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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561–580 / 732

File	Label	Size
microbiome_L7_species_Holdemania_massiliensis_QCed_sumstats.tsv.gz	Holdemania_massiliensis	525 MB
microbiome_L7_species_Hungatella_hathewayi_QCed_sumstats.tsv.gz	Hungatella_hathewayi	525 MB
microbiome_L7_species_Intestinibacter_bartlettii_QCed_sumstats.tsv.gz	Intestinibacter_bartlettii	526 MB
microbiome_L7_species_Intestinimonas_massiliensis_QCed_sumstats.tsv.gz	Intestinimonas_massiliensis	526 MB
microbiome_L7_species_Johnsonella_ignava_QCed_sumstats.tsv.gz	Johnsonella_ignava	524 MB
microbiome_L7_species_Klebsiella_aerogenes_QCed_sumstats.tsv.gz	Klebsiella_aerogenes	524 MB
microbiome_L7_species_Klebsiella_michiganensis_QCed_sumstats.tsv.gz	Klebsiella_michiganensis	525 MB
microbiome_L7_species_Klebsiella_oxytoca_QCed_sumstats.tsv.gz	Klebsiella_oxytoca	524 MB
microbiome_L7_species_Klebsiella_pneumoniae_QCed_sumstats.tsv.gz	Klebsiella_pneumoniae	525 MB
microbiome_L7_species_Klebsiella_quasipneumoniae_QCed_sumstats.tsv.gz	Klebsiella_quasipneumoniae	526 MB
microbiome_L7_species_Klebsiella_sp_QCed_sumstats.tsv.gz	Klebsiella_sp	522 MB
microbiome_L7_species_Klebsiella_variicola_QCed_sumstats.tsv.gz	Klebsiella_variicola	524 MB
microbiome_L7_species_Lachnoanaerobaculum_sp_QCed_sumstats.tsv.gz	Lachnoanaerobaculum_sp	525 MB
microbiome_L7_species_Lachnoclostridium_sp_QCed_sumstats.tsv.gz	Lachnoclostridium_sp	525 MB
microbiome_L7_species_Lachnospira_pectinoschiza_QCed_sumstats.tsv.gz	Lachnospira_pectinoschiza	526 MB
microbiome_L7_species_Lachnospira_sp_QCed_sumstats.tsv.gz	Lachnospira_sp	522 MB
microbiome_L7_species_Lachnospiraceae_bacterium_QCed_sumstats.tsv.gz	Lachnospiraceae_bacterium	526 MB
microbiome_L7_species_Lachnotalea_sp_QCed_sumstats.tsv.gz	Lachnotalea_sp	522 MB
microbiome_L7_species_Lactobacillus_amylovorus_QCed_sumstats.tsv.gz	Lactobacillus_amylovorus	526 MB
microbiome_L7_species_Lactobacillus_casei_QCed_sumstats.tsv.gz	Lactobacillus_casei	524 MB

561–580 / 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)