Power and Predictive Accuracy of Polygenic Risk Scores

PLoS Genetics

Volumn 9, Issue 3, 2013, Pages

  Dudbridge, Frank ^a  

^a LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYTICAL PARAMETERS; AREA UNDER THE CURVE; ARTICLE; GENETIC ASSOCIATION; GENETIC RISK; GENETIC TRAIT; GENETIC VARIABILITY; HUMAN; POLYGENIC SCORE; PREDICTION; QUANTITATIVE ANALYSIS; RISK ASSESSMENT; SCORING SYSTEM; STATISTICAL ANALYSIS;

GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINEAR MODELS; MODELS, THEORETICAL; MULTIFACTORIAL INHERITANCE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84876007072     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003348     Document Type: Article

References (41)

1. Visscher PM, Brown MA, McCarthy MI, Yang J, (2012) Five years of GWAS discovery. Am J Hum Genet 90: 7-24.
2. Wray NR, Goddard ME, Visscher PM, (2007) Prediction of individual genetic risk to disease from genome-wide association studies. Genome Res 17: 1520-1528.
3. Purcell SM, Wray NR, Stone JL, Visscher PM, O'Donovan MC, et al. (2009) Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 460: 748-752.
4. Ripke S, Sanders AR, Kendler KS, Levinson DF, Sklar P, et al. (2011) Genome-wide association study identifies five new schizophrenia loci. Nat Genet 43: 969-976.
5. Hamshere ML, O'Donovan MC, Jones IR, Jones L, Kirov G, et al. (2011) Polygenic dissection of the bipolar phenotype. Br J Psychiatry 198: 284-288.
6. Bush WS, Sawcer SJ, de Jager PL, Oksenberg JR, McCauley JL, et al. (2010) Evidence for polygenic susceptibility to multiple sclerosis-the shape of things to come. Am J Hum Genet 86: 621-625.
7. Lango Allen H, Estrada K, Lettre G, Berndt SI, Weedon MN, et al. (2010) Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467: 832-838.
8. Simonson MA, Wills AG, Keller MC, McQueen MB, (2011) Recent methods for polygenic analysis of genome-wide data implicate an important effect of common variants on cardiovascular disease risk. BMC Med Genet 12: 146.
9. Stahl EA, Wegmann D, Trynka G, Gutierrez-Achury J, Do R, et al. (2012) Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis. Nat Genet 44: 483-489.
10. Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, et al. (2010) Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet 42: 937-948.
11. Peterson RE, Maes HH, Holmans P, Sanders AR, Levinson DF, et al. (2011) Genetic risk sum score comprised of common polygenic variation is associated with body mass index. Hum Genet 129: 221-230.
12. Carayol J, Schellenberg GD, Tores F, Hager J, Ziegler A, et al. (2010) Assessing the impact of a combined analysis of four common low-risk genetic variants on autism risk. Mol Autism 1: 4.
13. Kang J, Kugathasan S, Georges M, Zhao H, Cho JH, (2011) Improved risk prediction for Crohn's disease with a multi-locus approach. Hum Mol Genet 20: 2435-2442.
14. Machiela MJ, Chen CY, Chen C, Chanock SJ, Hunter DJ, et al. (2011) Evaluation of polygenic risk scores for predicting breast and prostate cancer risk. Genet Epidemiol 35: 506-514.
15. Witte JS, Hoffmann TJ, (2011) Polygenic modeling of genome-wide association studies: an application to prostate and breast cancer. OMICS 15: 393-398.
16. Pharoah PD, Antoniou AC, Easton DF, Ponder BA, (2008) Polygenes, risk prediction, and targeted prevention of breast cancer. N Engl J Med 358: 2796-2803.
17. Clayton DG, (2009) Prediction and interaction in complex disease genetics: experience in type 1 diabetes. PLoS Genet 5: e1000540 doi:10.1371/journal.pgen.1000540.
18. Sawcer S, Ban M, Wason J, Dudbridge F, (2010) What role for genetics in the prediction of multiple sclerosis? Ann Neurol 67: 3-10.
19. Evans DM, Visscher PM, Wray NR, (2009) Harnessing the information contained within genome-wide association studies to improve individual prediction of complex disease risk. Hum Mol Genet 18: 3525-3531.
20. Pharoah PD, Antoniou A, Bobrow M, Zimmern RL, Easton DF, et al. (2002) Polygenic susceptibility to breast cancer and implications for prevention. Nat Genet 31: 33-36.
21. Wray NR, Yang J, Goddard ME, Visscher PM, (2010) The genetic interpretation of area under the ROC curve in genomic profiling. PLoS Genet 6: e1000864 doi:10.1371/journal.pgen.1000864.
22. Janssens AC, Aulchenko YS, Elefante S, Borsboom GJ, Steyerberg EW, et al. (2006) Predictive testing for complex diseases using multiple genes: fact or fiction? Genet Med 8: 395-400.
23. Daetwyler HD, Villanueva B, Woolliams JA, (2008) Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLoS ONE 3: e3395 doi:10.1371/journal.pone.0003395.
24. So HC, Sham PC, (2010) A unifying framework for evaluating the predictive power of genetic variants based on the level of heritability explained. PLoS Genet 6: e1001230 doi:10.1371/journal.pgen.1001230.
25. Lee SH, Goddard ME, Wray NR, Visscher PM, (2012) A better coefficient of determination for genetic profile analysis. Genet Epidemiol 36: 214-224.
26. Shi J, Levinson DF, Duan J, Sanders AR, Zheng Y, et al. (2009) Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature 460: 753-757.
27. Lee SH, DeCandia TR, Ripke S, Yang J, Sullivan PF, et al. (2012) Estimating the proportion of variation in susceptibility to schizophrenia captured by common SNPs. Nat Genet 44: 247-250.
28. Sklar P, Ripke S, Scott LJ, Andreassen OA, Cichon S, et al. (2011) Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. Nat Genet 43: 977-983.
29. Risch N, (2001) The genetic epidemiology of cancer: interpreting family and twin studies and their implications for molecular genetic approaches. Cancer Epidemiol Biomarkers Prev 10: 733-741.
30. Lee SH, Wray NR, Goddard ME, Visscher PM, (2011) Estimating missing heritability for disease from genome-wide association studies. Am J Hum Genet 88: 294-305.
31. Janssens AC, Moonesinghe R, Yang Q, Steyerberg EW, van Duijn CM, et al. (2007) The impact of genotype frequencies on the clinical validity of genomic profiling for predicting common chronic diseases. Genet Med 9: 528-535.
32. Dudbridge F, Gusnanto A, (2008) Estimation of significance thresholds for genomewide association scans. Genet Epidemiol 32: 227-234.
33. Yang J, Weedon MN, Purcell S, Lettre G, Estrada K, et al. (2011) Genomic inflation factors under polygenic inheritance. Eur J Hum Genet 19: 807-812.
34. Wacholder S, Hartge P, Prentice R, Garcia-Closas M, Feigelson HS, et al. (2010) Performance of common genetic variants in breast-cancer risk models. N Engl J Med 362: 986-993.
35. Goddard ME, Wray NR, Verbyla K, Visscher PM, (2009) Estimating Effects and Making Predictions from Genome-Wide Marker Data. Statistical Science 24: 517-529.
36. Greenland S, (2000) Principles of multilevel modelling. Int J Epidemiol 29: 158-167.
37. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, et al. (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42: 565-569.
38. Wu TT, Chen YF, Hastie T, Sobel E, Lange K, (2009) Genome-wide association analysis by lasso penalized logistic regression. Bioinformatics 25: 714-721.
39. Hoggart CJ, Whittaker JC, De Iorio M, Balding DJ, (2008) Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies. PLoS Genet 4: e1000130 doi:10.1371/journal.pgen.1000130.
40. Falconer DS, Mackay TFC (1996) Introduction to Quantitative Genetics: Longman.
41. Ruppert D, Wand MP, Carroll RJ (2003) Semiparametric regression: Cambridge University Press.