Logic regression is an adaptive regression
method which searches for Boolean (logic) combinations of binary variables that
best explain the variability in the outcome, and thus, it reveals interaction
effects which are associated with the response. In this study, we extended
logic regression to longitudinal data with binary response and proposed
“Transition Logic Regression Method” to find interactions related to response.
In this method, interaction effects over time were found by Annealing Algorithm
with AIC (Akaike Information Criterion) as the score function of the model.
Also, first and second orders Markov dependence were allowed to capture the
correlation among successive observations of the same individual in
longitudinal binary response. Performance of the method was evaluated with
simulation study in various conditions. Proposed method was used to find
interactions of SNPs and other risk factors related to low HDL over time in
data of 329 participants of longitudinal TLGS study.
References
[1]
Ruczinski, I., Kooperberg, C. and Le Blanc, M. (2003) Logic Regression. Journal of Computational and Graphical Statistics, 12, 475-511. http://dx.doi.org/10.1198/1061860032238
[2]
Schwender, H. and Ruczinski, I. (2010) Logic Regression and Its Extensions. Advances in Genetics, 72, 25-45.
http://dx.doi.org/10.1016/B978-0-12-380862-2.00002-3
[3]
Li, Q., Fallin, M.D., Louis, T.A., Lasseter, V.K., McGrath, J.A., Avramopoulos, D., Wolyniec, P.S., Valle, D., Liang, K.Y., Pulver, A.E. and Ruczinski, I. (2010) Detection of SNP-SNP Interactions in Trios of Parents with Schizophrenic Children. Genetic Epidemiology, 34, 396-406. http://dx.doi.org/10.1002/gepi.20488
[4]
Kooperberg, C. and Ruczinski, I. (2005) Identifying Interacting SNPs Using Monte Carlo Logic Regression. Genetic Epidemiology, 28, 157-170. http://dx.doi.org/10.1002/gepi.20042
[5]
Schwender, H. and Ickstadt, K. (2008) Identification of SNP Interactions Using Logic Regression. Biostatistics, 9, 187- 198. http://dx.doi.org/10.1093/biostatistics/kxm024
[6]
Nunkesser, R., Bernholt, T., Schwender, H., Ickstadt, K. and Wegener, I. (2007) Detecting High-Order Interactions of Single Nucleotide Polymorphisms Using Genetic Programming. Bioinformatics, 23, 3280-3288.
http://dx.doi.org/10.1093/bioinformatics/btm522
[7]
Diggle, P.J., Liang, K.Y. and Zeger, S.L. (1994) Analysis of Longitudinal Data. Oxford University Press, New York.
[8]
Mehrabi, Y., Sarbakhsh, P., Houwing-Duistermaat, J.J., Zayeri, F. and Sadat Daneshpour, M. (2015) Assessment of SNP Interactions Affecting Total Cholesterol over Time Using Logic Mixed Model: TLGS Study. Gene Cell Tissue, 2, e25572. http://dx.doi.org/10.17795/gct-25572
[9]
Goncalves, M.H. and Azzalini, A. (2008) Using Markov Chains for Marginal Modelling of Binary Longitudinal Data in an Exact Likelihood Approach. Metron-International Journal of Statistics, LXVI, 157-181.
[10]
Garte, S. (2001) Metabolic Susceptibility Genes as Cancer Risk Factors: Time for a Reassessment? Cancer Epidemiology Biomarkers & Prevention, 10, 1233-1237.
[11]
Azizi, F., Rahmani, M., Emami, H., Mirmiran, P., Hajipour, R., Madjid, M., Ghanbili, J., Ghanbarian, A., Mehrabi, J., Saadat, N., Salehi, P., Mortazavi, N., Heydarian, P., Sarbazi, N., Allahverdian, S., Saadati, N., Ainy, E. and M?ini, S. (2002) Cardiovascular Risk Factors in an Iranian Urban Population: Tehran Lipid and Glucose Study (Phase 1). Sozial- und Pr?ventivmedizin/Social and Preventive Medicine, 47, 408-426. http://dx.doi.org/10.1007/s000380200008
[12]
Azizi F Fau-Ghanbarian, A., Ghanbarian A Fau-Momenan, A.A., Momenan Aa Fau-Hadaegh, F., Hadaegh F Fau- Mirmiran, P., Mirmiran P Fau-Hedayati, M., Hedayati M Fau-Mehrabi, Y., Mehrabi Y Fau-Zahedi-Asl, S. and Zahedi-Asl, S. (2009) Prevention of Non-Communicable Disease in a Population in Nutrition Transition: Tehran Lipid and Glucose Study phase II.
[13]
Azizi, F., Khalili, D., Aghajani, H., Esteghamati, A., Hosseinpanah, F., Delavari, A., Larijani, B., Mirmiran, P., Mehrabi, Y., Kelishadi, R. and Hadaegh, F. (2010) Appropriate Waist Circumference Cut-Off Points among Iranian Adults: The First Report of the Iranian National Committee of Obesity. Archives of Iranian Medicine, 13, 243-244.
[14]
NCEP (2001) Executive Summary of the Third Report of The National Cholesterol Education Program (NCEP) Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults (Adult Treatment Panel III). JAMA, 285, 2486-2497. http://dx.doi.org/10.1001/jama.285.19.2486
[15]
NCEP (2001) Executive Summary of the Third Report of The National Cholesterol Education Program (NCEP) Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults (Adult Treatment Panel III). JAMA, 285, 2486-2497. http://dx.doi.org/10.1001/jama.285.19.2486
[16]
Daneshpour, M.S., Faam, B., Hedayati, M., Eshraghi, P. and Azizi, F. (2011) ApoB (XbaI) Polymorphism and Lipid Variation in Teharnian Population. European Journal of Lipid Science and Technology, 113, 436-440.
http://dx.doi.org/10.1002/ejlt.201000346
[17]
Brown, C.M., Rea, T.J., Hamon, S.C., Hixson, J.E., Boerwinkle, E., Clark, A.G. and Sing, C.F. (2006) The Contribution of Individual and Pairwise Combinations of SNPs in the APOA1 and APOC3 Genes to Interindividual HDL-C Variability. Journal of Molecular Medicine, 84, 561-572.
[18]
Daneshpour, M.S., Hedayati, M., Eshraghi, P. and Azizi, F. (2010) Association of Apo E Gene Polymorphism with HDL Level in Tehranian Population. European Journal of Lipid Science and Technology, 112, 810-816.
http://dx.doi.org/10.1002/ejlt.200900207
[19]
McCarthy, J.J., Lehner, T., Reeves, C., Moliterno, D.J., Newby, L.K., Rogers, W.J. and Topol, E.J. (2003) Association of Genetic Variants in the HDL Receptor, SR-B1, with Abnormal Lipids in Women with Coronary Artery Disease. Journal of Medical Genetics, 40, 453-458. http://dx.doi.org/10.1136/jmg.40.6.453
[20]
Frikke-Schmidt, R. (2000) Context-Dependent and Invariant Associations between APOE Genotype and Levels of Lipoproteins and Risk of Ischemic Heart Disease: A Review. Scandinavian Journal of Clinical and Laboratory Investigation, 233, 3-25.