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Dataset ID

NHA000154

Type of data
GWAS for autoimmune pulmonary alveolar proteinosis
Access criteria
Unrestricted-access
Total data volume
410 MB
File formats
  • HTML
  • ZIP
Research
hum0197
Date published
2020-11-27
Date modified
2020-11-27
Secondary ID
hum0197.v2.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0197.v2.gwas.v1.zip410 MB
hum0197_v2_gwas_v1_header.htmlDictionary file27.8 KB

Analysis method

genome wide SNPs

Materials and participants
Autoimmune pulmonary alveolar proteinosis cases (ICD10: J840): 198
Control participants: 395
Disease
Autoimmune pulmonary alveolar proteinosis cases (J840)
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 Infinium Asian Screening Array
QC and filtering
Sample QC: We excluded samples with low genotyping call rates (call rate < 98%) and in close genetic relation (PI_HAT > 0.175). We included samples of the estimated East Asian ancestry.
Variant QC: We excluded variants with (1) genotyping call rate < 98%, (2) P value for Hardy-Weinberg equilibrium < 1.0 × 10−6, and (3) minor allele count < 5, or (4) > 10% frequency difference with the imputation reference panel.
Analysis method
GenomeStudio for genotyping, shapeit2 for haplotype phasing, and minimac3 for imputation
PLINK2
Variant count
Autosomes: 12,153,232 variants (After QC)
X chromosome: 242,876 variants (After QC)
Data use policy
NBDC data sharing policy (JGAP000001)