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Volumn 23, Issue 5, 2018, Pages 1368-1374

Multi-polygenic score approach to trait prediction

Author keywords

[No Author keywords available]

Indexed keywords

ACADEMIC ACHIEVEMENT; ADOLESCENT; ARTICLE; BODY MASS; CONTROLLED STUDY; GENETIC PARAMETERS; GENETIC TRAIT; GENETIC VARIABILITY; GENOME-WIDE ASSOCIATION STUDY; HUMAN; MENTAL CAPACITY; MULTIFACTORIAL INHERITANCE; MULTIPOLYGENIC SCORE; OUTCOME ASSESSMENT; PREDICTION; PRIORITY JOURNAL; PROPENSITY SCORE; SAMPLE SIZE; SCORING SYSTEM; COGNITION; COMPUTER SIMULATION; EDUCATIONAL STATUS; FEMALE; FORECASTING; GENETIC PREDISPOSITION; GENETIC SCREENING; GENETICS; MALE; PHENOTYPE; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 85034049516     PISSN: 13594184     EISSN: 14765578     Source Type: Journal    
DOI: 10.1038/mp.2017.163     Document Type: Article
Times cited : (147)

References (45)
  • 1
    • 84941053261 scopus 로고    scopus 로고
    • GRASP v2 0: An update on the Genome-Wide Repository of Associations between SNPs and phenotypes
    • Eicher JD, Landowski C, Stackhouse B, Sloan A, Chen W, Jensen N et al. GRASP v2.0: an update on the Genome-Wide Repository of Associations between SNPs and phenotypes. Nucleic Acids Res 2015; 43: D799-D804.
    • (2015) Nucleic Acids Res , vol.43 , pp. D799-D804
    • Eicher, J.D.1    Landowski, C.2    Stackhouse, B.3    Sloan, A.4    Chen, W.5    Jensen, N.6
  • 3
    • 84908890496 scopus 로고    scopus 로고
    • Defining the role of common variation in the genomic and biological architecture of adult human height
    • Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S et al. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet 2014; 46: 1173-1186.
    • (2014) Nat Genet , vol.46 , pp. 1173-1186
    • Wood, A.R.1    Esko, T.2    Yang, J.3    Vedantam, S.4    Pers, T.H.5    Gustafsson, S.6
  • 4
    • 84923171580 scopus 로고    scopus 로고
    • Genetic studies of body mass index yield new insights for obesity biology
    • Locke AE, Kahali B, Berndt SI, Justice AE, Pers TH, Day FR et al. Genetic studies of body mass index yield new insights for obesity biology. Nature 2015; 518: 197-206.
    • (2015) Nature , vol.518 , pp. 197-206
    • Locke, A.E.1    Kahali, B.2    Berndt, S.I.3    Justice, A.E.4    Pers, T.H.5    Day, F.R.6
  • 5
    • 84876007072 scopus 로고    scopus 로고
    • Power and predictive accuracy of polygenic risk scores
    • Dudbridge F. Power and predictive accuracy of polygenic risk scores. PLoS Genet 2013; 9: e1003348.
    • (2013) PLoS Genet , vol.9 , pp. e1003348
    • Dudbridge, F.1
  • 6
    • 84938971555 scopus 로고    scopus 로고
    • A fast method that uses polygenic scores to estimate the variance explained by genome-wide marker panels and the proportion of variants affecting a trait
    • Palla L, Dudbridge F. A fast method that uses polygenic scores to estimate the variance explained by genome-wide marker panels and the proportion of variants affecting a trait. Am J Hum Genet 2015; 97: 250-259.
    • (2015) Am J Hum Genet , vol.97 , pp. 250-259
    • Palla, L.1    Dudbridge, F.2
  • 7
    • 84946158905 scopus 로고    scopus 로고
    • PRSice: Polygenic risk score software
    • btu848
    • Euesden J, Lewis CM, O'Reilly PF. PRSice: polygenic risk score software. Bioinformatics 2014; 31: 1466-1468, btu848.
    • (2014) Bioinformatics , vol.31 , pp. 1466-1468
    • Euesden, J.1    Lewis, C.M.2    O'Reilly, P.F.3
  • 8
    • 84976604384 scopus 로고    scopus 로고
    • A plethora of pleiotropy across complex traits
    • Visscher PM, Yang J. A plethora of pleiotropy across complex traits. Nat Genet 2016; 48: 707-708.
    • (2016) Nat Genet , vol.48 , pp. 707-708
    • Visscher, P.M.1    Yang, J.2
  • 13
    • 16244401458 scopus 로고    scopus 로고
    • Regularization and variable selection via the elastic net
    • Zou H, Hastie T. Regularization and variable selection via the elastic net. J R Stat Soc Ser B Stat Methodol 2005; 67: 301-320.
    • (2005) J R Stat Soc ser B Stat Methodol , vol.67 , pp. 301-320
    • Zou, H.1    Hastie, T.2
  • 14
    • 84925130699 scopus 로고    scopus 로고
    • Joint analysis of psychiatric disorders increases accuracy of risk prediction for schizophrenia, bipolar disorder, and major depressive disorder
    • Cross-Disorder Working Group of the Psychiatric Genomics Consortium
    • Maier R, Moser G, Chen G-B, Ripke S, Cross-Disorder Working Group of the Psychiatric Genomics Consortium, Coryell W et al. Joint analysis of psychiatric disorders increases accuracy of risk prediction for schizophrenia, bipolar disorder, and major depressive disorder. Am J Hum Genet 2015; 96: 283-294.
    • (2015) Am J Hum Genet , vol.96 , pp. 283-294
    • Maier, R.1    Moser, G.2    Chen, G.-B.3    Ripke, S.4    Coryell, W.5
  • 15
    • 85046789976 scopus 로고    scopus 로고
    • Multivariate genome-wide and integrated transcriptome and epigenome-wide analyses of the well-being spectrum
    • Baselmans BM, Jansen R, Dongen J, van, Bao Y, Smart M, Kumari M et al. Multivariate genome-wide and integrated transcriptome and epigenome-wide analyses of the well-being spectrum. bioRxiv 2017; doi: 10.1101/115915.
    • (2017) BioRxiv
    • Baselmans, B.M.1    Jansen, R.2    Dongen, J.3    Van4    Bao, Y.5    Smart, M.6    Kumari, M.7
  • 16
  • 19
    • 84958839102 scopus 로고    scopus 로고
    • Genetic link between family socioeconomic status and children's educational achievement estimated from genome-wide SNPs
    • Krapohl E, Plomin R. Genetic link between family socioeconomic status and children's educational achievement estimated from genome-wide SNPs. Mol Psychiatry 2016; 21: 437-443.
    • (2016) Mol Psychiatry , vol.21 , pp. 437-443
    • Krapohl, E.1    Plomin, R.2
  • 20
    • 36049033420 scopus 로고    scopus 로고
    • The genetic and environmental origins of learning abilities and disabilities in the early school years
    • Kovas Y, Haworth CMA, Dale PS, Plomin R. The genetic and environmental origins of learning abilities and disabilities in the early school years. Monogr Soc Res Child Dev 2007; 72, vii 1-144.
    • (2007) Monogr Soc Res Child Dev , vol.72 , pp. 1-144
    • Kovas, Y.1    Haworth, C.M.A.2    Dale, P.S.3    Plomin, R.4
  • 22
    • 85028296791 scopus 로고    scopus 로고
    • LD Hub: A centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis
    • Zheng J, Erzurumluoglu AM, Elsworth BL, Kemp JP, Howe L, Haycock PC et al. LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis. Bioinformatics 2017; 33: 272-279.
    • (2017) Bioinformatics , vol.33 , pp. 272-279
    • Zheng, J.1    Erzurumluoglu, A.M.2    Elsworth, B.L.3    Kemp, J.P.4    Howe, L.5    Haycock, P.C.6
  • 23
    • 84923946495 scopus 로고    scopus 로고
    • LD score regression distinguishes confounding from polygenicity in genome-wide association studies
    • Schizophrenia Working Group of the Psychiatric Genomics Consortium
    • Bulik-Sullivan BK, Loh P-R, Finucane HK, Ripke S, Yang J, Schizophrenia Working Group of the Psychiatric Genomics Consortium et al. LD score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat Genet 2015; 47: 291-295.
    • (2015) Nat Genet , vol.47 , pp. 291-295
    • Bulik-Sullivan, B.K.1    Loh, P.-R.2    Finucane, H.K.3    Ripke, S.4    Yang, J.5
  • 25
    • 56249113343 scopus 로고    scopus 로고
    • Building predictive models in R using the caret package
    • Kuhn M. Building predictive models in R using the caret package. J Stat Softw 2008; 28: 1-26.
    • (2008) J Stat Softw , vol.28 , pp. 1-26
    • Kuhn, M.1
  • 26
    • 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: 267-288.
    • (1996) J R Stat Soc ser B Methodol , vol.58 , pp. 267-288
    • Tibshirani, R.1
  • 27
    • 84879166428 scopus 로고    scopus 로고
    • On grouping effect of elastic net
    • Zhou D-X. On grouping effect of elastic net. Stat Probab Lett 2013; 83: 2108-2112.
    • (2013) Stat Probab Lett , vol.83 , pp. 2108-2112
    • Zhou, D.-X.1
  • 28
    • 77950537175 scopus 로고    scopus 로고
    • Regularization paths for generalized linear models via coordinate descent
    • Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Softw 2010; 33: 1-22.
    • (2010) J Stat Softw , vol.33 , pp. 1-22
    • Friedman, J.1    Hastie, T.2    Tibshirani, R.3
  • 29
    • 85164392958 scopus 로고    scopus 로고
    • A study of cross-validation and bootstrap for accuracy estimation and model selection
    • Morgan Kaufmann Publishers Inc. : San Francisco, CA, USA, 1995 (cited 14 December
    • Kohavi R. A study of cross-validation and bootstrap for accuracy estimation and model selection. In: Proceedings of the 14th International Joint Conference on Artificial Intelligence- Volume 2. Morgan Kaufmann Publishers Inc.: San Francisco, CA, USA, 1995 (cited 14 December 2016), pp 1137-1143. Available from http://dl. acm.org/citation.cfm?id = 1643031.1643047.
    • (2016) Proceedings of the 14th International Joint Conference on Artificial Intelligence- Volume 2 , pp. 1137-1143
    • Kohavi, R.1
  • 30
    • 84950461478 scopus 로고
    • Estimating the error rate of a prediction rule: Improvement on cross-validation
    • Efron B. Estimating the error rate of a prediction rule: improvement on cross-validation. J Am Stat Assoc 1983; 78: 316-331.
    • (1983) J Am Stat Assoc , vol.78 , pp. 316-331
    • Efron, B.1
  • 31
    • 0031536511 scopus 로고    scopus 로고
    • Improvements on cross-validation: The 632+ bootstrap method
    • Efron B, Tibshirani R. Improvements on cross-validation: the 632+ bootstrap method. J Am Stat Assoc 1997; 92: 548-560.
    • (1997) J Am Stat Assoc , vol.92 , pp. 548-560
    • Efron, B.1    Tibshirani, R.2
  • 32
    • 65749119811 scopus 로고    scopus 로고
    • Estimating classification error rate: Repeated cross-validation, repeated hold-out and bootstrap
    • Kim J-H. Estimating classification error rate: repeated cross-validation, repeated hold-out and bootstrap. Comput Stat Data Anal 2009; 53: 3735-3745.
    • (2009) Comput Stat Data Anal , vol.53 , pp. 3735-3745
    • Kim, J.-H.1
  • 34
    • 0344643407 scopus 로고    scopus 로고
    • Inhibition of subliminally primed responses is mediated by the caudate and thalamus: Evidence from functional MRI and Huntington's disease
    • Aron AR, Schlaghecken F, Fletcher PC, Bullmore ET, Eimer M, Barker R et al. Inhibition of subliminally primed responses is mediated by the caudate and thalamus: evidence from functional MRI and Huntington's disease. Brain 2003; 126: 713-723.
    • (2003) Brain , vol.126 , pp. 713-723
    • Aron, A.R.1    Schlaghecken, F.2    Fletcher, P.C.3    Bullmore, E.T.4    Eimer, M.5    Barker, R.6
  • 35
    • 84948069327 scopus 로고    scopus 로고
    • A fronto-striato-subthalamicpallidal network for goal-directed and habitual inhibition
    • Jahanshahi M, Obeso I, Rothwell JC, Obeso JA. A fronto-striato-subthalamicpallidal network for goal-directed and habitual inhibition. Nat Rev Neurosci 2015; 16: 719-732.
    • (2015) Nat Rev Neurosci , vol.16 , pp. 719-732
    • Jahanshahi, M.1    Obeso, I.2    Rothwell, J.C.3    Obeso, J.A.4
  • 36
    • 15244353512 scopus 로고    scopus 로고
    • The roles of the caudate nucleus in human classification learning
    • Seger CA, Cincotta CM. The roles of the caudate nucleus in human classification learning. J Neurosci 2005; 25: 2941-2951.
    • (2005) J Neurosci , vol.25 , pp. 2941-2951
    • Seger, C.A.1    Cincotta, C.M.2
  • 37
    • 43049090829 scopus 로고    scopus 로고
    • A probability-based measure of effect size: Robustness to base rates and other factors
    • Ruscio J. A probability-based measure of effect size: robustness to base rates and other factors. Psychol Methods 2008; 13: 19-30.
    • (2008) Psychol Methods , vol.13 , pp. 19-30
    • Ruscio, J.1
  • 39
    • 84957109611 scopus 로고    scopus 로고
    • Body mass index is associated with inflammatory bowel disease: A systematic review and meta-analysis
    • Dong J, Chen Y, Tang Y, Xu F, Yu C, Li Y et al. Body mass index is associated with inflammatory bowel disease: a systematic review and meta-analysis. PLoS ONE 2015; 10: e0144872.
    • (2015) PLoS ONE , vol.10 , pp. e0144872
    • Dong, J.1    Chen, Y.2    Tang, Y.3    Xu, F.4    Yu, C.5    Li, Y.6
  • 41
    • 85037364395 scopus 로고    scopus 로고
    • An efficient Bayesian meta-analysis approach for studying cross-phenotype genetic associations
    • Majumdar A, Haldar T, Bhattacharya S, Witte J. An efficient Bayesian meta-analysis approach for studying cross-phenotype genetic associations. bioRxiv. 2017; doi: 10.1101/101543.
    • (2017) BioRxiv.
    • Majumdar, A.1    Haldar, T.2    Bhattacharya, S.3    Witte, J.4
  • 42
    • 84920858732 scopus 로고    scopus 로고
    • Meta-analysis of correlated traits via summary statistics from GWASs with an application in hypertension
    • Zhu X, Feng T, Tayo BO, Liang J, Young JH, Franceschini N et al. Meta-analysis of correlated traits via summary statistics from GWASs with an application in hypertension. Am J Hum Genet 2015; 96: 21-36.
    • (2015) Am J Hum Genet , vol.96 , pp. 21-36
    • Zhu, X.1    Feng, T.2    Tayo, B.O.3    Liang, J.4    Young, J.H.5    Franceschini, N.6
  • 43
    • 84860771128 scopus 로고    scopus 로고
    • A subset-based approach improves power and interpretation for the combined analysis of genetic association studies of heterogeneous traits
    • Bhattacharjee S, Rajaraman P, Jacobs KB, Wheeler WA, Melin BS, Hartge P et al. A subset-based approach improves power and interpretation for the combined analysis of genetic association studies of heterogeneous traits. Am J Hum Genet 2012; 90: 821-835.
    • (2012) Am J Hum Genet , vol.90 , pp. 821-835
    • Bhattacharjee, S.1    Rajaraman, P.2    Jacobs, K.B.3    Wheeler, W.A.4    Melin, B.S.5    Hartge, P.6
  • 44
    • 84928253865 scopus 로고    scopus 로고
    • A multivariate genome-wide association analysis of 10 LDL subfractions, and their response to statin treatment, in 1868 Caucasians
    • Shim H, Chasman DI, Smith JD, Mora S, Ridker PM, Nickerson DA et al. A multivariate genome-wide association analysis of 10 LDL subfractions, and their response to statin treatment, in 1868 Caucasians. PLOS ONE 2015; 10: e0120758.
    • (2015) PLOS ONE , vol.10 , pp. e0120758
    • Shim, H.1    Chasman, D.I.2    Smith, J.D.3    Mora, S.4    Ridker, P.M.5    Nickerson, D.A.6
  • 45
    • 84897389512 scopus 로고    scopus 로고
    • A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle
    • Bolormaa S, Pryce JE, Reverter A, Zhang Y, Barendse W, Kemper K et al. A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle. PLOS Genet 2014; 10: e1004198.
    • (2014) PLOS Genet , vol.10 , pp. e1004198
    • Bolormaa, S.1    Pryce, J.E.2    Reverter, A.3    Zhang, Y.4    Barendse, W.5    Kemper, K.6


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