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Dataset ID

NHA000198

Type of data
Summary statistics of the genome-wide meta-analysis of NMOSD
Access criteria
Unrestricted-access
Total data volume
141 MB
File formats
  • TXT
  • DOCX
Research
hum0197
Date published
2024-12-18
Date modified
2024-12-18
Secondary ID
hum0197.v23.gwas-nmosd.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
Dictionary_NMOSD_meta.docxDictionary file17.5 KB
hum0197.v23.gwas-nmosd.v1.txt.gz141 MB

Analysis method

genome wide SNPs

Materials and participants
NMOSD (ICD10: G36.0): 240 cases
control participants: 50,578
  • Health status
    Mixed
  • Subject count
    50,818 (Individual)
Disease
NMOSD (G360)
Sample description
DNAs extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Reagent kit
Infinium Asian Screening Array Kit
Platform
Illumina Infinium Asian Screening Array
QC and filtering
Sample QC: We excluded samples with low genotyping call rates (call rate < 98%) or potential sex chromosome aneuploidy. We included only the individuals of the estimated East Asian ancestry using the principal component (PC) analysis, and then further restricted to those in Japanese Hondo (the main island of Japan) clusters.
Variant QC: We excluded variants with (1) genotyping call rate < 99%, (2) minor allele count < 5, (3) P-value for Hardy-Weinberg equilibrium < 1.0 × 10−10, and (4) > 5% allele frequency difference compared with the imputation reference panel or the allele frequency panel of Tohoku Medical Megabank Project and in-house reference panel.
Post-imputation QC: We excluded imputed variants with Rsq < 0.7 and minor allele frequency < 0.5%.
Imputation
Haplotype phasing: shapeit4
Imputation: minimac4
Analysis method
Genotyping: GenomeStudio
SAIGE
Variant count
8,894,915 variants
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)