Multi-locus stepwise regression: a haplotype-based algorithm for finding genetic associations applied to atopic dermatitis

Our proposed multi-locus stepwise regression starts with an evaluation of all pair-wise SNP combinations and then extends each SNP combination stepwise by one SNP from the region, carrying out haplotype regression in each step. The best associated haplotype patterns are kept for the next step and must be corrected for multiple testing at the end. These haplotypes should also be replicated in an independent data set. We applied the method to a region of 259 SNPs from the epidermal differentiation complex (EDC) on chromosome 1q21 of a German GWAS using a case control set (1,914 individuals) and to 268 families with at least two affected children as replication.A 4-SNP haplotype pattern with high statistical significance in the case control set (p = 4.13 × 10-7 after Bonferroni correction) could be identified which remained significant in the family set after Bonferroni correction (p = 0.0398). Further analysis revealed that this pattern reflects mainly the effect of the well-known FLG gene; however, a FLG-independent haplotype in case control set (OR = 1.71, 95% CI: 1.32-2.23, p = 5.6 × 10-5) and family set (OR = 1.68, 95% CI: 1.18-2.38, p = 2.19 × 10-3) could be found in addition.Our approach is a useful tool for finding allele combinations associated with diseases beyond single SNP analysis in chromosomal candidate regions.Single marker association analysis has been widely used to identify genetic risk factors involved in the genetics of complex diseases [1]. Previous studies have suggested that haplotypes, a collection of ordered markers along a chromosome, may be more appropriate as a unit for statistical analysis than single genetic markers [2,3]. As demonstrated by simulation studies, statistical approaches based on haplotypes can be a powerful method to characterize the genetic background of complex diseases [1,4-6]. However, since haplotypes are often not directly observable we have to use unphased genotypes to estimate haplotypes.The advent of the gene chip t