Statistical multilocus methods for disequilibrium analysis in complex traits

Hundreds of thousands of SNP markers are being generated with the purpose o f carrying out case-control association studies for complex traits, which a re thought to be due to multiple underlying susceptibility genes. The numbe r of markers is typically much larger than the number of observations so th at joins analysis of marker genotypes and their interactions is not feasibl e. We discuss a two-stage approach to first select a small subset of marker s and then model the effects of the selected markers on disease. Examples o f two procedures for marker selection are given with subsequent modeling of main and interaction effects. The approaches are applied to a data set wit h 89 SNPs in lieu of a genome screen with many more markers. Hum Mutat 17:2 85-288, 2001. (C) 2001 Wiley-Liss, Inc.