Penalized item response theory models: Application to epigenetic alterations in bladder cancer

Biometrics

Volumn 63, Issue 4, 2007, Pages 1269-1277

  Houseman, E Andrés ^a   Marsit, Carmen ^b   Karagas, Margaret ^c   Ryan, Louise M ^a  

^a UNIVERSITY OF MASSACHUSETTS LOWELL   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c NORRIS COTTON CANCER CENTER   (United States)

Author keywords

Bayesian hierarchical models; Bladder cancer; Constrained estimation; Latent trait models; Methylation silencing; Penalized likelihood; Rasch models; Ridge regression

Indexed keywords

ALKYLATION; BAYESIAN NETWORKS; DISEASES; GENE EXPRESSION; HIERARCHICAL SYSTEMS; MEAN SQUARE ERROR; REGRESSION ANALYSIS; TUMORS;

BAYESIAN HIERARCHICAL MODELLING; BLADDER CANCERS; CONSTRAINED ESTIMATION; ITEM RESPONSE THEORY; LATENT TRAIT MODEL; METHYLATION SILENCING; PENALIZED LIKELIHOOD; PENALIZED-LIKELIHOOD; RASCH MODELING; RIDGE REGRESSION;

METHYLATION;

AKAIKE INFORMATION CRITERION; BAYESIAN ANALYSIS; CANCER; GENETICS; METHYLATION; SMOKING; SURVIVAL; THEORETICAL STUDY;

BAYES THEOREM; BLADDER CANCER; CORRELATION ANALYSIS; EPIGENETICS; GENE EXPRESSION; GENE LOCUS; GENE SILENCING; METHYLATION; PARAMETER; PUBLIC HEALTH; REVIEW; SAMPLE SIZE;

EID: 36749057742     PISSN: 0006341X     EISSN: 15410420     Source Type: Journal    
DOI: 10.1111/j.1541-0420.2007.00806.x     Document Type: Review

References (48)

1. Adams, R. J., Wilson, M., and Wu, M. (1997). Multilevel item response models: An approach to errors in variables regression. Journal of Educational and Behavioral Statistics 22, 47 76.
2. Akaike, H. (1974). A new look at the statistical model identification. IEEE Transaction on Automatic Control AC-19, 716 723.
3. Bates, M. N., Smith, A. H., and Cantor, K. P. (1995). Case-control study of bladder cancer and arsenic in drinking water. American Journal of Epidemiology 141, 523 530.
4. Blozis, S. A. and Cudeck, R. (1999). Conditional linear mixed-effects model with latent variable covariates. Journal of Educational and Behavioral Statistics 24, 245 270.
5. Budtz-Jorgensen, E., Keiding, N., Grandjean, P., Weihe, P., and White, R. F. (2003). Statistical methods for the evaluation of health effects of prenatal mercury exposure. Environmetrics 14, 105 120.
6. Chan, M. W. Y., Chan, L. W., Tang, N. L. S., Tong, J. H. M., Lo, K. W., Lee, T. L., Cheung, H. Y., Wong, W. S., Chan, P. S. F., Lai, F. M. M., and To, K. F. (2002). Hypermethylation of multiple genes in tumor tissues and voided urine in urinary bladder cancer patients. Clinical Cancer Research 8, 464 470.
7. Chan, M. W. Y., Chan, L. W., Tang, N. L. S., Lo, K. W., Tong, J. H., Chan, A. W., Cheung, H. Y., Wong, W. S., Chan, P. S., Lai, F. M., and To, K. F. (2003). Frequent hypermethylation of promoter region of rassf1a in tumor tissues and voided urine of urinary bladder cancer patients. International Journal of Cancer 104, 611 616.
8. DiCiccio, T. and Efron, B. (1996). Bootstrap confidence intervals. Statistical Science 11, 189 228.
9. Dulaimi, E., Uzzo, R. G., Greenberg, R. E., Al-Saleem, T., and Cairns, P. (2004). Detection of bladder cancer in urine by a tumor suppressor gene hypermethylation panel. Clinical Cancer Research 10, 1887 1893.
10. Esrig, D., Freeman, J. A., Stein, J. P., and Skinner, D. G. (1997). Early cystectomy for clinical stage t1 transitional cell carcinoma of the bladder. Seminars in Urologic Oncology 15, 154 160.
11. Esrig, D., Elmajian, D., Groshen, S., Freeman, J. A., Stein, J. P., Chen, S.-C., Nichols, P. W., Skinner, D. G., Jones, P. A., and Cote, R. J. (2004). Accumulation of nuclear p53 and tumor progression in bladder cancer. New England Journal of Medicine 331, 1259 1264.
12. Friedrich, M. G., Weisenberger, D. J., Cheng, J. C. et al. 2004). Detection of methylated apoptosis-associated genes in urine sediments of bladder cancer patients. Clinical Cancer Research 10, 7457 7465.
13. Gao, F. R. and Chen, L. S. (2005). Bayesian or non-Bayesian: A comparison study of item parameter estimation in the three-parameter logistic model. Applied Measurement in Education 18, 351 380.
14. Gelfand, A. E., Sahu, S. K., and Carlin, B. P. (1995). Efficient parametrizations for normal linear mixed models. Biometrika 82, 479 488.
15. Hambleton, R. K. and Cook, L. L. (1977). Latent trait models and their use in analysis of educational test data. Journal of Educational Measurement 14, 75 96.
16. Hastie, T., Tibshirani, R., and Friedman, J. (2001). The Elements of Statistical Learning: Data Mining, Inference, and Prediction. New York : Springer-Verlag.
17. Houseman, E., Coull, B. and Betensky, B. (2006). Feature-specific penalized latent class analysis for genomic data. Biometrics 62, 1062 1070.
18. Ibrahim, J. G., Chen, M. H., and Sinha, D. (2001). Bayesian Survival Analysis. New York : Springer.
19. Jemal, A., Murray, T., Ward, E., Samuels, A., Tiwari, R. C., Ghafoor, A., Feuer, E. J., and Thun, M. J. (2005). Cancer statistics, 2005. CA: A Cancer Journal for Clinicians 55, 10 30.
20. Jones, P. A. and Laird, P. W. (1999). Cancer epigenetics comes of age. Nature Genetics 21, 163 167.
21. Jones, P. A., Gonzalgo, M. L., Tsutsumi, M., and Bender, C. M. (1998). DNA methylation in bladder cancer. Eur Urol 33 Suppl 4, 7 8.
22. Karagas, M., Tosteson, T., Blum, J., Morris, J., Baron, J., and Klaue, B. (1998). Design of an epidemiologic study of drinking water arsenic exposure and skin and bladder cancer risk in a US population. Environmental Health Perspectives 106, 1047 1050 (Suppl. 4).
23. Karagas, M. R., Tosteson, T. D., Morris, J. S., Demidenko, E., Mott, L. A., Heaney, J., and Schned, A. (2004). Incidence of transitional cell carcinoma of the bladder and arsenic exposure in New Hampshire. Cancer Causes Control 15, 465 472.
24. Kennedy, W. J. and Gentle, J. E. (1980). Statistical Computing. New York : Marcel Dekker, Inc.
25. L, L. E., Erkanli, A., Silberg, J., Angold, A., Maes, H. H., and Foley, D. (2005). Application of Bayesian inference using gibbs sampling to item-response theory modeling of multi-symptom genetic data. Behavior Genetics 35, 765 780.
26. Larsen, K. (2005). The cox proportional hazards model with a continuous latent variable measured by multiple binary indicators. Biometrics 61, 1049 1055.
27. Legler, J. and Ryan, L. (1997). Latent variable models for teratogenesis using multiple binary outcomes. Journal of the American Statistical Association 92, 13 20.
28. Lindsay, B., Clogg, C. C., and Grego, J. (1991). Semiparametric estimation in the Rasch model and related exponential response models, including a simple latent class model for item analysis. Journal of the American Statistical Association 86, 96 107.
29. Lord, F. M. (1986). Maximum-likelihood and Bayesian parameter estimation in item response theory. Journal of Educational Measurement 23, 157 162.
30. Marsit, C. J., Karagas, M. R., Andrew, A., Liu, M., Danaee, H., Schned, A. R., Nelson, H. H., and Kelsey, K. T. (2005). Epigenetic inactivation of sfrp genes and tp53 alteration act jointly as markers of invasive bladder cancer. Cancer Research 65, 7081 7085.
31. Masters, J. R., Vani, U. D., Grigor, K. M., Griffiths, G. O., Crook, A., Parmar, M. K., and Knowles, M. A. (2003). Can p53 staining be used to identify patients with aggressive superficial bladder cancer? J Pathol 200, 74 81.
32. May, M., Helke, C., Nitzke, T., Vogler, H., and Hoschke, B. (2004). Survival rates after radical cystectomy according to tumor stage of bladder carcinoma at first presentation. Urol Int 72, 103 111.
33. Rasch, G. (1960). Probabilistic Models for Some Intelligence and Attainment Tests. Copenhagen : The Danish Institute for Educational Research.
34. Rasch, G. (1966). An item analysis which takes individual differences into account. British Journal of Mathematical and Statistical Psychology 19, 49 57.
35. Sammel, M. and Ryan, L. (1996). Latent variable models with fixed effects. Biometrics 52, 650 663.
36. Sammel, M., Ryan, L., and Legler, J. (1997). Latent variable models for mixed discrete and continuous outcomes. Journal of the Royal Statistical Society, Series B 59, 667 678.
37. Sanchez, B., Budtz-Jorgensen, E., Ryan, L., and Hu, H. (2005). Structural equation models - a review with applications to environmental epidemiology. JASA 100, 1443 1455.
38. Sathyanarayana, U. G., Maruyama, R., Padar1, A., Suzuki, M., Bondaruk, J., Sagalowsky, A., Minna, J. D., Frenkel, E. P., Grossman, H. B., Czerniak, B., and Gazdar, A. F. (2004). Molecular detection of noninvasive and invasive bladder tumor tissues and exfoliated cells by aberrant promoter methylation of laminin-5 encoding genes. Cancer Research 64, 1425 1430.
39. Scott, S. L. and Ip, E. H. (2002). Empirical Bayes and item-clustering effects in a latent variable hierarchical model: A case study from the national assessment for educational progress. Journal of the American Statistical Association 97, 409 419.
40. Silverman, D., Morrison, A., and Devesa, S. (1996). Cancer Epidemiology and Prevention, chapter Bladder Cancer, 1156 1179. New York : Oxford Universty Press.
41. Sinharay, S. (2005). Assessing fit of unidimensional item response theory models using a Bayesian approach. Journal of Educational Measurement 42, 375 394.
42. Skrondal, A. and Rabe-Hesketh, S. (2004). Generalized Latent Variable Modeling: Multilevel, Longitudinal, and Structural Equation Models. CRC Interdisciplinary Statistics Series. Boca Raton, Florida : Chapman & Hall.
43. Spiegelhalter, D. J., Thomas, A., and Best, N. G. (1996). Computation on Bayesian graphical models. Bayesian Statistics 5, 407 425.
44. Spiegelhalter, D. J., Thomas, A., Best, N. G., and Lunn, D. (2003). WinBUGS User Manual Version 1.4. Cambridge, U.K : MRC Biostatistics Unit, Institute of Public Health.
45. Tibshirani, R. (1996). Regression shrinkage and selection via the lasso. Journal of the Royal Statistical Society, Series B 58, 267 288.
46. Vineis, P., Kogevinas, M., Simonato, L., Brennan, P., and Boffetta, P. (2000). Levelling-off of the risk of lung and bladder cancer in heavy smokers: An analysis based on multicentric case-control studies and a metabolic interpretation. Mutation Research 463, 103 110.
47. Vineis, P., Marinelli, D., Autrup, H., Brockmoller, J., Cascorbi, I., Daly, A. K., Golka, K., Okkels, H., Risch, A., Rothman, N., Sim, E., and Taioli, E. (2001). Current smoking, occupation, n-acetyltransferase-2 and bladder cancer: A pooled analysis of genotype-based studies. Cancer Epidemiology Biomarkers and Prevention 10, 1249 1252.
48. Wang, C. Y., Wang, N., and Wang, S. (2000). Regression analysis when covariates are regression parameters of a random effects model for observed longitudinal measurements. Biometrics 56, 487 495.