Permutation-based approaches do not adequately allow for linkage disequilibrium in gene-wide multi-locus association analysis.

Abstract excerpt

Additional information about risk genes or risk pathways for diseases can be extracted from genome-wide association studies through analyses of groups of markers. The most commonly employed approaches involve combining individual marker data by adding the test statistics, or summing the logarithms of their P-values, and then using permutation testing to derive empirical P-values that allow for the statistical...

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