NBDC Research ID: hum0197.v2
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SUMMARY
Aims: Elucidation of disease biology based on trans-omics analysis
Methods: Metagenome shotgun sequencing, genome-wide association study (GWAS)
Participants/Materials:
Metagenomic data of gut microbiome in the Japanese population (95 and 103 individuals)
Autoimmune pulmonary alveolar proteinosis cases: 198, Control participants: 395
| Data Set ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000205 | Metagenome | Controlled Access (Type I) | 2019/11/15 |
| hum0197.v2.gwas.v1 | GWAS for autoimmune pulmonary alveolar proteinosis | Un-restricted Access | 2020/11/27 |
| JGAS000260 | Metagenome | Controlled Access (Type I) | 2020/11/27 |
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*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials: | 95 Japanese individuals |
| Targets | Metagenome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 3000] |
| Library Source | DNA extracted from gut microbiome |
| Cell Lines | - |
| Library Construction (kit name) | KAPA Hyper Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000290 |
| Total Data Volume | 477 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Autoimmune pulmonary alveolar proteinosis cases (ICD10: J840): 198 Control participants: 395 |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium Asian Screening Array] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Infinium Asian Screening Array |
| Genotype Call Methods (software) | GenomeStudio for genotyping, shapeit2 for haplotype phasing, and minimac3 for imputation |
| Association Analysis (software) | PLINK2 |
| Filtering Methods |
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. |
| Marker Number (after QC) | 12,153,232 autosomal variants and 242,876 X-chromosomal variants after QC. |
| NBDC Data Set ID |
(Click the Data Set ID to download the file) |
| Total Data Volume | 390MB for autosome (txt.gz) and 19MB for X chromosome (txt.gz) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | 103 Japanese individuals |
| Targets | Metagenome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 3000] |
| Library Source | DNA extracted from gut microbiome |
| Cell Lines | - |
| Library Construction (kit name) | KAPA Hyper Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000363 |
| Total Data Volume | 408 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yukinori Okada
Affiliation: Department of Statistical Genetics, Osaka University Graduate School of Medicine
Project / Group Name： -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Precursory Research for Innovative Medical care (PRIME), Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED) | Crosstalk among microbiome, host, disease, and drug discovery enhanced by statistical genetics | JP19gm6010001 |
| FORCE, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED) | Elucidation of disease-specific microbiota and personalized medicine by metagenome-wide association studies | JP20gm4010006 |
| Practical Research Project for Rare / Intractable Diseases, Japan Agency for Medical Research and Development (AMED) | Biology and in silico drug repositioning of pulmonary alveolar proteinosis using trans-layer omics analysis | JP20ek0109413 |
PUBLICATIONS
| Title | DOI | Data Set ID | |
|---|---|---|---|
| 1 | Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population. | doi: 10.1136/annrheumdis-2019-215743 | JGAD000290 |
| 2 | Genetic determinants of risk in autoimmune pulmonary alveolar proteinosis. | doi: 10.1038/s41467-021-21011-y | hum0197.v2.gwas.v1 |
| 3 | A metagenome-wide association study of gut microbiome in patients with multiple sclerosis revealed novel disease pathology. | doi: 10.3389/fcimb.2020.585973 | JGAD000363 |
USRES (Controlled-Access Data)
| Principal Investigator: | Affiliation: | Data in Use (Data Set ID) | Period of Data Use |
|---|---|---|---|
