Risk prediction for complex diseases: Application to Parkinson disease

Genetics in Medicine

Volumn 15, Issue 5, 2013, Pages 361-367

  Hall, Taryn O ^a   Wan, Jia Y ^a   Mata, Ignacio F ^a   Kerr, Kathleen F ^a   Snapinn, Katherine W ^a   Samii, Ali ^a   Roberts, John W ^b   Agarwal, Pinky ^c   Zabetian, Cyrus P ^a   Edwards, Karen L ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b VIRGINIA MASON MEDICAL CENTER   (United States)

^c Evergreen Hospital Medical Center   (United States)

Author keywords

genetics; Parkinson disease; risk prediction

Indexed keywords

AGED; ALLELE; ARTICLE; CONTROLLED STUDY; ENVIRONMENTAL FACTOR; FAMILY HISTORY; FEMALE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MALE; PARKINSON DISEASE; PREDICTION; SCORING SYSTEM; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84877297227     PISSN: 10983600     EISSN: 15300366     Source Type: Journal    
DOI: 10.1038/gim.2012.109     Document Type: Article

References (34)

1. de Lau LM, Breteler MM. Epidemiology of Parkinson's disease. Lancet Neurol 2006;5:525-535.
2. Hughes AJ, Daniel SE, Ben-Shlomo Y, Lees AJ. The accuracy of diagnosis of parkinsonian syndromes in a specialist movement disorder service. Brain 2002;125(Pt 4):861-870.
3. Gagne JJ, Power MC. Anti-inflammatory drugs and risk of Parkinson disease: a meta-analysis. Neurology 2010;23(74):12.
4. Bekris LM, Mata IF, Zabetian CP. The genetics of Parkinson disease. J Geriatr Psychiatry Neurol 2010;23:228-242.
5. Lesage S, Condroyer C, Klebe S, et al. Identification of VPS35 mutations replicated in French families with Parkinson disease. Neurology 2012;78: 1449-1450.
6. Vilariño-Güell C, Wider C, Ross OA, et al. VPS35 mutations in Parkinson disease. Am J Hum Genet 2011;89:162-167.
7. Zimprich A, Benet-Pagès A, Struhal W, et al. A mutation in VPS35, encoding a subunit of the retromer complex, causes late-onset Parkinson disease. Am J Hum Genet 2011;89:168-175.
8. International Parkinson's Disease Genomics Consortium. Imputation of sequence variants for identification of genetic risks for Parkinson's disease: a meta-analysis of genome-wide association studies. Lancet 2011;377: 641-649.
9. International Parkinson's Disease Genomics Consortium (IPDGC); Wellcome Trust Case Control Consortium 2 (WTCCC2). A two-stage meta-analysis identifies several new loci for Parkinson's disease. PLoS Genetics 2011;7(8):e1002142.
10. Do CB, Tung JY, Dorfman E, et al. Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson's disease. PLoS Genet 2011;7:e1002141.
11. Hamza TH, Zabetian CP, Tenesa A, et al. Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease. Nat Genet 2010;42:781-785.
12. Pankratz N, Wilk JB, Latourelle JC, et al. Genomewide association study for susceptibility genes contributing to familial Parkinson disease. Hum Genet 2009;124:593-605.
13. Saad M, Lesage S, Saint-Pierre A, et al. Genome-wide association study confirms BST1 and suggests a locus on 12q24 as the risk loci for Parkinson's disease in the European population. Hum Mol Genet 2011;20:615-627.
14. Satake W, Nakabayashi Y, Mizuta I, et al. Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease. Nat Genet 2009;41:1303-1307.
15. Simón-Sánchez J, Schulte C, Bras JM, et al. Genome-wide association study reveals genetic risk underlying Parkinson's disease. Nat Genet 2009;41:1308-1312.
16. Simón-Sánchez J, van Hilten JJ, van de Warrenburg B, et al. Genome-wide association study confirms extant PD risk loci among the Dutch. Eur J Hum Genet 2011;19:655-661.
17. Gibb WR, Lees AJ. The relevance of the Lewy body to the pathogenesis of idiopathic Parkinson's disease. J Neurol Neurosurg Psychiatr 1988;51:745-752.
18. Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009;5:e1000529.
19. Kay DM, Zabetian CP, Factor SA, et al. Parkinson's disease and LRRK2: frequency of a common mutation in U.S. movement disorder clinics. Mov Disord 2006;21:519-523.
20. Robin X, Turck N, Hainard A, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics 2011; 12:77.
21. Pepe MS, Janes H, Longton G, Leisenring W, Newcomb P. Limitations of the odds ratio in gauging the performance of a diagnostic, prognostic, or screening marker. Am J Epidemiol 2004;159:882-890.
22. Davies RW, Dandona S, Stewart AF, et al. Improved prediction of cardiovascular disease based on a panel of single nucleotide polymorphisms identified through genome-wide association studies. Circ Cardiovasc Genet 2010;3: 468-474.
23. Machiela MJ, Chen CY, Chen C, Chanock SJ, Hunter DJ, Kraft P. Evaluation of polygenic risk scores for predicting breast and prostate cancer risk. Genet Epidemiol 2011;35:506-514.
24. Mealiffe ME, Stokowski RP, Rhees BK, Prentice RL, Pettinger M, Hinds DA. Assessment of clinical validity of a breast cancer risk model combining genetic and clinical information. J Natl Cancer Inst 2010;102:1618-1627.
25. Meigs JB, Shrader P, Sullivan LM, et al. Genotype score in addition to common risk factors for prediction of type 2 diabetes. N Engl J Med 2008; 359:2208-2219.
26. van Hoek M, Dehghan A, Witteman JC, et al. Predicting type 2 diabetes based on polymorphisms from genome-wide association studies: a population-based study. Diabetes 2008;57:3122-3128.
27. Chen H, Poon A, Yeung C, et al. A genetic risk score combining ten psoriasis risk loci improves disease prediction. PLoS ONE 2011;6:e19454.
28. Hageman GS, Gehrs K, Lejnine S, et al. Clinical validation of a genetic model to estimate the risk of developing choroidal neovascular age-related macular degeneration. Hum Genomics 2011;5:420-440.
29. Kang J, Kugathasan S, Georges M, Zhao H, Cho JH; NIDDK IBD Genetics Consortium. Improved risk prediction for Crohn's disease with a multi-locus approach. Hum Mol Genet 2011;20:2435-2442.
30. Bansal A, Pepe MS. When does combining markers improve classification performance and what are the implications for practice. UW Biostatistics Working Paper Series. The Berkley Electronic Press: Berkley, CA, 2011 (Paper 378).
31. Moonesinghe R, Khoury MJ, Liu T, Janssens ACJW. Discriminative accuracy of genomic profiling comparing mulitplicative and additive risk models. Eur J Hum Genet 2011;19:180-185.
32. Brenner H, Gefeller O. Variation of sensitivity, specificity, likelihood ratios and predictive values with disease prevalence. Stat Med 1997;16:981-991.
33. Moons KG, van Es GA, Deckers JW, Habbema JD, Grobbee DE. Limitations of sensitivity, specificity, likelihood ratio, and bayes' theorem in assessing diagnostic probabilities: a clinical example. Epidemiology 1997;8:12-17.
34. Keller MF, Saad M, Bras J, et al. Using genome-wide complex trait analysis to quantify 'missing heritability' in Parkinson's disease. Hum Mol Genet 2012;21:4996-5009.