메뉴 건너뛰기




Volumn 95, Issue 5, 2014, Pages 477-489

Structural architecture of SNP effects on complex traits

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COPY NUMBER VARIATION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC TRAIT; GENETIC VARIABILITY; GENOMICS; GENOTYPE; HUMAN; PHENOTYPE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGICAL MODEL; GENETICS; PROCEDURES;

EID: 84922414574     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2014.09.009     Document Type: Article
Times cited : (21)

References (57)
  • 2
    • 46249093584 scopus 로고    scopus 로고
    • Strong association of de novo copy number mutations with sporadic schizophrenia
    • Xu, B., Roos, J.L., Levy, S., van Rensburg, E.J., Gogos, J.A., and Karayiorgou, M. (2008). Strong association of de novo copy number mutations with sporadic schizophrenia. Nat. Genet. 40, 880-885.
    • (2008) Nat. Genet , vol.40 , pp. 880-885
    • Xu, B.1    Roos, J.L.2    Levy, S.3    Van Rensburg, E.J.4    Gogos, J.A.5    Karayiorgou, M.6
  • 4
    • 77952887857 scopus 로고    scopus 로고
    • Rare structural variants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes
    • Elia, J., Gai, X., Xie, H.M., Perin, J.C., Geiger, E., Glessner, J.T., D'arcy, M., deBerardinis, R., Frackelton, E., Kim, C., et al. (2010). Rare structural variants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes. Mol. Psychiatry 15, 637-646.
    • (2010) Mol. Psychiatry , vol.15 , pp. 637-646
    • Elia, J.1    Gai, X.2    Xie, H.M.3    Perin, J.C.4    Geiger, E.5    Glessner, J.T.6    D'arcy, M.7    De Berardinis, R.8    Frackelton, E.9    Kim, C.10
  • 11
    • 35948984173 scopus 로고    scopus 로고
    • PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
    • Wang, K., Li, M., Hadley, D., Liu, R., Glessner, J., Grant, S.F., Hakonarson, H., and Bucan, M. (2007). PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 17, 1665-1674.
    • (2007) Genome Res , vol.17 , pp. 1665-1674
    • Wang, K.1    Li, M.2    Hadley, D.3    Liu, R.4    Glessner, J.5    Grant, S.F.6    Hakonarson, H.7    Bucan, M.8
  • 12
    • 67649199562 scopus 로고    scopus 로고
    • A Bayesian segmentation approach to ascertain copy number variations at the population level
    • Wu, L.Y., Chipman, H.A., Bull, S.B., Briollais, L., andWang, K. (2009). A Bayesian segmentation approach to ascertain copy number variations at the population level. Bioinformatics 25, 1669-1679.
    • (2009) Bioinformatics , vol.25 , pp. 1669-1679
    • Wu, L.Y.1    Chipman, H.A.2    Bull, S.B.3    Briollais, L.4    Wang, K.5
  • 13
    • 3042604472 scopus 로고    scopus 로고
    • Real-time PCR based on SYBR-Green i fluorescence: An alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions
    • Ponchel, F., Toomes, C., Bransfield, K., Leong, F.T., Douglas, S.H., Field, S.L., Bell, S.M., Combaret, V., Puisieux, A., Mighell, A.J., et al. (2003). Real-time PCR based on SYBR-Green I fluorescence: an alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions. BMC Biotechnol. 3, 18.
    • (2003) BMC Biotechnol , vol.3 , pp. 18
    • Ponchel, F.1    Toomes, C.2    Bransfield, K.3    Leong, F.T.4    Douglas, S.H.5    Field, S.L.6    Bell, S.M.7    Combaret, V.8    Puisieux, A.9    Mighell, A.J.10
  • 14
    • 84876287827 scopus 로고    scopus 로고
    • Effect of combining multiple CNV defining algorithms on the reliability of CNV calls from SNP genotyping data
    • Kim, S.Y., Kim, J.H., and Chung, Y.J. (2012). Effect of combining multiple CNV defining algorithms on the reliability of CNV calls from SNP genotyping data. Genomics Inform. 10, 194-199.
    • (2012) Genomics Inform , vol.10 , pp. 194-199
    • Kim, S.Y.1    Kim, J.H.2    Chung, Y.J.3
  • 15
    • 84860352109 scopus 로고    scopus 로고
    • An integrative segmentation methodfor detecting germline copy number variations in SNP arrays
    • Shi, J., and Li, P. (2012). An integrative segmentation methodfor detecting germline copy number variations in SNP arrays. Genet. Epidemiol. 36, 373-383.
    • (2012) Genet. Epidemiol , vol.36 , pp. 373-383
    • Shi, J.1    Li, P.2
  • 17
    • 77953974065 scopus 로고    scopus 로고
    • Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays
    • Dellinger, A.E., Saw, S.M., Goh, L.K., Seielstad, M., Young, T.L., and Li, Y.J. (2010). Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays. Nucleic Acids Res. 38, e105.
    • (2010) Nucleic Acids Res , vol.38 , pp. e105
    • Dellinger, A.E.1    Saw, S.M.2    Goh, L.K.3    Seielstad, M.4    Young, T.L.5    Li, Y.J.6
  • 18
    • 79960840650 scopus 로고    scopus 로고
    • Characterization of copy number-stable regions in the human genome
    • Johansson, A.C., and Feuk, L. (2011). Characterization of copy number-stable regions in the human genome. Hum. Mutat. 32, 947-955.
    • (2011) Hum. Mutat , vol.32 , pp. 947-955
    • Johansson, A.C.1    Feuk, L.2
  • 20
    • 85030404101 scopus 로고    scopus 로고
    • Commentary "in search of genomicstability: Characterizing copy number stable regions"
    • Davis, L. (2011). Commentary "In Search of GenomicStability: Characterizing Copy Number Stable Regions".Hum. Mutat. 32, v.
    • (2011) Hum. Mutat , vol.32 , pp. v
    • Davis, L.1
  • 22
    • 77951439152 scopus 로고    scopus 로고
    • Trait-associated SNPs are more likely to be eQTLs: Annotation to enhance discovery from GWAS
    • Nicolae, D.L., Gamazon, E., Zhang,W., Duan, S., Dolan, M.E.,and Cox, N.J. (2010). Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS.PLoS Genet. 6, e1000888.
    • (2010) PLoS Genet , vol.6 , pp. e1000888
    • Nicolae, D.L.1    Gamazon, E.2    Zhang, W.3    Duan, S.4    Dolan, M.E.5    Cox, N.J.6
  • 26
    • 84969213492 scopus 로고    scopus 로고
    • Genomewide association study of 14,000 cases of seven common diseases and 3,000 shared controls
    • Wellcome Trust Case Control Consortium (2007). Genomewide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661-678.
    • (2007) Nature , vol.447 , pp. 661-678
    • Wellcome Trust Case Control Consortium1
  • 33
    • 79952269948 scopus 로고    scopus 로고
    • A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci
    • Gamazon, E.R., Nicolae, D.L., and Cox, N.J. (2011). A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. PLoS Genet. 7, e1001292.
    • (2011) PLoS Genet , vol.7 , pp. e1001292
    • Gamazon, E.R.1    Nicolae, D.L.2    Cox, N.J.3
  • 35
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey, J.D., and Tibshirani, R. (2003). Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100, 9440-9445.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 36
    • 79960923810 scopus 로고    scopus 로고
    • Genome-wide assocation and meta-analysis in populations from Starr County, Texas, and Mexico City identify type 2 diabetes susceptibility loci and enrichment for expression quantitative trait loci in top signals
    • Below, J.E., Gamazon, E.R., Morrison, J.V., Konkashbaev, A., Pluzhnikov, A., McKeigue, P.M., Parra, E.J., Elbein, S.C., Hallman, D.M., Nicolae, D.L., et al. (2011). Genome-wide assocation and meta-analysis in populations from Starr County, Texas, and Mexico City identify type 2 diabetes susceptibility loci and enrichment for expression quantitative trait loci in top signals. Diabetologia 54, 2047-2055.
    • (2011) Diabetologia , vol.54 , pp. 2047-2055
    • Below, J.E.1    Gamazon, E.R.2    Morrison, J.V.3    Konkashbaev, A.4    Pluzhnikov, A.5    McKeigue, P.M.6    Parra, E.J.7    Elbein, S.C.8    Hallman, D.M.9    Nicolae, D.L.10
  • 37
    • 84867805626 scopus 로고    scopus 로고
    • Loci nominally associated with autism from genome-wide analysis show enrichment of brain expression quantitative trait loci but not lymphoblastoid cell line expression quantitative trait loci
    • Davis, L.K., Gamazon, E.R., Kistner-Griffin, E., Badner, J.A., Liu, C., Cook, E.H., Sutcliffe, J.S., and Cox, N.J. (2012). Loci nominally associated with autism from genome-wide analysis show enrichment of brain expression quantitative trait loci but not lymphoblastoid cell line expression quantitative trait loci. Mol. Autism 3, 3.
    • (2012) Mol. Autism , vol.3 , pp. 3
    • Davis, L.K.1    Gamazon, E.R.2    Kistner-Griffin, E.3    Badner, J.A.4    Liu, C.5    Cook, E.H.6    Sutcliffe, J.S.7    Cox, N.J.8
  • 38
    • 84887265151 scopus 로고    scopus 로고
    • Partitioning the heritability of Tourette syndrome and obsessive compulsive disorder reveals differences in genetic architecture
    • Davis, L.K., Yu, D., Keenan, C.L., Gamazon, E.R., Konkashbaev, A.I., Derks, E.M., Neale, B.M., Yang, J., Lee, S.H., Evans, P., et al. (2013). Partitioning the heritability of Tourette syndrome and obsessive compulsive disorder reveals differences in genetic architecture. PLoS Genet. 9, e1003864.
    • (2013) PLoS Genet , vol.9 , pp. e1003864
    • Davis, L.K.1    Yu, D.2    Keenan, C.L.3    Gamazon, E.R.4    Konkashbaev, A.I.5    Derks, E.M.6    Neale, B.M.7    Yang, J.8    Lee, S.H.9    Evans, P.10
  • 39
    • 84880346737 scopus 로고    scopus 로고
    • SCAN: Asystems biology approach to pharmacogenomic discovery
    • Gamazon, E.R., Huang, R.S., and Cox, N.J. (2013). SCAN: asystems biology approach to pharmacogenomic discovery. Methods Mol. Biol. 1015, 213-224.
    • (2013) Methods Mol. Biol , vol.1015 , pp. 213-224
    • Gamazon, E.R.1    Huang, R.S.2    Cox, N.J.3
  • 40
    • 78650747491 scopus 로고    scopus 로고
    • Discovery and characterization of chromatin states for systematic annotation of the human genome
    • Ernst, J., and Kellis, M. (2010). Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat. Biotechnol. 28, 817-825.
    • (2010) Nat. Biotechnol , vol.28 , pp. 817-825
    • Ernst, J.1    Kellis, M.2
  • 42
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A.R., and Hall, I.M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 44
    • 84891783452 scopus 로고    scopus 로고
    • The Database of Genomic Variants: A curatedcollection of structural variation in the human genome
    • Database issue
    • MacDonald, J.R., Ziman, R., Yuen, R.K., Feuk, L., and Scherer,S.W. (2014). The Database of Genomic Variants: a curatedcollection of structural variation in the human genome.Nucleic Acids Res. 42 (Database issue), D986-D992.
    • (2014) Nucleic Acids Res , vol.42 , pp. D986-D992
    • Macdonald, J.R.1    Ziman, R.2    Yuen, R.K.3    Feuk, L.4    Scherers, W.5
  • 45
    • 77955128564 scopus 로고    scopus 로고
    • Using GWAS data to identify copy number variants contributing to common complex diseases
    • Zollner, S., and Teslovich, T.M. (2009). Using GWAS data to identify copy number variants contributing to common complex diseases. Stat. Sci. 24, 530-546.
    • (2009) Stat. Sci , vol.24 , pp. 530-546
    • Zollner, S.1    Teslovich, T.M.2
  • 48
    • 62549090133 scopus 로고    scopus 로고
    • Great genotypic and phenotypic diversities associated with copynumber variations of complement C4 and RP-C4-CYP21- TNX (RCCX) modules: A comparison of Asian-Indian and European American populations
    • Saxena, K., Kitzmiller, K.J., Wu, Y.L., Zhou, B., Esack, N., Hiremath, L., Chung, E.K., Yang, Y., and Yu, C.Y. (2009). Great genotypic and phenotypic diversities associated with copynumber variations of complement C4 and RP-C4-CYP21- TNX (RCCX) modules: a comparison of Asian-Indian and European American populations. Mol. Immunol. 46, 1289-1303.
    • (2009) Mol. Immunol , vol.46 , pp. 1289-1303
    • Saxena, K.1    Kitzmiller, K.J.2    Wu, Y.L.3    Zhou, B.4    Esack, N.5    Hiremath, L.6    Chung, E.K.7    Yang, Y.8    Yu, C.Y.9
  • 49
    • 44649198581 scopus 로고    scopus 로고
    • The molecular genetics of type 1 diabetes: New genes and emerging mechanisms
    • Ounissi-Benkalha, H., and Polychronakos, C. (2008). The molecular genetics of type 1 diabetes: new genes and emerging mechanisms. Trends Mol. Med. 14, 268-275.
    • (2008) Trends Mol. Med , vol.14 , pp. 268-275
    • Ounissi-Benkalha, H.1    Polychronakos, C.2
  • 50
    • 57749191212 scopus 로고    scopus 로고
    • The genetic basis for type 1 diabetes
    • Mehers, K.L., and Gillespie, K.M. (2008). The genetic basis for type 1 diabetes. Br. Med. Bull. 88, 115-129.
    • (2008) Br. Med. Bull , vol.88 , pp. 115-129
    • Mehers, K.L.1    Gillespie, K.M.2
  • 51
    • 84878682420 scopus 로고    scopus 로고
    • The Genotype- Tissue Expression (GTEx) project
    • Consortium, G.; GTEx Consortium (2013). The Genotype- Tissue Expression (GTEx) project. Nat. Genet. 45, 580-585.
    • (2013) Nat. Genet , vol.45 , pp. 580-585
    • Consortium, G.1    Consortium, G.2
  • 52
    • 84860817223 scopus 로고    scopus 로고
    • Recent explosive human population growth has resulted in an excess of rare genetic variants
    • Keinan, A., and Clark, A.G. (2012). Recent explosive human population growth has resulted in an excess of rare genetic variants. Science 336, 740-743.
    • (2012) Science , vol.336 , pp. 740-743
    • Keinan, A.1    Clark, A.G.2
  • 54
    • 54149118995 scopus 로고    scopus 로고
    • Reduced purifying selection prevails over positive selection in human copy number variant evolution
    • Nguyen, D.Q.,Webber, C., Hehir-Kwa, J., Pfundt, R., Veltman, J., and Ponting, C.P. (2008). Reduced purifying selection prevails over positive selection in human copy number variant evolution. Genome Res. 18, 1711-1723.
    • (2008) Genome Res , vol.18 , pp. 1711-1723
    • Nguyen, D.Q.1    Webber, C.2    Hehir-Kwa, J.3    Pfundt, R.4    Veltman, J.5    Ponting, C.P.6
  • 55
    • 4243882278 scopus 로고
    • On the problem of hidden variables in quantum mechanics
    • Bell, J. (1966). On the problem of hidden variables in quantum mechanics. Rev. Mod. Phys. 38, 447-452.
    • (1966) Rev. Mod. Phys , vol.38 , pp. 447-452
    • Bell, J.1
  • 56
    • 84899487356 scopus 로고    scopus 로고
    • Integrative genomics: Quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data
    • Gamazon, E.R., Huang, R.S., Dolan, M.E., Cox, N.J., and Im, H.K. (2012). Integrative genomics: quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data. Front. Genet. 3, 202.
    • (2012) Front. Genet , vol.3 , pp. 202
    • Gamazon, E.R.1    Huang, R.S.2    Dolan, M.E.3    Cox, N.J.4    Im, H.K.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.