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Dataset ID

NHA000209

Type of data
GWAS for multiple sclerosis
Access criteria
Unrestricted-access
Total data volume
1.2 GB
File formats
  • TXT
  • ZIP
Research
hum0197
Date published
2026-07-31
Date modified
2026-07-31
Secondary ID
hum0197.v31.MS-gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0197.v31.MS-gwas.v1.zip1.2 GB
hum0197_v31_MS-gwas-v1_readme.txtDictionary file1.2 KB

Analysis method

genome wide SNPs

Materials and participants
multiple sclerosis (MS) (ICD10: G35):
Japanese: 688 MS patients and 205,199 controls
European: 27,572 MS patients and 1,436,801 controls
African: 819 MS patients and 155,904 controls
Cross-population: 29,374 MS patients and 1,843,563 controls (293 MS patients and 45,569 controls in the US population was included)
  • Health status
    Mixed
  • Subject count
    1,872,937 (Individual)
  • Population
    African, American, European, Japanese
Disease
multiple sclerosis (MS) (G35)
Sample description
DNAs extracted from peripheral blood cells
  • Tissue
    Peripheral blood
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Platform
Illumina HumanExome
Illumina HumanOmniExpress
Illumina HumanOmniExpressExome
Illumina Infinium Asian Screening Array
QC and filtering
Sample QC:
Japanese: We excluded samples with a genotyping call rate < 0.98. We included samples of estimated East Asian ancestry, based on principal component analysis (PCA).
UK Biobank: We included samples based on the following criteria: (1) concordant with sex information, (2) genotyping call rate > 0.95, (3) heterozygosity rate < +3 S.D., and (4) the white British subset previously reported.
All of Us: We included samples based on the following criteria: (1) genotyping call rate > 0.98, (2) heterozygosity rate < +3 S.D., and (3) subjects of European, African and American ancestries identified by PCA-based criteria.
Genomics England: We included samples of European ancestry, identified by PCA-based criteria.
Post-imputation QC:
We excluded variants with Rsq < 0.7 or minor allele frequency (MAF) < 0.5% (1% for All of Us).
Imputation
Haplotype phasing: SHAPEIT4
Imputation: Minimac4
Analysis method
Genotyping: GenomeStudio
Association analysis: SAIGE, REGENIE, METAL
Variant count
Japanese population: 8,858,017 variants
European population: 9,970,295 variants
African population: 12,996,649 variants
Multi-ancestry population: 19,056,190 variants
Data use policy
NBDC data sharing policy (JGAP000001)