A genome-wide association scan comprising a total of 2,657 unrelated Sardinian Multiple Sclerosis (MS) patients and 2,877 controls using the Affymetrix genotyping platform. A total of 575,678 unique SNPs were genotyped.  To maximise genome-wide coverage, the MACH algorithm was used to impute ~6M SNPs using HapMap CEU and TSI haplotypes as well as 56 unrelated individuals of European decent from the 1000 Genomes Project.  Association at genome-wide significance (P<5x10-8) was confirmed for the HLA region, showing strong correlation for the DRB1*0301-DQB1*0201 haplotype as previously found.  Of the non-HLA SNPs only one showed genome-wide significance, rs9657904 located in intron 1 of CBLB on chromosome 3q13.11.

Study Type
Whole Genome Association Study
Exclusion Criteria

Samples were excluded due to:-

  • genotype call rate <90%
  • sex/gender discordance
  • detection of a relative using RELPAIR

Markers were excluded due to:-

  • Hardy-Weinberg equilibrium p<10-6
  • minor allele frequency (MAF) <0.05%
  • genotype call rate ≤90%

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
3q13.11chr3:105653463-105954342CBLB  rs9657904T > C0.1741.60e-10C1.59 (1.32-1.89)D
MHCchr6:32414162-32714887HLA-DQA1  HLA-DQA2  rs2040406A > G0.2611.45e-20C2.05C


GDXHsS00043 meets the following criteria:

Criteria Name
Disease Tags
Study for a Disease 


PMIDTitleFirst AuthorJournalDisease(s)Date