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

Sven Knüppel17, Jorge Esparza-Gordillo12, Ingo Marenholz12, Hermann-Georg Holzhütter3, Anja Bauerfeind1, Andreas Ruether4, Stephan Weidinger56, Young-Ae Lee12 and Klaus Rohde1*

Author Affiliations

1 Max Delbrück Center for Molecular Medicine Berlin-Buch, Berlin, Germany

2 Pediatric Pneumology and Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany

3 Institute of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany

4 Institute for Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany

5 Department of Dermatology and Allergy, Technische Universität München, Munich, Germany

6 Division of Environmental Dermatology and Allergy, Helmholtz Zentrum Munich and ZAUM-Center for Allergy and Environment, Technische Universität München, Munich, Germany

7 German Institute of Human Nutrition Potsdam-Rehbrücke, Department of Epidemiology, Nuthetal, Germany

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BMC Medical Genetics 2012, 13:8  doi:10.1186/1471-2350-13-8

Published: 27 January 2012

Additional files

Additional file 1:

Table S1. 10 best SNP patterns in each step of the Multi-locus stepwise regression (MSR) based on case control set (n = 1914). The results of the global test statistic (Likelihood ratio p value) and model criteria (Nagelkerke R2, AIC, and BIC) of the haplotype logistic regression models of the best 10 SNP patterns in each step are shown. Figure S1. LD plot of the four SNPs of the best 4-SNP pattern and the four FLG mutations based on the case control set. An LD plot (Haploview 4.2) shows on the basis of D' the LD-structure of the best 4-SNP pattern formed together with the known four FLG mutations in physical locus order. Figure S2. Mean of -log10(p values) of best 10 p values in each step of the Multi-locus stepwise regression based on case control sample. This figure shows the saturation effect of decrease of the mean of the ten best transformed p values with increasing pattern length.

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