Projecting the performance of risk prediction based on polygenic analyses of genome-wide association studies (original) (raw)

• Bowles Biesecker, B. & Marteau, T.M. The future of genetic counselling: an international perspective. Nat. Genet. 22, 133–137 (1999).
  Article CAS Google Scholar
• Pharoah, P.D. et al. Polygenic susceptibility to breast cancer and implications for prevention. Nat. Genet. 31, 33–36 (2002).
  Article CAS Google Scholar
• van Hoek, M. et al. Predicting type 2 diabetes based on polymorphisms from genome-wide association studies: a population-based study. Diabetes 57, 3122–3128 (2008).
  Article CAS Google Scholar
• Pharoah, P.D., Antoniou, A.C., Easton, D.F. & Ponder, B.A. Polygenes, risk prediction, and targeted prevention of breast cancer. N. Engl. J. Med. 358, 2796–2803 (2008).
  Article CAS Google Scholar
• Wacholder, S. et al. Performance of common genetic variants in breast-cancer risk models. N. Engl. J. Med. 362, 986–993 (2010).
  Article CAS Google Scholar
• Lango Allen, H. et al. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467, 832–838 (2010).
  Article CAS Google Scholar
• Speliotes, E.K. et al. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat. Genet. 42, 937–948 (2010).
  Article CAS Google Scholar
• Teslovich, T.M. et al. Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466, 707–713 (2010).
  Article CAS Google Scholar
• Jostins, L. & Barrett, J.C. Genetic risk prediction in complex disease. Hum. Mol. Genet. 20, R182–R188 (2011).
  Article CAS Google Scholar
• Franke, A. et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat. Genet. 42, 1118–1125 (2010).
  Article CAS Google Scholar
• Kraft, P. & Hunter, D.J. Genetic risk prediction–are we there yet? N. Engl. J. Med. 360, 1701–1703 (2009).
  Article CAS Google Scholar
• Manolio, T.A. et al. Finding the missing heritability of complex diseases. Nature 461, 747–753 (2009).
  Article CAS Google Scholar
• Zuk, O., Hechter, E., Sunyaev, S.R. & Lander, E.S. The mystery of missing heritability: Genetic interactions create phantom heritability. Proc. Natl. Acad. Sci. USA 109, 1193–1198 (2012).
  Article CAS Google Scholar
• Park, J.H. et al. Estimation of effect size distribution from genome-wide association studies and implications for future discoveries. Nat. Genet. 42, 570–575 (2010).
  Article CAS Google Scholar
• Park, J.H. et al. Distribution of allele frequencies and effect sizes and their interrelationships for common genetic susceptibility variants. Proc. Natl. Acad. Sci. USA 108, 18026–18031 (2011).
  Article CAS Google Scholar
• Yang, J. et al. Common SNPs explain a large proportion of the heritability for human height. Nat. Genet. 42, 565–569 (2010).
  Article CAS Google Scholar
• Yang, J. et al. Genome partitioning of genetic variation for complex traits using common SNPs. Nat. Genet. 43, 519–525 (2011).
  Article CAS Google Scholar
• Park, J.H. & Dunson, D.B. Bayesian generalized product partition model. Statist. Sinica 20, 1203–1226 (2010).
  Google Scholar
• Lee, S.H. et al. Estimating the proportion of variation in susceptibility to schizophrenia captured by common SNPs. Nat. Genet. 44, 247–250 (2012).
  Article CAS Google Scholar
• Stahl, E.A. et al. Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis. Nat. Genet. 44, 483–489 (2012).
  Article CAS Google Scholar
• Vattikuti, S., Guo, J. & Chow, C.C. Heritability and Genetic Correlations Explained by Common SNPs for Metabolic Syndrome Traits. PLoS Genet. 8, e1002637 (2012).
  Article CAS Google Scholar
• Purcell, S.M. et al. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 460, 748–752 (2009).
  Article CAS Google Scholar
• Clayton, D.G. Prediction and interaction in complex disease genetics: experience in type 1 diabetes. PLoS Genet. 5, e1000540 (2009).
  Article Google Scholar
• Wray, N.R., Goddard, M.E. & Visscher, P.M. Prediction of individual genetic risk to disease from genome-wide association studies. Genome Res. 17, 1520–1528 (2007).
  Article CAS Google Scholar
• Daetwyler, H.D., Villanueva, B. & Woolliams, J.A. Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLoS ONE 3, e3395 (2008).
  Article Google Scholar
• Janssens, A.C. et al. Predictive testing for complex diseases using multiple genes: fact or fiction? Genet. Med. 8, 395–400 (2006).
  Article Google Scholar
• Mihaescu, R., Moonesinghe, R., Khoury, M.J. & Janssens, A.C. Predictive genetic testing for the identification of high-risk groups: a simulation study on the impact of predictive ability. Genome Med. 3, 51 (2011).
  Article Google Scholar
• Roberts,, N.J. et al. The predictive capacity of personal genome sequencing. Sci Transl. Med. 4, 133ra58 (2012).
  Article Google Scholar
• Tibshirani, R. Regression shrinkage and selection via the lasso. J. R. Stat. Soc. Series B Stat. Methodol. 58, 267–288 (1996).
  Google Scholar
• Yang, J. et al. Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nat. Genet. 44, 369–375 (2012).
  Article CAS Google Scholar
• Goddard, M.E., Wray, N.R., Verbyla, K. & Visscher, P.M. Estimating effects and making predictions from genome-wide marker data. Stat. Sci. 24, 517–529 (2009).
  Article Google Scholar
• Guan, Y. & Stephens, M. Bayesian variable selection regression for genome-wide association studies and other large-scale problems. Ann. Appl. Stat. 5, 1780–1815 (2011).
  Article Google Scholar
• Li, B. & Leal, S.M. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am. J. Hum. Genet. 83, 311–321 (2008).
  Article CAS Google Scholar
• Gail, M.H. Personalized estimates of breast cancer risk in clinical practice and public health. Stat. Med. 30, 1090–1104 (2011).
  Article Google Scholar
• Lee, S.H., Wray, N.R., Goddard, M.E. & Visscher, P.M. Estimating missing heritability for disease from genome-wide association studies. Am. J. Hum. Genet. 88, 294–305 (2011).
  Article Google Scholar
• Barrett, J.C. et al. Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat. Genet. 41, 703–707 (2009).
  Article CAS Google Scholar
• Voight, B.F. et al. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat. Genet. 42, 579–589 (2010).
  Article CAS Google Scholar
• Eeles, R.A. et al. Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. Nat. Genet. 41, 1116–1121 (2009).
  Article CAS Google Scholar
• Schunkert, H. et al. Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat. Genet. 43, 333–338 (2011).
  Article CAS Google Scholar
• Scheuner, M.T. Genetic evaluation for coronary artery disease. Genet. Med. 5, 269–285 (2003).
  Article Google Scholar
• Mai, P.L., Wideroff, L., Greene, M.H. & Graubard, B.I. Prevalence of family history of breast, colorectal, prostate, and lung cancer in a population-based study. Public Health Genomics 13, 495–503 (2010).
  Article CAS Google Scholar
• Annis, A.M., Caulder, M.S., Cook, M.L. & Duquette, D. Family history, diabetes, and other demographic and risk factors among participants of the National Health and Nutrition Examination Survey 1999–2002. Prev. Chronic Dis. 2, A19 (2005).
  PubMed PubMed Central Google Scholar
• Wray, N.R., Yang, J., Goddard, M.E. & Visscher, P.M. The genetic interpretation of area under the ROC curve in genomic profiling. PLoS Genet. 6, e1000864 (2010).
  Article Google Scholar
• So, H.C., Kwan, J.S., Cherny, S.S. & Sham, P.C. Risk prediction of complex diseases from family history and known susceptibility loci, with applications for cancer screening. Am. J. Hum. Genet. 88, 548–565 (2011).
  Article CAS Google Scholar
• Park, J.H., Gail, M.H., Greene, M.H. & Chatterjee, N. Potential usefulness of single nucleotide polymorphisms to identify persons at high cancer risk: an evaluation of seven common cancers. J. Clin. Oncol. 30, 2157–2162 (2012).
  Article Google Scholar
• Ghosh, A., Zou, F. & Wright, F.A. Estimating odds ratios in genome scans: an approximate conditional likelihood approach. Am. J. Hum. Genet. 82, 1064–1074 (2008).
  Article CAS Google Scholar
• Spiegelhalter, D.J., Best, N.G., Carlin, B.R. & van der Linde, A. Bayesian measures of model complexity and fit. J. R. Stat. Soc. Series B Stat. Methodol. 64, 583–616 (2002).
  Article Google Scholar