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MSGene - Overview of all published large-scale and genome-wide association studies in MS
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 Status: Updated 26 November 2011;  

***Note that content for MSGene is still being curated and that most currently displayed pages (including this page) contain preliminary summaries and are still incomplete.***
GWAS (genome-wide association studies)
              MS Cases Normal Controls  
Study Design Type Population Source Platform # of SNPs Genotype Data Publicly Available DX # Subjects
(GWAS)		 # Subjects
(follow-up)		 # Subjects
(GWAS)		 # Subjects
(follow-up)		 Featured Genes
 Caucasian
ANZgene, 2009
CCGWAS Australia, New Zealand, UK, USA CL,PO Illumina (370CNV)302,098 Yes O/M1618225634132310
Aulchenko, 2008
CC, FBATGWAS Netherlands, Sweden, Canada PO Affymetrix (250K)211,555 No O/M4526341952930
Baranzini, 2008
CCGWAS USA, Netherlands, Switzerland CL Illumina (550K)551,642 Yes MD1&2978974883-
Comabella, 2008
CCGWAS (pooled) Spain, USA CL Affymetrix (500K)428,867 No P2425532421033
Goedde, 2005
CCGWAS Germany (HLA-DR2+) CL Affymetrix (10K)11,555 No P100280100280
IMSGC, 2007
CC, FBATGWAS USA, UK CL,PO Affymetrix (500K)334,923 Yes MD1&2931293133623596
IMSGC, 2011
CCGWAS GWAS: Europe, USA, Australia, New Zealand, REP: published GWAS CL,PO Illumina (multiple chips)465,434 No O/M97724218173767296
Jakkula, 2010
CCGWAS Finland, Norway, Denmark, and other CL,PO Illumina (300K, 610Quad)297,343 No O/M68457013610139
McWhirter, 2011
CCGWAS (homozygosity) UK (Orkney and Shetland Islands) CL Illumina (Omni1-Quad)794,367 No O/M88-178-  
Nischwitz, 2010
CCGWAS Germany CL Illumina (300K, CNV370-2)n.g. No O/M592-825-
Sanna, 2010
CCGWAS Italy (Sardinia) CL Affymetrix (6.0)555,335 No MD188217758722005
WTCCC, 2007
CCGWAS UK CL,PO Illumina (nsSNPs)12,374 Yes O/M975-1466-
Contact us if you are an author of an association study regarding this gene and do not find your study in this table or find errors in the representation of your study details.
Other large-scale studies
              MS Cases Normal Controls  
Study Design Type Population Source Platform # of SNPs Genotype Data Publicly Available DX # Subjects
(GWAS)		 # Subjects
(follow-up)		 # Subjects
(GWAS)		 # Subjects
(follow-up)		 Featured Genes
 Caucasian
Ban, 2010
CCGWAS follow-up (WTCCC, 2007) UK, USA, Australia, Italy CL,PO See primary studies1,664 No O/M-3444-2595
Briggs, 2010a
CCDNA repair pathways USA, UK CL,PO See IMSGC, 2009485 No MD11343-1379-
Briggs, 2010b
CCHypothalamic-pituitary-adrenal axis pathway USA, UK CL,PO See IMSGC, 2009326 No MD1&21343-1379-
Cotsapas, 2011
CCCross Phenotype Meta-Analysis (autoimmune diseases) IMSGC (2007), Baranzini (2008), unpublished GWAS (BWH) CL,PO See primary studies107 No MD12624-7220-  
De Jager, 2009
CCGWAS meta-analysis, and follow-up IMSGC (2007), Baranzini (2008), unpublished GWAS (BWH); follow-up: USA, UK CL,PO See primary studies2,557,248 No MD1-2214-2116
GAMES, 2006
CC, FBATMulticentric GWAS (STRs), meta-analysis, and follow-up Multiple CL customized6,000 No O/M51319374452937
Giedraitis, 2003
FBATGWAS (STRs) Sweden CO deCODE834 No U54-114-
IMSGC, 2009
CCComprehensive GWAS follow-up (IMSGC, 2007) USA, UK CL,PO Illumina iSelect (customized)29,561 No MD1-3507-5593
IMSGC, 2010
CCGWAS re-analysis IMSGC (2007), unpublished GWAS (BWH) CL,PO See primary studies311,315 No MD11737-4151-  
McCauley, 2009
FBATFollow-up of chr.1q43 linkage region USA CL Illumina (customized)629 No P173831173831
Omont, 2008
CCRe-analysis of three unpublished GWAS France, Sweden, USA CL Affymetrix (100K)116,204 No U882-942-
Patsopoulos, 2011
CCGWAS meta-analysis IMSGC (2007), Baranzini (2008), ANZgene (2009), unpublished GWAS (Boston) CL,PO See primary studies2,529,394 No MD15545-12153-  
Vyshkina, 2008
FBATChr. 19p USA, Canada CL Sequenom MassARRAY569 No O/M257-257-  
Zuvich, 2010
CCIL7RA/IL7 pathway USA, UK CL,PO Illumina Infinium (customized)7,865 No MD11343211113792037
 African Descent
Reich, 2005
CCGenome-wide admixture scan USA, Martinique, UK CL Illumina/Sequenom1,082 No O/M60514310431143
Contact us if you are an author of an association study regarding this gene and do not find your study in this table or find errors in the representation of your study details.
Design: "CC" (case-control), "FBAT" (family-based)
Type: "GWAS" (genome-wide association study); "LSS" (other large-scale association study); "STRs" (short tandem repeats)
Source: Source of case population -> "CL" (clinic-based), "PO" (population-based), or "CO" (community-based).
Platform: Please refer to orignal publication for exact description.
# SNPs: Approximate number of polymorphisms covered.
DX: Criteria used to determine MS diagnosis -> "P" (Poser criteria, 1983), "MD1" (McDonald criteria, 2001), "MD2" (revised McDonald criteria, 2005), "MD1&2" (McDonald criteria, 2001 and 2005), "O/M" (other/mixed), "U" (Unknown).
# Subjects: For studies with mixed study design (CC and FBAT) and no data provided about # of affected and unaffected subjects in the FBAT study, one subject per pedigree was added for both "MS cases" and "Normal Controls".
Featured Genes: Dropdown menu of genes highlighted ("featured") in original publication as potential MS susceptibility genes/loci after completion of all analyses, e.g. replication in multiple samples.
(-): No information provided or not applicable.
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MSGene Top Results
Top Results Details
1. HLA-DRB1
2. IL2RA
3. IL7R
4. TAGAP
5. CLEC16A
6. EVI5
7. GWA_16q24.1
8. GWA_5p13.1
9. TTC34
10. AHI1   
[see more]
MSGene Stats
Studies: 789
Genes: 809
Polymorphisms: 2907
Meta-analyses: 324
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An up-to-date collection of all published genetic association studies.
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