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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
Per page
50
2050100

151–200 / 732

FileLabelSizeCopy URL
metabo_C_0146_QCed_sumstats.tsv.gzIsobutyrylcarnitine319 MB
metabo_C_0147_QCed_sumstats.tsv.gzButyrylcarnitine319 MB
metabo_C_0148_QCed_sumstats.tsv.gzCystine318 MB
metabo_C_0153_QCed_sumstats.tsv.gzUridine318 MB
metabo_C_0158_QCed_sumstats.tsv.gzDyphylline318 MB
metabo_C_0165_QCed_sumstats.tsv.gz1-Methyladenosine318 MB
metabo_C_0167_QCed_sumstats.tsv.gzOctanoylcarnitine318 MB
metabo_C_0168_QCed_sumstats.tsv.gzArgininosuccinic acid318 MB
metabo_C_0169_QCed_sumstats.tsv.gzXC0120318 MB
metabo_C_0170_QCed_sumstats.tsv.gzGlutathione (GSSG)_divalent319 MB
metabo_C_0172_QCed_sumstats.tsv.gzXC0132318 MB
metabo_C_0174_QCed_sumstats.tsv.gzCysteine glutathione disulfide318 MB
metabo_N_0002_QCed_sumstats.tsv.gzFatty acid(12:0)318 MB
metabo_N_0005_QCed_sumstats.tsv.gzFatty acid(14:3)318 MB
metabo_N_0006_QCed_sumstats.tsv.gzFatty acid(14:2)318 MB
metabo_N_0007_QCed_sumstats.tsv.gzFatty acid(14:1)-1318 MB
metabo_N_0008_QCed_sumstats.tsv.gzFatty acid(14:1)-2319 MB
metabo_N_0009_QCed_sumstats.tsv.gzMyristic acid319 MB
metabo_N_0012_QCed_sumstats.tsv.gzFatty acid(15:0)318 MB
metabo_N_0013_QCed_sumstats.tsv.gzPentadecanoic acid318 MB
metabo_N_0014_QCed_sumstats.tsv.gz3-Hydroxytetradecanoic acid319 MB
metabo_N_0017_QCed_sumstats.tsv.gzFatty acid(16:2)-2318 MB
metabo_N_0020_QCed_sumstats.tsv.gzPalmitoleic acid319 MB
metabo_N_0021_QCed_sumstats.tsv.gzPalmitic acid319 MB
metabo_N_0024_QCed_sumstats.tsv.gzFatty acid(17:1)-2319 MB
metabo_N_0027_QCed_sumstats.tsv.gzHeptadecanoic acid-1;Fatty acid(17:0)-1319 MB
metabo_N_0028_QCed_sumstats.tsv.gzHeptadecanoic acid-2;Fatty acid(17:0)-2319 MB
metabo_N_0030_QCed_sumstats.tsv.gzStearidonic acid319 MB
metabo_N_0031_QCed_sumstats.tsv.gzLinolenic acid319 MB
metabo_N_0032_QCed_sumstats.tsv.gzLinoleic acid319 MB
metabo_N_0033_QCed_sumstats.tsv.gzOleic acid319 MB
metabo_N_0034_QCed_sumstats.tsv.gzStearic acid319 MB
metabo_N_0037_QCed_sumstats.tsv.gzFatty acid(19:2)318 MB
metabo_N_0038_QCed_sumstats.tsv.gzFatty acid(19:1)319 MB
metabo_N_0040_QCed_sumstats.tsv.gzRicinoleic acid-2319 MB
metabo_N_0041_QCed_sumstats.tsv.gzRicinoleic acid-3319 MB
metabo_N_0045_QCed_sumstats.tsv.gzcis-5,8,11,14,17-Eicosapentaenoic acid318 MB
metabo_N_0046_QCed_sumstats.tsv.gzArachidonic acid318 MB
metabo_N_0047_QCed_sumstats.tsv.gzFatty acid(20:3)319 MB
metabo_N_0048_QCed_sumstats.tsv.gzcis-8,11,14-Eicosatrienoic acid319 MB
metabo_N_0049_QCed_sumstats.tsv.gzcis-11,14-Eicosadienoic acid318 MB
metabo_N_0050_QCed_sumstats.tsv.gzcis-11-Eicosenoic acid319 MB
metabo_N_0051_QCed_sumstats.tsv.gzArachidic acid318 MB
metabo_N_0053_QCed_sumstats.tsv.gzcis-4,7,10,13,16,19-Docosahexaenoic acid-1318 MB
metabo_N_0055_QCed_sumstats.tsv.gzFatty acid(22:5)-1318 MB
metabo_N_0056_QCed_sumstats.tsv.gzFatty acid(22:5)-2319 MB
metabo_N_0057_QCed_sumstats.tsv.gzFatty acid(22:5)-3319 MB
metabo_N_0058_QCed_sumstats.tsv.gzFatty acid(22:4)-1319 MB
metabo_N_0059_QCed_sumstats.tsv.gzFatty acid(22:4)-2319 MB
metabo_N_0060_QCed_sumstats.tsv.gzFatty acid(22:3)-1319 MB

151–200 / 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)