Background Multiple sclerosis has a clinically significant heritable component. We conducted a genomewide association study to identify alleles associated with the risk of multiple sclerosis.
Methods We used DNA microarray technology to identify common DNA sequence variants in 931 family trios (consisting of an affected child and both parents) and tested them for association. For replication, we genotyped another 609 family trios, 2322 case subjects, and 789 control subjects and used genotyping data from two external control data sets. A joint analysis of data from 12,360 subjects was performed to estimate the overall significance and effect size of associations between alleles and the risk of multiple sclerosis.
Results A transmission disequilibrium test of 334,923 single-nucleotide polymorphisms (SNPs) in 931 family trios revealed 49 SNPs having an association with multiple sclerosis (P<1x10–4); of these SNPs, 38 were selected for the second-stage analysis. A comparison between the 931 case subjects from the family trios and 2431 control subjects identified an additional nonoverlapping 32 SNPs (P<0.001).> P values (<0.01)> for the second-stage analysis. Of these SNPs, two within the interleukin-2 receptor 
gene (IL2RA) were strongly associated with multiple sclerosis (P=2.96x10–8), as were a nonsynonymous SNP in the interleukin-7 receptor gene (IL7RA) (P=2.94x10–7) and multiple SNPs in the HLA-DRA locus (P=8.94x10–81).
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