Risk Factor Searching Heuristics for SNP Case-Control Studies
Brinza, D.; Zelikovsky, A.
Bioinformatics and Biomedicine, 2007. BIBM 2007. IEEE International Conference on
Volume , Issue , 2-4 Nov. 2007 Page(s):282 - 287
Digital Object Identifier   10.1109/BIBM.2007.7
Summary:This paper addresses the computational challenge facing association analysis of case-control studies - searching an enormous amount of possible gene interactions. A complex risk factor (RF) is proposed to be modeled as close (weighted) match to a diplotype (e.g., no more than k mismatches) and the optimization formulation asks for RF with the maximum odds ratio. We have applied and cross-validated previously known and two proposed search methods for finding basic RF's with large odds ratios on 5 real case-control studies. New proposed methods find RF's that are statistically significant on all data including two datasets where no significant RF's were found before. The found RF's explain 1.5-4 times more cases than previously known RF's. The new methods also have significantly higher leave-half-out cross-validation rate.

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