Genomic prediction of complex human traits: Relatedness, trait architecture and predictive meta-models

Human Molecular Genetics

Volumn 24, Issue 14, 2015, Pages 4167-4182

  Spiliopoulou, Athina ^a,b   Nagy, Reka ^a   Bermingham, Mairead L ^a   Huffman, Jennifer E ^a   Hayward, Caroline ^a   Vitart, Veronique ^a   Rudan, Igor ^c   Campbell, Harry ^c   Wright, Alan F ^a   Wilson, James F ^c   Pong Wong, Ricardo ^d   Agakov, Felix ^b   Navarro, Pau ^a   Haley, Chris S ^a,d  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b PHARMATICS LIMITED   (United Kingdom)

^c UNIVERSITY OF EDINBURGH   (United Kingdom)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HIGH DENSITY LIPOPROTEIN; GENETIC MARKER;

ACCURACY; ARTICLE; BODY HEIGHT; BODY MASS; CLINICAL DECISION MAKING; EFFECT SIZE; GENE FREQUENCY; GENE LOCUS; GENETIC ASSOCIATION; GENETIC SIMILARITY; GENETIC TRAIT; GENETIC VARIABILITY; GENOME; GENOMICS; GENOTYPE; HEREDITY; HERITABILITY; HUMAN; INDEL MUTATION; META ANALYSIS; PEDIGREE; PHENOTYPE; POPULATION GENETICS; POPULATION STRUCTURE; PREDICTION; PRIORITY JOURNAL; BIOLOGICAL MODEL; BLOOD; COHORT ANALYSIS; COMPARATIVE STUDY; CROATIA; EMPIRICAL RESEARCH; GENETIC DATABASE; GENETIC MARKER; GENOME-WIDE ASSOCIATION STUDY; PROCEDURES; QUANTITATIVE TRAIT LOCUS; SAMPLE SIZE; SCOTLAND; SINGLE NUCLEOTIDE POLYMORPHISM;

BODY MASS INDEX; COHORT STUDIES; CROATIA; DATABASES, GENETIC; EMPIRICAL RESEARCH; GENETIC MARKERS; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; GENOTYPE; HUMANS; LIPOPROTEINS, HDL; MODELS, GENETIC; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SAMPLE SIZE; SCOTLAND;

EID: 84936743760     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddv145     Document Type: Article

References (53)

1. Guttmacher, A.E. and Collins, F.S. (2002) Genomic medicine-a primer. N. Engl. J. Med., 347, 1512-1520.
2. Guttmacher, A.E., McGuire, A.L., Ponder, B. and Stefansson, K. (2010) Personalized genomic information: preparing for the future of genetic medicine. Nat. Rev. Genet., 11, 161-165.
3. Manolio, T.A. (2013) Bringing genome-wide association findings into clinical use. Nat. Rev. Genet., 14, 549-558.
4. Clayton, D.G. (2009) Prediction and interaction in complex disease genetics: experience in type 1 diabetes. PLoS Genet., 5, e1000540.
5. Thanabalasingham, G., Shah, N., Vaxillaire, M., Hansen, T., Tuomi, T., Gasperikova, D., Szopa, M., Tjora, E., James, T.J., Kokko, P. et al. (2011) A large multi-centre European study validates high-sensitivity C-reactive protein (hsCRP) as a clinical biomarker for the diagnosis of diabetes subtypes. Diabetologia, 54, 2801-2810.
6. Wilke, R.A., Ramsey, L.B., Johnson, S.G., Maxwell, W.D., McLeod, H.L., Voora, D., Krauss, R.M., Roden, D.M., Feng, Q., Cooper-Dehoff, R.M. et al. (2012) The clinical pharmacogenomics implementation consortium: CPIC guideline for SLCO1B1 and simvastatininduced myopathy. Clin. Pharmacol. Ther., 92, 112-117.
7. Lamberts, S.W. and Uitterlinden, A.G. (2009) Genetic testing in clinical practice. Annu. Rev. Med., 60, 431-442.
8. Phimister, E.G., Feero, W.G. and Guttmacher, A.E. (2012) Realizing Genomic Medicine. N. Engl. J. Med., 366, 757-759.
9. Aschard, H., Chen, J., Cornelis, M.C., Chibnik, L.B., Karlson, E.W. and Kraft, P. (2012) Inclusion of gene-gene and gene-environment interactions unlikely to dramatically improve risk prediction for complex diseases. Am. J. Hum. Genet., 90, 962-972.
10. Jakobsdottir, J., Gorin, M.B., Conley, Y.P., Ferrell, R.E. and Weeks, D.E. (2009) Interpretation of genetic association studies: markers with replicated highly significant odds ratios may be poor classifiers. PLoS Genet., 5, e1000337.
11. Janssens, A.C. and van Duijn, C.M. (2008) Genome-based prediction of common diseases: advances and prospects. Hum. Mol. Genet., 17, R166-R173.
12. Evans, D.M., Visscher, P.M. and Wray, N.R. (2009) Harnessing the information contained within genome-wide association studies to improve individual prediction of complex disease risk. Hum. Mol. Genet., 18, 3525-3531.
13. International Schizophrenia ConsortiumPurcell, S.M., Wray, N.R., Stone, J.L., Visscher, P.M., O'Donovan, M.C., Sullivan, P.F. and Sklar, P. (2009) Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature, 460, 748-752.
14. Pharoah, P.D., Antoniou, A.C., Easton, D.F. and Ponder, B.A. (2008) Polygenes, risk prediction, and targeted prevention of breast cancer. N. Engl. J. Med., 358, 2796-2803.
15. Machiela, M.J., Chen, C.Y., Chen, C., Chanock, S.J., Hunter, D.J. andKraft, P. (2011)Evaluationofpolygenicriskscoresforpredictingbreastandprostatecancer risk. Genet. Epidemiol., 35, 506-514.
16. de los Campos, G., Gianola, D. and Allison, D.B. (2010) Predicting genetic predisposition in humans: the promise of wholegenome markers. Nat. Rev. Genet., 11, 880-886.
17. Meuwissen, T.H.E., Hayes, B.J. and Goddard, M.E. (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157, 1819-1829.
18. Yang, J., Benyamin, B., McEvoy, B.P., Gordon, S., Henders, A.K., Nyholt, D.R., Madden, P.A., Heath, A.C., Martin, N.G., Montgomery, G.W., Goddard, M.E. and Visscher, P.M. (2010) Common SNPs explain a large proportion of the heritability for human height. Nat. Genet., 42, 565-569.
19. de los Campos, G., Hickey, J.M., Pong-Wong, R., Daetwyler, H. D. and Calus, M.P.L. (2013) Whole-genome regression and prediction methods applied to plant and animal breeding. Genetics, 193, 327-345.
20. Wimmer, V., Lehermeier, C., Albrecht, T., Auinger, H.J., Wang, Y. and Schon, C.C. (2013) Genome-wide prediction of traits with different genetic architecture through efficient variable selection. Genetics, 195, 573-587.
21. Abraham, G., Kowalczyk, A., Zobel, J. and Inouye, M. (2013) Performance and robustness of penalized and unpenalized methods for genetic prediction of complex human disease. Genet. Epidemiol., 37, 184-195.
22. Warren, H., Casas, J.P., Hingorani, A., Dudbridge, F. and Whittaker, J. (2014) Genetic prediction of quantitative lipid traits: comparing shrinkage models to gene scores. Genet. Epidemiol., 38, 72-83.
23. Makowsky, R., Pajewski, N.M., Klimentidis, Y.C., Vazquez, A.I., Duarte, C.W., Allison, D.B. and de los Campos, G. (2011) Beyond missing heritability: prediction of complex traits. PLoS Genet., 7, e1002051.
24. Vazquez, A.I., de los Campos, G., Klimentidis, Y.C., Rosa, G.J., Gianola, D., Yi, N. and Allison, D.B. (2012) A comprehensive genetic approach for improving prediction of skin cancer risk in humans. Genetics, 192, 1493-1502.
25. de los Campos, G., Vazquez, A.I., Fernando, R., Klimentidis, Y. C. and Sorensen, D. (2013) Prediction of Complex Human Traits Using the Genomic Best Linear Unbiased Predictor. PLoS Genet., 9, e1003608.
26. Wray, N.R., Yang, J., Hayes, B.J., Price, A.L., Goddard, M.E. and Visscher, P.M. (2013) Pitfalls of predicting complex traits from SNPs. Nat. Rev. Genet., 14, 507-515.
27. Zaitlen, N., Kraft, P., Patterson, N., Pasaniuc, B., Bhatia, G., Pollack, S. and Price, A.L. (2013) Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits. PLoS Genet., 9, e1003520.
28. Dudbridge, F. (2013) Power and predictive accuracy of polygenic risk scores. PLoS Genet., 9, e1003348.
29. Chatterjee, N., Wheeler, B., Sampson, J., Hartge, P., Chanock, S.J. and Park, J.H. (2013) Projecting the performance of risk prediction based on polygenic analyses of genome-wide association studies. Nat. Genet., 45, 400-405.
30. Hoerl, A.E.andKennard, R.W. (1970) Ridge regression: biased estimation for nonorthogonal problems. Technometrics, 12, 55-67.
31. Tibshirani, R. (1996) Regression shrinkage and selection via the Lasso. J. R. Stat. Soc. Series B Stat. Methodol., 58, 267-288.
32. Zou, H. and Hastie, T. (2005) Regularization and variable selection via the elastic net. J. R. Stat. Soc. Series B Stat. Methodol., 67, 301-320.
33. Allen, H.L., Estrada, K., Lettre, G., Berndt, S.I., Weedon, M.N., Rivadeneira, F., Willer, C.J., Jackson, A.U., Vedantam, S., Raychaudhuri, S. et al. (2010) Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature, 467, 832-838.
34. Speliotes, E.K., Willer, C.J., Berndt, S.I., Monda, K.L., Thorleifsson, G., Jackson, A.U., Allen, H.L., Lindgren, C.M., Luan, J., Magi, R. et al. (2010) Association analyses of 249, 796 individuals reveal 18 new loci associated with body mass index. Nat. Genet., 42, 937-948.
35. Global Lipids Genetics Consortium, Willer, C.J., Schmidt, E.M., Sengupta, S., Peloso, G.M., Gustafsson, S., Kanoni, S., Ganna, A., Chen, J., Buchkovich, M.L. et al. (2013) Discovery and refinement of loci associated with lipid levels. Nat. Genet., 45, 1274-1283.
36. Vattikuti, S., Guo, J. and Chow, C.C. (2012) Heritability and genetic correlations explained by common SNPs for metabolic syndrome traits. PLoS Genet., 8, e1002637.
37. Legarra, A., Robert-Granie, C., Manfredi, E. and Elsen, J.M. (2008) Performance of genomic selection in mice. Genetics, 180, 611-618.
38. de los Campos, G., Klimentidis, Y.C., Vazquez, A.I. and Allison, D.B. (2012) Prediction of expected years of life using whole-genome markers. PloS One, 7, e40964.
39. Zuk, O., Hechter, E., Sunyaev, S.R. and Lander, E.S. (2012) The mystery of missing heritability: Genetic interactions create phantom heritability. Proc. Natl Acad. Sci. USA, 109, 1193-1198.
40. Ripke, S., O'Dushlaine, C., Chambert, K., Moran, J.L., Kahler, A. K., Akterin, S., Bergen, S.E., Collins, A.L., Crowley, J.J., Fromer, M. et al. (2013) Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat. Genet., 45, 1150-1159.
41. Kooperberg, C., LeBlanc, M. and Obenchain, V. (2010) Risk prediction using genome-wide association studies. Genet. Epidemiol., 34, 643-652.
42. Wheeler, H.E., Aquino-Michaels, K., Gamazon, E.R., Trubetskoy, V.V., Dolan, M.E., Huang, R.S., Cox, N.J. and Im, H.K. (2014) Poly-omic prediction of complex traits: OmicKriging. Genet. Epidemiol., 38, 402-415.
43. Vitart, V., Biloglav, Z., Hayward, C., Janicijevic, B., Smolej-Narancic, N., Barac, L., Pericic, M., Klaric, I.M., Skaric-Juric, T., Barbalic, M. et al. (2006) 3000 years of solitude: extreme differentiation in the island isolates of Dalmatia, Croatia. Eur. J. Hum. Genet., 14, 478-487.
44. Polasek, O., Marusic, A., Rotim, K., Hayward, C., Vitart, V., Huffman, J., Campbell, S., Jankovic, S., Boban, M., Biloglav, Z. et al. (2009) Genome-wide association study of anthropometric traits in Korcula Island, Croatia. Croat. Med. J., 50, 7-16.
45. Rudan, I., Marusic, A., Jankovic, S., Rotim, K., Boban, M., Lauc, G., Grkovic, I., Dogas, Z., Zemunik, T., Vatavuk, Z. et al. (2009) "10001 Dalmatians:" Croatia launches its national biobank. Croat. Med. J., 50, 4-6.
46. McQuillan, R., Leutenegger, A.-L., Abdel-Rahman, R., Franklin, C.S., Pericic, M., Barac-Lauc, L., Smolej-Narancic, N., Janicijevic, B., Polasek, O., Tenesa, A. et al. (2008) Runs of homozygosity in European populations. Am. J. Hum. Genet., 83, 359-372.
47. Delaneau, O., Zagury, J.F. and Marchini, J. (2013) Improved whole-chromosome phasing for disease and population genetic studies. Nat. Methods, 10, 5-6.
48. Howie, B.N., Donnelly, P. and Marchini, J. (2009) A flexible and accurate genotype imputationmethod for the next generation of genome-wide association studies. PLoS Genet., 5, e1000529.
49. Hoeting, J.A., Madigan, D., Raftery, A.E. and Volinsky, C.T. (1999) Bayesian model averaging: a tutorial. Stat. Sci., 14, 382-401.
50. Kittler, J., Hatef, M., Duin, R.P.W. andMatas, J. (1998)On combining classifiers. IEEE Trans. Pattern. Anal. Mach. Intell., 20, 226-239.
51. Dietterich, T.G. (2000) Ensemble methods in machine learning. Lect. Notes Comput. Sc., 1857, 1-15.
52. Gianola, D., Weigel, K.A., Kramer, N., Stella, A. and Schon, C.C. (2014) Enhancing genome-enabled prediction by bagging genomic BLUP. PLoS One, 9, e91693.
53. Friedman, J., Hastie, T. and Tibshirani, R. (2010) Regularization Paths for Generalized Linear Models via Coordinate Descent. J. Stat. Softw., 33, 1-22.