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Dataset ID

NHA000190

Type of data
GWAS for gut microbiome
GWAS for plasma metabolite
GWAS for KEGG Gene Ortholog and KEGG Pathway
Access criteria
Unrestricted-access
Total data volume
320 GB
File formats
  • TSV
  • DOCX
Research
hum0197
Date published
2023-10-02
Date modified
2023-10-02
Secondary ID
hum0197.v18.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
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1–20 / 732

FileLabelSizeCopy URL
KO_1e_4_GWAS.tsv.gzKEGG Gene Ortholog300 MB
PATH_1e_4_GWAS.tsv.gzKEGG Pathway9.4 MB
ReadMe_hum0197.v18.docxDictionary file24.3 KB
metabo_A_0003_QCed_sumstats.tsv.gzPyruvic acid318 MB
metabo_A_0005_QCed_sumstats.tsv.gzLactic acid318 MB
metabo_A_0007_QCed_sumstats.tsv.gzIsovaleric acid;Valeric acid318 MB
metabo_A_0009_QCed_sumstats.tsv.gz3-Hydroxybutyric acid318 MB
metabo_A_0010_QCed_sumstats.tsv.gz2-Hydroxybutyric acid319 MB
metabo_A_0012_QCed_sumstats.tsv.gzGlyceric acid318 MB
metabo_A_0015_QCed_sumstats.tsv.gz2-Oxoisovaleric acid318 MB
metabo_A_0016_QCed_sumstats.tsv.gzHexanoic acid318 MB
metabo_A_0017_QCed_sumstats.tsv.gzN-Acetylglycine318 MB
metabo_A_0018_QCed_sumstats.tsv.gzSuccinic acid318 MB
metabo_A_0019_QCed_sumstats.tsv.gz2-Hydroxyvaleric acid318 MB
metabo_A_0021_QCed_sumstats.tsv.gzIsethionic acid319 MB
metabo_A_0022_QCed_sumstats.tsv.gz5-Oxoproline318 MB
metabo_A_0024_QCed_sumstats.tsv.gz4-Methyl-2-oxovaleric acid;3-Methyl-2-oxovaleric acid319 MB
metabo_A_0027_QCed_sumstats.tsv.gzN-Acetylalanine318 MB
metabo_A_0029_QCed_sumstats.tsv.gz2-Hydroxy-4-methylvaleric acid318 MB
metabo_A_0030_QCed_sumstats.tsv.gz6-Hydroxyhexanoic acid319 MB

1–20 / 732

Analysis method

genome wide SNPs

Materials and participants
524 Japanese individuals (423 species in the gut microbiome)
306 Japanese individuals (306 plasma metabolites)
524 Japanese individuals (KEGG Gene Ortholog and KEGG Pathway)
  • Subject count
    524 (Individual)
  • Population
    Japanese
Sample description
DNAs extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Experimental method
Genotyping by array
WGS
Reagent kit
Infinium Asian Screening Array Kit
KAPA Hyper Prep Kit
TruSeq DNA PCR-Free Library Prep Kit
Platform
Illumina HiSeq 2500
Illumina HiSeq 3000
Illumina HiSeq X
Illumina Infinium Asian Screening Array
Illumina NovaSeq 6000
Reference genome
GRCh37
QC and filtering
SNP array data:
Sample QC: We excluded individuals with low genotyping call rates (call rate < 98%). We included individuals of the estimated Asian ancestry using PCA.
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.
Post-imputation QC: We excluded imputed variants with Rsq < 0.7 and minor allele frequency < 1%.
WGS:
We excluded variants with genotype call rate <90%, ExcessHet > 60, Hardy-Weinberg P<1.0×10−10
After imputation with Beagle v5.1, we excluded imputed variants with minor allele frequency < 1%.
Imputation
Haplotype phasing: shapeit4
Imputation: minimac4
Analysis method
SNP array:
Genotyping: GenomeStudio
WGS:
WA-MEM v0.7.13 + GATK v3.8-0
PLINK2
Variant count
Gut microbiota/KEGG (SNP array): 7,213,470 variants
Blood metabolites (WGS): 6,840,258 variants
Processed data type
GWAS summary statistics
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)