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Methods

Automated Detection of Informative Combined Effects in Genetic Association Studies of Complex Traits

¹ INSERM U525, Faculté de Médecine, Hôpital Pitié-Salpêtrière, 75634 Paris, France ² Genset-Serono Group, RN7, 91030 Evry, France

There is a growing body of evidence suggesting that the relationships between gene variability and common disease are more complex than initially thought and require the exploration of the whole polymorphism of candidate genes as well as several genes belonging to biological pathways. When the number of polymorphisms is relatively large and the structure of the relationships among them complex, the use of data mining tools to extract the relevant information is a necessity. Here, we propose an automated method for the detection of informative combined effects (DICE) among several polymorphisms (and nongenetic covariates) within the framework of association studies. The algorithm combines the advantages of the regressive approaches with those of data exploration tools. Importantly, DICE considers the problem of interaction between polymorphisms as an effect of interest and not as a nuisance effect. We illustrate the method with three applications on the relationship between (1) the P-selectin gene and myocardial infarction, (2) the cholesteryl ester transfer protein gene and plasma high-density-lipoprotein cholesterol concentration, and (3) genes of the renin-angiotensin-aldosterone system and myocardial infarction. The applications demonstrated that the method was able to recover results already found using other approaches, but in addition detected biologically sensible effects not previously described.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1254203.

³ Corresponding author. E-MAIL laurence.tiret{at}chups.jussieu.fr; FAX 33-1-40-77-9728.

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