A comparison of bayesian and frequentist approaches to incorporating external information for the prediction of prostate cancer risk

Genetic Epidemiology

Volumn 36, Issue 1, 2012, Pages 71-83

  Newcombe, Paul J ^a   Reck, Brian H ^b   Sun, Jielin ^c   Platek, Greg T ^b   Verzilli, Claudio ^a   Kader, A Karim ^c   Kim, Seong Tae ^c   Hsu, Fang Chi ^c   Zhang, Zheng ^c   Zheng, S Lilly ^c   Mooser, Vincent E ^b   Condreay, Lynn D ^b   Spraggs, Colin F ^a   Whittaker, John C ^a   Rittmaster, Roger S ^b   Xu, Jianfeng ^c  

^a GLAXOSMITHKLINE   (United Kingdom)

^b GLAXOSMITHKLINE   (United States)

^c WAKE FOREST SCHOOL OF MEDICINE   (United States)

Author keywords

Bayesian logistic regression; Genetic clinical risk prediction; Genetic scores; Predictive assessment; Prostate cancer

Indexed keywords

ARTICLE; BAYES THEOREM; CALIBRATION; CANCER GENETICS; CANCER RISK; COMPARATIVE STUDY; FREQUENTIST LOGISTIC REGRESSION; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GENOTYPE; HUMAN; LOGISTIC REGRESSION ANALYSIS; META ANALYSIS (TOPIC); PREDICTION; PREDICTIVE VALUE; PROSTATE CANCER; SINGLE NUCLEOTIDE POLYMORPHISM;

AGED; ALGORITHMS; AREA UNDER CURVE; BAYES THEOREM; CALIBRATION; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LOGISTIC MODELS; MALE; MIDDLE AGED; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; PROSTATIC NEOPLASMS; RANDOMIZED CONTROLLED TRIALS AS TOPIC; ROC CURVE;

EID: 84859083855     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21600     Document Type: Article

References (43)

1. Amundadottir LT, Sulem P, Gudmundsson J, Helgason A, Baker A, Agnarsson BA, Sigurdsson A, Benediktsdottir KR, Cazier J-B, Sainz J, Jakobsdottir M, Kostic J, Magnusdottir DN, Ghosh S, Agnarsson K, Birgisdottir B, Le Roux L, Olafsdottir A, Blondal T, Andresdottir M, Gretarsdottir OS, Bergthorsson JT, Gudbjartsson D, Gylfason A, Thorleifsson G, Manolescu A, Kristjansson K, Geirsson G, Isaksson H, Douglas J, Johansson J-E, Bälter K, Wiklund F, Montie JE, Yu X, Suarez BK, Ober C, Cooney KA, Gronberg H, Catalona WJ, Einarsson GV, Barkardottir RB, Gulcher JR, Kong A, Thorsteinsdottir U, Stefansson K. 2006. A common variant associated with prostate cancer in European and African populations. Nat Genet 38:652-658.
2. Andriole GL, Bostwick DG, Brawley OW, Gomella LG, Marberger M, Montorsi F, Pettaway CA, Tammela TL, Teloken C, Tindall DJ, Somerville MC, Wilson TH, Fowler IL, Rittmaster RS, the REDUCE Study Group. 2010. Effect of Dutasteride on the risk of prostate cancer. N Engl J Med 362:1192-1202.
3. Bayarri MJ, Berger JO. 2000. P values for composite null models. J Am Stat Assoc 95:1127-1142.
4. DeLong ER, DeLong DM, Clarke-Pearson DL. 1988. Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics 44:837-845.
5. Duggan D, Zheng SL, Knowlton M, Benitez D, Dimitrov L, Wiklund F, Robbins C, Isaacs SD, Cheng Y, Li G, Sun J, Chang B-L, Marovich L, Wiley KE, Bälter K, Stattin P, Adami H-O, Gielzak M, Yan G, Sauvageot J, Liu W, Kim JW, Bleecker ER, Meyers DA, Trock BJ, Partin AW, Walsh PC, Isaacs WB, Grönberg H, Xu J, Carpten JD. 2007. Two genome-wide association studies of aggressive prostate cancer implicate putative prostate tumor suppressor gene DAB2IP. J Natl Cancer Inst 99:1836-1844.
6. Easton DF, Eeles RA. 2008. Genome-wide association studies in cancer. Hum Mol Genet 17:R109-R115.
7. Eeles RA, Kote-Jarai Z, Al Olama AA, Giles GG, GuyM, Severi G, Muir K, Hopper JL, Henderson BE, Haiman CA, Schleutker J, Hamdy FC, Neal DE, Donovan JL, Stanford JL, Ostrander EA, Ingles SA, John EM, Thibodeau SN, Schaid D, Park JY, Spurdle A, Clements J, Dickinson JL, Maier C, Vogel W, Dork T, Rebbeck TR, Cooney KA, Cannon-Albright L, Chappuis PO, Hutter P, Zeegers M, Kaneva R, Zhang H-W, Lu Y-J, FoulkesWD, English DR, Leongamornlert DA, Tymrakiewicz M, Morrison J, Ardern-Jones AT, Hall AL, O'Brien LT, Wilkinson RA, Saunders EJ, Page EC, Sawyer EJ, Edwards SM, Dearnaley DP, Horwich A, Huddart RA, Khoo VS, Parker CC, Van As N, Woodhouse CJ, Thompson A, Christmas T, Ogden C, Cooper CS, Southey MC, Lophatananon A, Liu J-F, Kolonel LN, Le Marchand L, Wahlfors T, Tammela TL, Auvinen A, Lewis SJ, Cox A, FitzGerald LM, Koopmeiners JS, Karyadi DM, Kwon EM, SternMC, Corral R, Joshi AD, Shahabi A, McDonnell SK, Sellers TA, Pow-SangJ, Chambers S, Aitken J, Gardiner RA (Frank), Batra J, Kedda MA, Lose F, Polanowski A, Patterson B, Serth J, Meyer A, Luedeke M, Stefflova K, Ray AM, Lange EM, Farnham J, KhanH, Slavov C, et al. 2009. Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. Nat Genet 41:1116-1121.
8. Eeles RA, Kote-Jarai Z, Giles GG, Olama AAA, Guy M, Jugurnauth SK, Mulholland S, Leongamornlert DA, Edwards SM, Morrison J, Field HI, Southey MC, Severi G, Donovan JL, Hamdy FC, Dearnaley DP, Muir KR, Smith C, Bagnato M, Ardern-Jones AT, Hall AL, O'Brien LT, Gehr-Swain BN, Wilkinson RA, Cox A, Lewis S, Brown PM, Jhavar SG, Tymrakiewicz M, Lophatananon A, Bryant SL, Horwich A, Huddart RA, Khoo VS, Parker CC, Woodhouse CJ, Thompson A, Christmas T, Ogden C, Fisher C, Jamieson C, Cooper CS, English DR, Hopper JL, Neal DE, Easton DF. 2008. Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet 40:316-321.
9. FitzGerald LM, Kwon EM, Koopmeiners JS, Salinas CA, Stanford JL, Ostrander EA. 2009. Analysis of recently identified prostate cancer susceptibility loci in a population-based study: associationswith family history and clinical features. Clin Cancer Res 15:3231-3237.
10. Gelman A, Meng XL, Stern H. 1996. Posterior predictive assessment of model fitness via realized discrepancies. Stat Sin 6:733-759.
11. Gilks WR, Richardson S, Spiegelhalter DJ. 1996. Markov Chain Monte Carlo In Practice, 2nd Edition. London: Chapman & Hall CRC Press.
12. Gion M, Mione R, Barioli P, Barichello M, Zattoni F, Prayer-Galetti T, Plebani M, Aimo G, Terrone C, Manferrari F, Madeddu G, Caberlotto L, Fandella A, Pianon C, Vianello L. 1998. Percent free prostatespecific antigen in assessing the probability of prostate cancer under optimal analytical conditions. Clin Chem 44:2462-2470.
13. Green PJ. 1995. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82:711.
14. Gudmundsson J, Sulem P, Manolescu A, Amundadottir LT, Gudbjartsson D, HelgasonA, Rafnar T, Bergthorsson JT, Agnarsson BA, Baker A, Sigurdsson A, Benediktsdottir KR, Jakobsdottir M, Xu J, Blondal T, Kostic J, Sun J, Ghosh S, Stacey SN, Mouy M, Saemundsdottir J, Backman VM, Kristjansson K, Tres A, Partin AW, Albers-Akkers MT, Godino-Ivan Marcos J, Walsh PC, Swinkels DW, Navarrete S, Isaacs SD, Aben KK, Graif T, Cashy J, Ruiz-Echarri M, Wiley KE, Suarez BK, Witjes JA, Frigge M, Ober C, Jonsson E, Einarsson GV, Mayordomo JI, Kiemeney LA, Isaacs WB, Catalona WJ, Barkardottir RB, Gulcher JR, Thorsteinsdottir U, Kong A, Stefansson K. 2007a. Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat Genet 39:631-637.
15. Gudmundsson J, Sulem P, Steinthorsdottir V, Bergthorsson JT, Thorleifsson G, Manolescu A, Rafnar T, Gudbjartsson D, Agnarsson BA, Baker A, Sigurdsson A, Benediktsdottir KR, JakobsdottirM, Blondal T, Stacey SN, Helgason A, Gunnarsdottir S, Olafsdottir A, Kristinsson KT, Birgisdottir B, Ghosh S, Thorlacius S, Magnusdottir D, Stefansdottir G, Kristjansson K, Bagger Y, Wilensky RL, Reilly MP, Morris AD, Kimber CH, AdeyemoA, Chen Y, Zhou J, SoW-Y, Tong PCY, Ng MCY, Hansen T, Andersen G, Borch-Johnsen K, Jorgensen T, Tres A, Fuertes F, Ruiz-Echarri M, Asin L, Saez B, van Boven E, Klaver S, Swinkels DW, Aben KK, Graif T, Cashy J, Suarez BK, van Vierssen Trip O, Frigge ML, Ober C, Hofker MH, Wijmenga C, Christiansen C, Rader DJ, Palmer CNA, Rotimi C, Chan JCN, Pedersen O, Sigurdsson G, Benediktsson R, Jonsson E, Einarsson GV, Mayordomo JI, Catalona WJ, Kiemeney LA, Barkardottir RB, Gulcher JR, Thorsteinsdottir U, Kong A, Stefansson K. 2007b. Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. Nat Genet 39:977-983.
16. Hernandez DJ, HanM, Humphreys EB, Mangold LA, Taneja SS, Childs SJ, Bartsch G, Partin AW. 2009. Predicting the outcome of prostate biopsy: comparison of a novel logistic regression-based model, the prostate cancer risk calculator, and prostate-specific antigen level alone. BJU International 103:609-614.
17. Hsu F-C, Sun J, Zhu Y, Kim S-T, Jin T, Zhang Z, Wiklund F, Kader AK, Zheng SL, Isaacs W, Gr ̈onberg H, Xu J. 2010. Comparison of two methods for estimating absolute risk of prostate cancer based on single nucleotide polymorphisms and family history. Cancer Epidemiol Biomarkers Prev 19:1083-1088.
18. Jakobsdottir J, Gorin MB, Conley YP, Ferrell RE, Weeks DE. 2009. Interpretation of genetic association studies: markers with replicated highly significant odds ratios may be poor classifiers. PLoS Genet 5: e1000337.
19. Kim S-T, Cheng Y, Hsu F-C, Jin T, Kader AK, Zheng SL, Isaacs WB, Xu J, Sun J. 2010. Prostate cancer risk-associated variants reported from genome-wide association studies: meta-analysis and their contribution to genetic Variation. Prostate 70:1729-1738.
20. Lango H, Palmer CNA, Morris AD, Zeggini E, Hattersley AT, Mc-Carthy MI, Frayling TM, Weedon MN. 2008. Assessing the combined impact of 18 common genetic variants of modest effect sizes on type 2 diabetes risk. Diabetes 57:3129-3135.
21. Lin X, Song K, Lim N, Yuan X, Johnson T, Abderrahmani A, Vollenweider P, Stirnadel H, Sundseth S, Lai E, Burns D, Middleton L, Roses A, Matthews P, Waeber G, Cardon L, Waterworth D, Mooser V. 2009. Risk prediction of prevalent diabetes in a Swiss population using a weighted genetic score-the CoLaus study. Diabetologia 52:600-608.
22. Lunn DJ, Whittaker JC, Best N. 2006. A Bayesian toolkit for genetic association studies. Genet Epidemiol 30:231-247.
23. Meigs JB, Shrader P, Sullivan LM, McAteer JB, Fox CS, Dupuis J, Manning AK, Florez JC, Wilson PWF, D'Agostino RB, Cupples LA. 2008. Genotype score in addition to common risk factors for prediction of type 2 diabetes. N Engl J Med 359:2208-2219.
24. Nguyen CT, Yu C, Moussa A, Kattan MW, Jones JS. 2010. Performance of prostate cancer prevention trial risk calculator in a contemporary cohort screened for prostate cancer and diagnosed by extended prostate biopsy. J Urol 183:529-533.
25. Ntzoufras I. 2009. Bayesian Modeling Using WinBUGS. JohnWiley and Sons.
26. Optenberg SA, Clark JY, Brawer MK, Thompson IM, Stein CR, Friedrichs P. 1997. Development of a decision-making tool to predict risk of prostate cancer: the Cancer of the Prostate Risk Index (CAPRI) test. Urology 50:665-672.
27. Paynter NP, Chasman DI, Pare G, Buring JE, Cook NR, Miletich JP, Ridker PM. 2010. Association between a literature-based genetic risk score and cardiovascular events in women. JAMA 303:631-637.
28. Salinas CA, Koopmeiners JS, Kwon EM, FitzGerald L., Lin DW, Ostrander EA, Feng Z, Stanford JL. 2009. Clinical utility of five genetic variants for predicting prostate cancer risk and mortality. Prostate 69:363-372.
29. Schroder FH, Hugosson J, Roobol MJ, Tammela TLJ, Ciatto S, Nelen V, Kwiatkowski M, Lujan M, Lilja H, Zappa M, Denis LJ, Recker F, Berenguer A, Maattanen L, Bangma CH, Aus G, Villers A, Rebillard X, van der Kwast T, Blijenberg BG, Moss SM, de Koning HJ, Auvinen A, the ERSPC Investigators. 2009. Screening and prostatecancer mortality in a randomized European study. N Engl J Med 360:1320-1328.
30. Serfling R, Shulman M, Thompson GL, Xiao Z, Benaim E, Roehrborn CG, Rittmaster R. 2007. Quantifying the impact of prostate volumes, number of biopsy cores and 5alpha-reductase inhibitor therapy on the probability of prostate cancer detection using mathematical modeling. J Urol 177:2352-2356.
31. Spiegelhalter DJ, Best NG. 2003. Bayesian approaches to multiple sources of evidence and uncertainty in complex cost-effectiveness modelling. Stat Med 22:3687-3709.
32. Thomas G, Jacobs KB, Yeager M, Kraft P, Wacholder S, Orr N, Yu K, Chatterjee N, Welch R, Hutchinson A, Crenshaw A, Cancel-Tassin G, Staats BJ, Wang Z, Gonzalez-Bosquet J, Fang J, Deng X, Berndt SI, Calle EE, Feigelson HS, Thun MJ, Rodriguez C, Albanes D, Virtamo J, Weinstein S, Schumacher FR, Giovannucci E, Willett WC, Cussenot O, Valeri A, Andriole GL, Crawford ED, Tucker M, Gerhard DS, Fraumeni JF, Hoover R, Hayes RB, Hunter DJ, Chanock SJ. 2008. Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet 40:310-315.
33. Thompson IM, Ankerst DP, Chi C, Goodman PJ, Tangen CM, Lucia MS, Feng Z, Parnes HL, Coltman CA. 2006. Assessing prostate cancer risk: results from the Prostate Cancer Prevention trial. J Natl Cancer Inst 98:529-534.
34. Thompson IM, Pauler Ankerst D, Chi C, Goodman PJ, Tangen CM, Lippman SM, Lucia MS, Parnes HL, Coltman CA. 2007. Prediction of prostate cancer for patients receiving Finasteride: results from the Prostate Cancer Prevention trial. J Clin Oncol 25:3076-3081.
35. Thompson IM, Tangen CM, Ankerst DP, Chi C, Lucia MS, Goodman P, Parnes H, Coltman Jr CA. 2008. The performance of prostate specific antigen for predicting prostate cancer is maintained after a prior negative prostate biopsy. J Urol 180:544-547.
36. Todd JA, Walker NM, Cooper JD, Smyth DJ, Downes K, Plagnol V, Bailey R, Nejentsev S, Field SF, Payne F, Lowe CE, Szeszko JS, Hafler JP, Zeitels L, Yang JHM, Vella A, Nutland S, Stevens HE, Schuilenburg H, Coleman G, Maisuria M, Meadows W, Smink LJ, Healy B, Burren OS, Lam AAC, Ovington NR, Allen J, Adlem E, Leung H-T, Wallace C, Howson JMM, Guja C, Ionescu-T̂ i{dotless}rgovişte C, Simmonds MJ, Heward JM, Gough SCL, Dunger DB, Wicker LS, Clayton DG. 2007. Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Nat Genet 39:857-864.
37. Vlaeminck-Guillem V, Ruffion A, André J, Devonec M, Paparel P. 2010. Urinary prostate cancer 3 test: toward the age of reason? Urology 75:447-453.
38. Wacholder S, Hartge P, Prentice R, Garcia-Closas M, Feigelson HS, Diver WR, ThunMJ, Cox DG, Hankinson SE, Kraft P, Rosner B, Berg CD, Brinton LA, Lissowska J, Sherman ME, Chlebowski R, Kooperberg, C, Jackson RD, Buckman DW, Hui P, Pfeiffer R, Jacobs KB, Thomas GD, Hoover RN, Gail MH, Chanock SJ, Hunter DJ. 2010. Performance of common genetic variants in breast-cancer risk models. N Engl J Med 362:986-993.
39. Wakefield J. 2008. Bayes factors for genome-wide association studies: comparison with P-values. Genet Epidemiol 33:79-86.
40. Xu J, Sun J, Kader AK, Lindstr̈om S, Wiklund F, Hsu F-C, Johansson JE, Zheng SL, Thomas G, Hayes RB, Kraft P, Hunter DJ, Chanock SJ, Isaacs WB, Gr̈onberg H. 2009. Estimation of absolute risk for prostate cancer using genetic markers and family history. Prostate 69:1565-1572.
41. Yeager M, Chatterjee N, Ciampa J, Jacobs KB, Gonzalez-Bosquet J, Hayes RB, Kraft P, Wacholder S, Orr N, Berndt S, Yu K, Hutchinson A, Wang Z, Amundadottir L, Feigelson HS, Thun MJ, Diver WR, Albanes D, Virtamo J, Weinstein S, Schumacher FR, Cancel-Tassin G, Cussenot O, Valeri A, Andriole GL, Crawford ED, Haiman CA, Henderson B, Kolonel L, Le Marchand L, Siddiq A, Riboli E, Key TJ, Kaaks R, IsaacsW, Isaacs S, Wiley KE, Gronberg H, Wiklund F, Stattin P, Xu J, Zheng SL, Sun J, Vatten LJ, Hveem K, Kumle M, Tucker M, Gerhard DS, Hoover RN, Fraumeni JF, Hunter DJ, Thomas G, Chanock SJ. 2009. Identification of a new prostate cancer susceptibility locus on chromosome 8q24. Nat Genet 41:1055-1057.
42. Yeager M, Orr N, Hayes RB, Jacobs KB, Kraft P, Wacholder S, Minichiello MJ, Fearnhead P, Yu K, Chatterjee N, Wang Z, Welch R, Staats BJ, Calle EE, Feigelson HS, ThunMJ, Rodriguez C, Albanes D, Virtamo J, Weinstein S, Schumacher FR, Giovannucci E, Willett WC, Cancel-Tassin G, Cussenot O, Valeri A, Andriole GL, Gelmann EP, TuckerM, Gerhard DS, Fraumeni JF, Hoover R, Hunter DJ, Chanock SJ, Thomas G. 2007. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 39:645-649.
43. Zheng SL, Sun J, Wiklund F, Smith S, Stattin P, Li G, Adami HO, Hsu F-C, Zhu Y, Bälter K, Kader AK, Turner AR, Liu W, Bleecker ER, Meyers DA, Duggan D, Carpten JD, Chang B-L, Isaacs WB, Xu J, Grönberg H. 2008. Cumulative association of five genetic variants with prostate cancer. N Engl J Med 358:910-919.