Siscovick, D.S.9    Zhu, X.10
  • 15
    • 84881083007 scopus 로고    scopus 로고
    • Genome-wide variation of cytosine modifications between European and African populations and the implications for complex traits
    • 1:CAS:528:DC%2BC3sXhsV2lu7%2FM 23792949 3730924
    • Moen EL, Zhang X, Mu W, Delaney SM, Wing C, McQuade J, Myers J, Godley LA, Dolan ME, Zhang W. Genome-wide variation of cytosine modifications between European and African populations and the implications for complex traits. Genetics. 2013;194(4):987-96.
    • (2013) Genetics. , vol.194 , Issue.4 , pp. 987-996
    • Moen, E.L.1    Zhang, X.2    Mu, W.3    Delaney, S.M.4    Wing, C.5    McQuade, J.6    Myers, J.7    Godley, L.A.8    Dolan, M.E.9    Zhang, W.10
  • 16
    • 84897545981 scopus 로고    scopus 로고
    • Methylation quantitative trait loci (meQTLs) are consistently detected across ancestry, developmental stage, and tissue type
    • Smith AK, Kilaru V, Kocak M, Almli LM, Mercer KB, Ressler KJ, Tylavsky FA, Conneely KN. Methylation quantitative trait loci (meQTLs) are consistently detected across ancestry, developmental stage, and tissue type. BMC Genom. 2014;15(1):145.
    • (2014) BMC Genom. , vol.15 , Issue.1 , pp. 145
    • Smith, A.K.1    Kilaru, V.2    Kocak, M.3    Almli, L.M.4    Mercer, K.B.5    Ressler, K.J.6    Tylavsky, F.A.7    Conneely, K.N.8
  • 18
    • 46249117780 scopus 로고    scopus 로고
    • Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation
    • 1:CAS:528:DC%2BD1cXnslKrsr4%3D 18568024
    • Kerkel K, Spadola A, Yuan E, Kosek J, Jiang L, Hod E, Li K, Murty VV, Schupf N, Vilain E, et al. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nature Genet. 2008;40(7):904-8.
    • (2008) Nature Genet. , vol.40 , Issue.7 , pp. 904-908
    • Kerkel, K.1    Spadola, A.2    Yuan, E.3    Kosek, J.4    Jiang, L.5    Hod, E.6    Li, K.7    Murty, V.V.8    Schupf, N.9    Vilain, E.10
  • 20
    • 84907584646 scopus 로고    scopus 로고
    • Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels
    • Banovich NE, Lan X, McVicker G, Van de Geijn B, Degner JF, Blischak JD, Roux J, Pritchard JK, Gilad Y. Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. PLoS Genet. 2014;10(9):1004663.
    • (2014) PLoS Genet. , vol.10 , Issue.9 , pp. 1004663
    • Banovich, N.E.1    Lan, X.2    McVicker, G.3    Van De Geijn, B.4    Degner, J.F.5    Blischak, J.D.6    Roux, J.7    Pritchard, J.K.8    Gilad, Y.9
  • 25
    • 23844472247 scopus 로고    scopus 로고
    • KORA-gen-resource for population genetics, controls and a broad spectrum of disease phenotypes
    • Wichmann H, Gieger C, Illig T, et al. KORA-gen-resource for population genetics, controls and a broad spectrum of disease phenotypes. Gesundheitswesen. 2005;67:26.
    • (2005) Gesundheitswesen. , vol.67 , pp. 26
    • Wichmann, H.1    Gieger, C.2    Illig, T.3
  • 28
    • 84886111619 scopus 로고    scopus 로고
    • DNA methylation age of human tissues and cell types
    • Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013;14(10):1-20.
    • (2013) Genome Biol. , vol.14 , Issue.10 , pp. 1-20
    • Horvath, S.1
  • 33
    • 84946495535 scopus 로고    scopus 로고
    • Estimation of blood cellular heterogeneity in newborns and children for epigenome-wide association studies
    • 1:CAS:528:DC%2BC2MXhsVagtL3E 26332589 4636959
    • Yousefi P, Huen K, Quach H, Motwani G, Hubbard A, Eskenazi B, Holland N. Estimation of blood cellular heterogeneity in newborns and children for epigenome-wide association studies. Environ Mol Mutagen. 2015;56(9):751-8.
    • (2015) Environ. Mol. Mutagen. , vol.56 , Issue.9 , pp. 751-758
    • Yousefi, P.1    Huen, K.2    Quach, H.3    Motwani, G.4    Hubbard, A.5    Eskenazi, B.6    Holland, N.7
  • 35
    • 84907375523 scopus 로고    scopus 로고
    • Organophosphate pesticide exposure, PON1, and neurodevelopment in school-age children from the CHAMACOS study
    • 1:CAS:528:DC%2BC2cXhsVOmsL7O 25171140 4338203
    • Eskenazi B, Kogut K, Huen K, Harley KG, Bouchard M, Bradman A, Boyd-Barr D, Johnson C, Holland N. Organophosphate pesticide exposure, PON1, and neurodevelopment in school-age children from the CHAMACOS study. Environ Res. 2014;134:149-57.
    • (2014) Environ. Res. , vol.134 , pp. 149-157
    • Eskenazi, B.1    Kogut, K.2    Huen, K.3    Harley, K.G.4    Bouchard, M.5    Bradman, A.6    Boyd-Barr, D.7    Johnson, C.8    Holland, N.9
  • 36
    • 84877049549 scopus 로고    scopus 로고
    • Associations of PON1 and genetic ancestry with obesity in early childhood
    • Huen K, Harley K, Beckman K, Eskenazi B, Holland N. Associations of PON1 and genetic ancestry with obesity in early childhood. PloS ONE. 2013;8(5):62565.
    • (2013) PloS ONE. , vol.8 , Issue.5 , pp. 62565
    • Huen, K.1    Harley, K.2    Beckman, K.3    Eskenazi, B.4    Holland, N.5
  • 38
    • 84905595372 scopus 로고    scopus 로고
    • Genome-wide association study and admixture mapping identify different asthma-associated loci in Latinos: The Genes-Environments & Admixture in Latino Americans Study
    • 1:CAS:528:DC%2BC2cXkvF2rtw%3D%3D 24406073 4085159
    • Galanter JM, Gignoux CR, Torgerson DG, Roth LA, Eng C, Oh SS, Nguyen EA, Drake KA, Huntsman S, Hu D, et al. Genome-wide association study and admixture mapping identify different asthma-associated loci in Latinos: the Genes-Environments & Admixture in Latino Americans Study. J Allergy Clin Immunol. 2014;134(2):295-305.
    • (2014) J. Allergy Clin. Immunol. , vol.134 , Issue.2 , pp. 295-305
    • Galanter, J.M.1    Gignoux, C.R.2    Torgerson, D.G.3    Roth, L.A.4    Eng, C.5    Oh, S.S.6    Nguyen, E.A.7    Drake, K.A.8    Huntsman, S.9    Hu, D.10
  • 40
    • 84872564830 scopus 로고    scopus 로고
    • A beta-mixture quantile normalization method for correcting probe design bias in Illumina infinium 450K DNA methylation data
    • 1:CAS:528:DC%2BC3sXhtFygsro%3D 23175756
    • Teschendorff AE, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, Beck S. A beta-mixture quantile normalization method for correcting probe design bias in Illumina infinium 450K DNA methylation data. Bioinformatics. 2013;29(2):189-96.
    • (2013) Bioinformatics. , vol.29 , Issue.2 , pp. 189-196
    • Teschendorff, A.E.1    Marabita, F.2    Lechner, M.3    Bartlett, T.4    Tegner, J.5    Gomez-Cabrero, D.6    Beck, S.7
  • 41
    • 84876806540 scopus 로고    scopus 로고
    • A data-driven approach to preprocessing Illumina 450K methylation array data
    • 1:CAS:528:DC%2BC3sXpslyis7w%3D
    • Pidsley R, Wong CC, Volta M, Lunnon K, Mill J, Schalkwyk LC. A data-driven approach to preprocessing Illumina 450K methylation array data. BMC Genom. 2013;14(1):293.
    • (2013) BMC Genom. , vol.14 , Issue.1 , pp. 293
    • Pidsley, R.1    Wong, C.C.2    Volta, M.3    Lunnon, K.4    Mill, J.5    Schalkwyk, L.C.6
  • 43
    • 81955167912 scopus 로고    scopus 로고
    • Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm
    • 1:CAS:528:DC%2BC3MXhsFWqsL3I 21903159 3502750
    • Hoffmann TJ, Zhan Y, Kvale MN, Hesselson SE, Gollub J, Iribarren C, Lu Y, Mei G, Purdy MM, Quesenberry C, et al. Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm. Genomics. 2011;98(6):422-30.
    • (2011) Genomics. , vol.98 , Issue.6 , pp. 422-430
    • Hoffmann, T.J.1    Zhan, Y.2    Kvale, M.N.3    Hesselson, S.E.4    Gollub, J.5    Iribarren, C.6    Lu, Y.7    Mei, G.8    Purdy, M.M.9    Quesenberry, C.10
  • 44
    • 84897548625 scopus 로고    scopus 로고
    • Minfi: A flexible and comprehensive bioconductor package for the analysis of infinium DNA methylation microarrays
    • 1:CAS:528:DC%2BC2cXnslOit78%3D 24478339 4016708
    • Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. Minfi: a flexible and comprehensive bioconductor package for the analysis of infinium DNA methylation microarrays. Bioinformatics. 2014;30(10):1363-9.
    • (2014) Bioinformatics. , vol.30 , Issue.10 , pp. 1363-1369
    • Aryee, M.J.1    Jaffe, A.E.2    Corrada-Bravo, H.3    Ladd-Acosta, C.4    Feinberg, A.P.5    Hansen, K.D.6    Irizarry, R.A.7
  • 45
    • 84862173149 scopus 로고    scopus 로고
    • SWAN: Subset-quantile within array normalization for Illumina infinium HumanMethylation450 BeadChips
    • Maksimovic J, Gordon L, Oshlack A, et al. SWAN: subset-quantile within array normalization for Illumina infinium HumanMethylation450 BeadChips. Genome Biol. 2012;13(6):44.
    • (2012) Genome Biol. , vol.13 , Issue.6 , pp. 44
    • Maksimovic, J.1    Gordon, L.2    Oshlack, A.3
  • 46
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • 16632515
    • Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007;8(1):118-27.
    • (2007) Biostatistics. , vol.8 , Issue.1 , pp. 118-127
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 47
    • 84887485993 scopus 로고    scopus 로고
    • Considerations for normalization of DNA methylation data by Illumina 450K BeadChip assay in population studies
    • 1:CAS:528:DC%2BC2cXntlWgt7s%3D 23959097
    • Yousefi P, Huen K, Schall RA, Decker A, Elboudwarej E, Quach H, Barcellos L, Holland N. Considerations for normalization of DNA methylation data by Illumina 450K BeadChip assay in population studies. Epigenetics. 2013;8(11):1141-52.
    • (2013) Epigenetics. , vol.8 , Issue.11 , pp. 1141-1152
    • Yousefi, P.1    Huen, K.2    Schall, R.A.3    Decker, A.4    Elboudwarej, E.5    Quach, H.6    Barcellos, L.7    Holland, N.8
  • 48
    • 29244479125 scopus 로고    scopus 로고
    • Comparison of three methods to estimate genetic ancestry and control for stratification in genetic association studies among admixed populations
    • 16208514
    • Tsai H-J, Choudhry S, Naqvi M, Rodriguez-Cintron W, Burchard EG, Ziv E. Comparison of three methods to estimate genetic ancestry and control for stratification in genetic association studies among admixed populations. Hum Genet. 2005;118(3-4):424-33.
    • (2005) Hum. Genet. , vol.118 , Issue.3-4 , pp. 424-433
    • Tsai, H.-J.1    Choudhry, S.2    Naqvi, M.3    Rodriguez-Cintron, W.4    Burchard, E.G.5    Ziv, E.6
  • 52
    • 0022000776 scopus 로고
    • A fraction of the mouse genome that is derived from islands of nonmethylated
    • 1:CAS:528:DyaL2MXhtVOgt7o%3D 2981636
    • Bird A, Taggart M, Frommer M, Miller OJ, Macleod D. A fraction of the mouse genome that is derived from islands of nonmethylated. CpG-rich DNA. Cell. 1985;40(1):91-9.
    • (1985) CpG-rich DNA. Cell. , vol.40 , Issue.1 , pp. 91-99
    • Bird, A.1    Taggart, M.2    Frommer, M.3    Miller, O.J.4    Macleod, D.5
  • 53
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores
    • 1:CAS:528:DC%2BD1MXntFGrtA%3D%3D 19151715 2729128
    • Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, et al. The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet. 2009;41(2):178-86.
    • (2009) Nat. Genet. , vol.41 , Issue.2 , pp. 178-186
    • Irizarry, R.A.1    Ladd-Acosta, C.2    Wen, B.3    Wu, Z.4    Montano, C.5    Onyango, P.6    Cui, H.7    Gabo, K.8    Rongione, M.9    Webster, M.10
  • 55
    • 31944432339 scopus 로고    scopus 로고
    • A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters
    • 1:CAS:528:DC%2BD28Xhs1Gnsrs%3D 16432200 1345710
    • Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci. 2006;103(5):1412-7.
    • (2006) Proc Natl Acad Sci. , vol.103 , Issue.5 , pp. 1412-1417
    • Saxonov, S.1    Berg, P.2    Brutlag, D.L.3
  • 63
    • 85194972808 scopus 로고    scopus 로고
    • Regression shrinkage and selection via the lasso
    • Tibshirani R. Regression shrinkage and selection via the lasso. J R Stat Soc Ser B (Methodol). 1996;58:267-88.
    • (1996) J R Stat Soc ser B (Methodol). , vol.58 , pp. 267-288
    • Tibshirani, R.1
  • 65
    • 84943171338 scopus 로고    scopus 로고
    • A global reference for human genetic variation
    • Consortium G.P., et al. A global reference for human genetic variation. Nature. 2015;526(7571):68-74.
    • (2015) Nature. , vol.526 , Issue.7571 , pp. 68-74
    • Consortium, G.P.1
  • 66
    • 84893192328 scopus 로고    scopus 로고
    • Accounting for cellular heterogeneity is critical in epigenome-wide association studies
    • Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol. 2014;15(2):31.
    • (2014) Genome Biol. , vol.15 , Issue.2 , pp. 31
    • Jaffe, A.E.1    Irizarry, R.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.