Dataset ID

NHA000190

Name: NHA000190: GWAS for gut microbiome, GWAS for plasma metabolite, GWAS for KEGG Gene Ortholog and KEGG Pathway
Published: 2023-10-02

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

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1–100 / 732

File	Label	Size
KO_1e_4_GWAS.tsv.gz	KEGG Gene Ortholog	300 MB
PATH_1e_4_GWAS.tsv.gz	KEGG Pathway	9.4 MB
ReadMe_hum0197.v18.docx	Dictionary file	24.3 KB
metabo_A_0003_QCed_sumstats.tsv.gz	Pyruvic acid	318 MB
metabo_A_0005_QCed_sumstats.tsv.gz	Lactic acid	318 MB
metabo_A_0007_QCed_sumstats.tsv.gz	Isovaleric acid;Valeric acid	318 MB
metabo_A_0009_QCed_sumstats.tsv.gz	3-Hydroxybutyric acid	318 MB
metabo_A_0010_QCed_sumstats.tsv.gz	2-Hydroxybutyric acid	319 MB
metabo_A_0012_QCed_sumstats.tsv.gz	Glyceric acid	318 MB
metabo_A_0015_QCed_sumstats.tsv.gz	2-Oxoisovaleric acid	318 MB
metabo_A_0016_QCed_sumstats.tsv.gz	Hexanoic acid	318 MB
metabo_A_0017_QCed_sumstats.tsv.gz	N-Acetylglycine	318 MB
metabo_A_0018_QCed_sumstats.tsv.gz	Succinic acid	318 MB
metabo_A_0019_QCed_sumstats.tsv.gz	2-Hydroxyvaleric acid	318 MB
metabo_A_0021_QCed_sumstats.tsv.gz	Isethionic acid	319 MB
metabo_A_0022_QCed_sumstats.tsv.gz	5-Oxoproline	318 MB
metabo_A_0024_QCed_sumstats.tsv.gz	4-Methyl-2-oxovaleric acid;3-Methyl-2-oxovaleric acid	319 MB
metabo_A_0027_QCed_sumstats.tsv.gz	N-Acetylalanine	318 MB
metabo_A_0029_QCed_sumstats.tsv.gz	2-Hydroxy-4-methylvaleric acid	318 MB
metabo_A_0030_QCed_sumstats.tsv.gz	6-Hydroxyhexanoic acid	319 MB
metabo_A_0031_QCed_sumstats.tsv.gz	Malic acid	318 MB
metabo_A_0032_QCed_sumstats.tsv.gz	Threonic acid	318 MB
metabo_A_0034_QCed_sumstats.tsv.gz	Ethanolamine phosphate	318 MB
metabo_A_0035_QCed_sumstats.tsv.gz	Octanoic acid	318 MB
metabo_A_0036_QCed_sumstats.tsv.gz	XA0004	318 MB
metabo_A_0038_QCed_sumstats.tsv.gz	2-Oxoglutaric acid	318 MB
metabo_A_0039_QCed_sumstats.tsv.gz	2-Hydroxyglutaric acid	318 MB
metabo_A_0043_QCed_sumstats.tsv.gz	3-Phenylpropionic acid	318 MB
metabo_A_0045_QCed_sumstats.tsv.gz	Pelargonic acid	318 MB
metabo_A_0047_QCed_sumstats.tsv.gz	8-Hydroxyoctanoic acid;2-Hydroxyoctanoic acid-1	318 MB
metabo_A_0051_QCed_sumstats.tsv.gz	Terephthalic acid	318 MB
metabo_A_0052_QCed_sumstats.tsv.gz	Perillic acid	318 MB
metabo_A_0054_QCed_sumstats.tsv.gz	Uric acid	318 MB
metabo_A_0058_QCed_sumstats.tsv.gz	Decanoic acid	318 MB
metabo_A_0059_QCed_sumstats.tsv.gz	XA0013	318 MB
metabo_A_0060_QCed_sumstats.tsv.gz	cis-Aconitic acid	319 MB
metabo_A_0062_QCed_sumstats.tsv.gz	Indole-3-acetic acid	318 MB
metabo_A_0064_QCed_sumstats.tsv.gz	Hippuric acid	318 MB
metabo_A_0065_QCed_sumstats.tsv.gz	Homovanillic acid	318 MB
metabo_A_0068_QCed_sumstats.tsv.gz	3-Phosphoglyceric acid	318 MB
metabo_A_0072_QCed_sumstats.tsv.gz	Citric acid	318 MB
metabo_A_0073_QCed_sumstats.tsv.gz	Isocitric acid	318 MB
metabo_A_0074_QCed_sumstats.tsv.gz	Quinic acid	318 MB
metabo_A_0076_QCed_sumstats.tsv.gz	Glucuronic acid-1;Galacturonic acid-1	318 MB
metabo_A_0078_QCed_sumstats.tsv.gz	Gluconic acid	318 MB
metabo_A_0080_QCed_sumstats.tsv.gz	Lauric acid	318 MB
metabo_A_0081_QCed_sumstats.tsv.gz	S-Sulfocysteine	318 MB
metabo_A_0083_QCed_sumstats.tsv.gz	Mucic acid	318 MB
metabo_A_0084_QCed_sumstats.tsv.gz	Glucaric acid	318 MB
metabo_A_0086_QCed_sumstats.tsv.gz	3-Indoxylsulfuric acid	318 MB
metabo_A_0089_QCed_sumstats.tsv.gz	Myristoleic acid	319 MB
metabo_A_0090_QCed_sumstats.tsv.gz	XA0027	319 MB
metabo_A_0100_QCed_sumstats.tsv.gz	Glucose 6-phosphate	319 MB
metabo_A_0101_QCed_sumstats.tsv.gz	Sulfotyrosine	318 MB
metabo_A_0102_QCed_sumstats.tsv.gz	N2-Phenylacetylglutamine	318 MB
metabo_A_0103_QCed_sumstats.tsv.gz	2,3-Diphosphoglyceric acid	318 MB
metabo_A_0125_QCed_sumstats.tsv.gz	Adenosine diphosphate	318 MB
metabo_A_0134_QCed_sumstats.tsv.gz	Adenosine triphosphate	319 MB
metabo_C_0002_QCed_sumstats.tsv.gz	Urea	319 MB
metabo_C_0003_QCed_sumstats.tsv.gz	Ethanolamine	318 MB
metabo_C_0005_QCed_sumstats.tsv.gz	Gly	318 MB
metabo_C_0007_QCed_sumstats.tsv.gz	Trimethylamine N-oxide	318 MB
metabo_C_0008_QCed_sumstats.tsv.gz	Piperidine	318 MB
metabo_C_0010_QCed_sumstats.tsv.gz	Sarcosine	319 MB
metabo_C_0011_QCed_sumstats.tsv.gz	β-Ala	318 MB
metabo_C_0012_QCed_sumstats.tsv.gz	Ala	318 MB
metabo_C_0013_QCed_sumstats.tsv.gz	Glycerol	318 MB
metabo_C_0016_QCed_sumstats.tsv.gz	N-Methylputrescine	318 MB
metabo_C_0018_QCed_sumstats.tsv.gz	N,N-Dimethylglycine	318 MB
metabo_C_0019_QCed_sumstats.tsv.gz	2-Aminoisobutyric acid;2-Aminobutyric acid	318 MB
metabo_C_0020_QCed_sumstats.tsv.gz	3-Aminoisobutyric acid	319 MB
metabo_C_0022_QCed_sumstats.tsv.gz	Choline	318 MB
metabo_C_0023_QCed_sumstats.tsv.gz	Ser	318 MB
metabo_C_0024_QCed_sumstats.tsv.gz	Diethanolamine	318 MB
metabo_C_0025_QCed_sumstats.tsv.gz	Hypotaurine	318 MB
metabo_C_0028_QCed_sumstats.tsv.gz	Creatinine	319 MB
metabo_C_0030_QCed_sumstats.tsv.gz	Pro	319 MB
metabo_C_0031_QCed_sumstats.tsv.gz	Guanidoacetic acid	318 MB
metabo_C_0032_QCed_sumstats.tsv.gz	Betaine	318 MB
metabo_C_0033_QCed_sumstats.tsv.gz	Val	318 MB
metabo_C_0034_QCed_sumstats.tsv.gz	Thr	318 MB
metabo_C_0039_QCed_sumstats.tsv.gz	Nicotinamide	318 MB
metabo_C_0042_QCed_sumstats.tsv.gz	Taurine	318 MB
metabo_C_0044_QCed_sumstats.tsv.gz	XC0016	318 MB
metabo_C_0046_QCed_sumstats.tsv.gz	Pipecolic acid	318 MB
metabo_C_0047_QCed_sumstats.tsv.gz	N-Acetylputrescine	318 MB
metabo_C_0048_QCed_sumstats.tsv.gz	cis-4-Hydroxyproline	318 MB
metabo_C_0049_QCed_sumstats.tsv.gz	Hydroxyproline	318 MB
metabo_C_0051_QCed_sumstats.tsv.gz	Creatine	318 MB
metabo_C_0053_QCed_sumstats.tsv.gz	Alloisoleucine	319 MB
metabo_C_0054_QCed_sumstats.tsv.gz	Ile	318 MB
metabo_C_0055_QCed_sumstats.tsv.gz	Leu	318 MB
metabo_C_0056_QCed_sumstats.tsv.gz	Asn	318 MB
metabo_C_0057_QCed_sumstats.tsv.gz	Ornithine	318 MB
metabo_C_0058_QCed_sumstats.tsv.gz	Thiaproline	318 MB
metabo_C_0059_QCed_sumstats.tsv.gz	Asp	318 MB
metabo_C_0061_QCed_sumstats.tsv.gz	S-Methylcysteine	318 MB
metabo_C_0063_QCed_sumstats.tsv.gz	Hypoxanthine	318 MB
metabo_C_0064_QCed_sumstats.tsv.gz	1-Methylnicotinamide	318 MB
metabo_C_0066_QCed_sumstats.tsv.gz	Trigonelline	318 MB

1–100 / 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)