<p>The goal of this study is to perform a comprehensive allelic and genotypic association analysis of the entire human genome
 in multiple sclerosis.  The recent definitive linkage genome screen demonstrated that there is no other MS risk gene with an
 effect size anywhere near that of the MHC.  However, linkage analysis is significantly hampered by reduced power in the face
 of heterogeneity and requires multiplex families, which also hampers acquiring an appropriate sample size.  In contrast,
 genotyping 500K SNPs allows us to survey a significant amount of the genome (we estimate >70%) directly for allelic
 or genotypic association.  This uses the improved power of association analysis and can also take advantage
 of the linkage disequilibrium relationships among SNPs to further increase power (e.g. haplotype analysis).  Quality control
 and data analysis are significant challenges.  We will initially perform substantial QC checks and analyze the data using both
 TDT and AFBAC approaches.  Multigenic interactions will also be tested using MDR.</p>

IMSGC Genome Wide Association Study of Multiple Sclerosis

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