NBDC Research ID: hum0014.v9
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SUMMARY
Aims: Identify disease-related genes in Japanese
Methods: Genomic DNA samples were genotyped by following methods: Human610-Quad BeadChip, HumanHap550v3 Genotyping BeadChip, HumanOmniExpress-12 BeadChip, HumanExome BeadChip, OmniExpressExome BeadChip (Illumina), high-density oligonucleotide arrays (Perlegen Sciences), or Invader (Hologic Japan). Genome-Wide Association Studies (GWAS) for myocardial infarction (MI) , type II diabetes mellitus (T2DM), Atopic dermatitis (AD), atrial fibrillation (AF), and Body Mass Index (BMI), primary open-angle glaucoma (POAG), 58 quantitative traits and age at menarche / menopause were performed using about 500-600K SNPs.
Participants/Materials: Participants for the Tailor-made Medical Treatment Program (BioBank Japan: BBJ)
| Data Set ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0014.v1.freq.v1 | GWAS for MI | Un-restricted Access | 2014/09/30 |
| hum0014.v2.jsnp.934ctrl.v1 |
Genotype frequencies in 934 healthy individuals (JSNP data) |
Un-restricted Access | 2015/12/28 |
| 35 Dieases |
Genotype frequencies in each disease (JSNP data) |
Un-restricted Access | 2015/12/28 |
| hum0014.v2.jsnp.182ec.v1 |
Genotype frequencies in 182 esophageal cancer patients (JSNP data) |
Un-restricted Access | 2015/12/28 |
| hum0014.v2.jsnp.92als.v1 |
Genotype frequencies in 92 amyotrophic lateral sclerosis (ALS) patients (JSNP data) |
Un-restricted Access | 2015/12/28 |
| hum0014.v3.T2DM-1.v1 | GWAS for T2DM [1] | Un-restricted Access | 2016/01/28 |
| hum0014.v3.T2DM-2.v1 | GWAS for T2DM [2] | Un-restricted Access | 2016/01/28 |
| hum0014.v4.AD.v1 | GWAS for AD | Un-restricted Access | 2016/02/02 |
| hum0014.v5.AF.v1 | GWAS for AF | Un-restricted Access | 2016/05/18 |
| JGAS000101 | Genotype and phenotype data for 8180 AF patients | Controlled Access (Type I) | 2016/05/18 |
| hum0014.v6.158k.v1 | GWAS for BMI | Un-restricted Access | 2017/09/08 |
| JGAS000114 |
BMI data for 158,284 individuals Genotype data for 182,505 individuals |
Controlled Access (Type I) | 2017/09/08 |
| hum0014.v7.POAG.v1 | GWAS for POAG | Un-restricted Access | 2018/04/04 |
| hum0014.v8.58qt.v1 | GWAS for 58 quantitative traits | Un-restricted Access | 2018/05/01 |
| JGAS000114 | 58 quantitative traits data for 200,849 individuals | Controlled Access (Type I) | 2018/05/01 |
| GWAS for age at menarche and menopause | Un-restricted Access | 2018/08/07 |
* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more
* 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 | 1666 MI patients and 3198 controls |
| Targets | genome wide SNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Human610-Quad BeadChip, HumanHap550v3 Genotyping BeadChip] |
| Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Illumina Human610-Quad Beadchip |
| Genotype Call Methods (software) | GenCall software (GenomeStudio) |
| Filtering Methods | sample call rate ≧ 0.98, SNP call rate ≧ 0.99, HWE P ≧ 1 x 10^-6 |
| Marker Number (after QC) | 455,781 SNPs (hg18/GRCh36) |
| NBDC Data Set ID |
(Click the Data Set ID to download the file) |
| Total Data Volume | 71.3 MB (xlsx) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 934 Japanese healthy individuals (JSNP) |
| Targets | genome wide SNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HumanHap550v3 Genotyping BeadChip] |
| Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Illumina HumanHap550v3 Genotyping BeadChip |
| Genotype Call Methods (software) | GenCall software (GenomeStudio) |
| Filtering Methods | sample call rate < 0.98, SNP call rate < 0.99, HWE P < 1 x 10^-6 |
| Marker Number (after QC) | 515,286 SNPs |
| NBDC Data Set ID |
(Click the Data Set ID to download the file) |
| Total Data Volume | 32.2 M (zip [xls]) |
| Comments (Policies) | NBDC policy |
35 Diseases (JSNP)
| Participants/Materials |
Cancer (Lung cancer, Breast cancer, Gastric cancer, Colorectal cancer, Prostate cancer) Cardiovascular diseases (Heart failure, Myocardial infarction, Unstable angina, Stable angina, Cardiac arrhythmias, Arteriosclerosis obliterans) Cerebrovascular disorders (Brain infarction, Intracranial aneurysm) Respiratory tract diseases (Interstitial pneumonitis & pulmonary fibrosis, Pulmonary emphysema, Bronchial asthma) Chronic liver diseases (Chronic hepatitis C, Liver cirrhosis) Eye diseases (Cataract, Glaucoma) Others (Epilepsy, Periodontal disease, Urolithiasis, Nephrotic syndrome, Uterine myoma, Endometriosis, Osteoporosis, Rheumatoid arthritis, Amyotrophic lateral sclerosis, Hay fever, Atopic dermatitis, Drug eruptions , Hyperlipidemias, Diabetes mellitus, Basedow disease )
about 190 patients in each disease set |
| Targets | genome wide SNVs |
| Target Loci for Capture Methods | - |
| Platform | Perlegen Sciences [high-density oligonucleotide arrays] |
| Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | - |
| Genotype Call Methods (software) | - |
| Filtering Methods | - |
| Marker Number (after QC) | About 200,000 SNPs (b129) |
| NBDC Data Set ID |
Cancer (Lung cancer, Breast cancer, Gastric cancer, Colorectal cancer, Prostate cancer) Cardiovascular diseases (Heart failure, Myocardial infarction, Unstable angina, Stable angina, Cardiac arrhythmias, Arteriosclerosis obliterans) Cerebrovascular disorders (Brain infarction, Intracranial aneurysm) Respiratory tract diseases (Interstitial pneumonitis & pulmonary fibrosis, Pulmonary emphysema, Bronchial asthma) Chronic liver diseases (Chronic hepatitis C, Liver cirrhosis) Eye diseases (Cataract, Glaucoma) Others (Epilepsy, Periodontal disease, Urolithiasis, Nephrotic syndrome, Uterine myoma, Endometriosis, Osteoporosis, Rheumatoid arthritis, Amyotrophic lateral sclerosis, Hay fever, Atopic dermatitis, Drug eruptions, Hyperlipidemias, Diabetes mellitus, Basedow disease) (Click the disease names to download the file) |
| Comments (Policies) | NBDC policy |
*Chromosomal position of each SNP is based on dbSNP build 129. If you need other mapping information, please contact us.
| Participants/Materials | 182 esophageal cancer patients (JSNP) |
| Targets | genome wide SNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HumanHap550v3 Genotyping BeadChip] |
| Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Illumina HumanHap550v3 Genotyping BeadChip |
| Genotype Call Methods (software) | GenCall software (GenomeStudio) |
| Filtering Methods | sample call rate < 0.98, SNP call rate < 0.99, HWE P < 1 x 10^-6 |
| Marker Number (after QC) | 503,734 SNPs |
| NBDC Data Set ID |
(Click the Data Set ID to download the file) |
| Total Data Volume | 6.6 MB (zip [txt]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 92 ALS patients (JSNP) |
| Targets | large-scale case-control association study |
| Target Loci for Capture Methods | - |
| Platform | Hologic Japan [Invader] |
| Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Invader assay system (Third Wave Technologies) |
| Genotype Call Methods (software) | ABI PRISM SDS versions 2.0 - 2.2 |
| Filtering Methods | SNP call rate ≥ 0.95, HWE P ≥1.0 x 10^-2 |
| Marker Number (after QC) | 48,939 SNPs |
| NBDC Data Set ID |
(Click the Data Set ID to download the file) |
| Total Data Volume | 3.2 MB (zip [txt]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
9817 T2DM patients 6763 controls (healthy individuals and patients with Intracranial aneurysm, Esophageal cancer, Uterine cancer, Pulmonary emphysema, or Glaucoma [without T2DM]) |
| Targets | genome wide SNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [OmniExpressExome Beadchip] |
| Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Illumina OmniExpressExome Beadchip kit |
| Genotype Call Methods (software) | GenCall software (GenomeStudio) |
| Filtering Methods | sample call rate < 0.98, SNP call rate < 0.99, MAF < 0.01, HWE P < 1 x 10^-6 in control |
| Marker Number (after QC) | 552,915 SNPs (hg19) |
| NBDC Data Set ID |
(Click the Data Set ID to download the file) |
| Total Data Volume | 84.0 MB (xlsx) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
5646 T2DM patients 19,420 controls (patients with Colorectal cancer, Breast cancer, Prostate cancer, Lung cancer, Gastric cancer, Arteriosclerosis obliterans, Cardiac arrhythmias, Brain infarction, Myocardial infarction, Gallbladder cancer and Cholangiocarcinoma, Pancreatic cancer, Drug eruptions, Rheumatoid arthritis, Amyotrophic lateral sclerosis, Liver cancer, Liver cirrhosis, Osteoporosis, or Uterine myoma [without T2DM]) |
| Targets | genome wide SNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Human610-Quad BeadChip] |
| Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Illumina Human610-Quad Beadchip kit |
| Genotype Call Methods (software) | GenCall software (GenomeStudio) |
| Filtering Methods | sample call rate < 0.98, SNP call rate < 0.99, MAF < 0.01, HWE P < 1 x 10^-6 in control |
| Marker Number (after QC) | 479,088 SNPs (hg18) |
| NBDC Data Set ID |
(Click the Data Set ID to download the file) |
| Total Data Volume | 72.6 MB (xlsx) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
1472 AD patients 7966 controls (healthy individuals and patients with Intracranial aneurysm, Esophageal cancer, Uterine cancer, Pulmonary emphysema, or Glaucoma [without AD and Bronchial asthma]) |
| Targets | genome wide SNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HumanOmniExpress BeadChip] |
| Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | HumanOmniExpress BeadChip |
| Genotype Call Methods (software) |
minimac [imputation (1000 genomes Phase I v3)] |
| Association Analysis (software) | mach2dat [GWAS] |
| Filtering Methods |
Genotyping QC: sample call rate < 0.98, SNV call rate < 0.99, HWE P < 1 x 10^-6 in the control samples Imputation QC: HWE P < 1 x 10^-6 or MAF < 0.01 in the reference panel Differences of MAF between the GWAS dataset and the reference panel > 0.16 |
| Marker Number (after QC) | About 7,700,000 SNPs (hg19) |
| NBDC Data Set ID |
(Click the Data Set ID to download the file) |
| Total Data Volume |
ADGWAS_auto.txt (525 MB) ADGWAS_X_females.txt (17 MB) ADGWAS_X_males.txt (15 MB) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
8180 atrial fibrillation patients and 28,612 controls |
| Targets | genome wide SNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HumanOmniExpress / HumanExome / OmniExpressExome BeadChip] |
| Source | DNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | HumanOmniExpress / HumanExome / OmniExpressExome BeadChip kit |
| Genotype Call Methods (software) |
minimac [imputation (1000 genomes Phase I v3)] GenCall software（GenomeStudio） |
| Association Analysis (software) | mach2dat [GWAS] |
| Filtering Methods |
Genotyping QC: sample call rate < 0.98, SNV call rate < 0.99, HWE P < 1 x 10^-6 in the control samples Imputation QC: HWE P < 1 x 10^-6 or MAF < 0.01 in the reference panel Differences of MAF between the GWAS dataset and the reference panel > 0.16 R square < 0.9 |
| Marker Number (after QC) | About 5,000,000 SNVs |
| Phenotype Data | Gender, Age |
|
NBDC Data Set ID / Japanese Genotype-phenotype Archive Data set ID |
[GWAS stats] (Click the Data Set ID to download the file) [Individual data sets] Phenotype: JGAD000101 Genotype: JGAD000102 |
| Total Data Volume |
GWAS: 473 MB (txt) Individual phenotype-genotype data: 1 GB (txt) |
| Comments (Policies) | NBDC policy |
JGAS000114 / hum0014.v6.158k.v1
| Participants/Materials | 182,505 individuals (158,284 individuals for BMI study) |
| Targets | genome wide SNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HumanOmniExpress / HumanExome / OmniExpressExome BeadChip] |
| Source | DNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | HumanOmniExpress / HumanExome / OmniExpressExome BeadChip kit |
| Genotype Call Methods (software) |
minimac [imputation (1000 genomes Phase I v3)] GenCall software (GenomeStudio) |
| Association Analysis (software) | mach2qtl (v1.1.3) |
| Filtering Methods |
Genotyping QC: sample call rate < 0.98, SNV call rate < 0.99, HWE P < 1 x 10^-6 QC for reference panel: After excluding 11 closely related individuals, variants with HWE P < 1.0 x 10^-6, MAF < 0.01 were excluded. QC after imputation: Variants with imputation quality of Rsq < 0.7 were excluded. |
| Marker Number (after QC) | About 6,000,000 and 150,000 SNVs on autosomes and X-chromosome, respectively. |
|
NBDC Data Set ID / Japanese Genotype-phenotype Archive Data set ID |
[GWAS] (Click the Data Set ID to download the file) [Individual data sets] Phenotype data (BMI): JGAD000124 Genotype data: JGAD000123 |
| Total Data Volume |
GWAS: 406 MB (zip) Phenotype data (BMI): 3.32 MB (txt.gz) Genotype data: 26.3GB (csv.gz) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
3980 POAG patients (Male: 1,997, Female: 1,983) 18,815 controls (Male: 7,817, Female: 10,998) |
| Targets | genome wide SNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HumanOmniExpress / HumanExome / OmniExpressExome BeadChip] |
| Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | HumanOmniExpress / HumanExome / OmniExpressExome BeadChip kit |
| Genotype Call Methods (software) |
minimac（ver. 0.1.1） [imputation (1000 genomes Phase I v3)] |
| Association Analysis (software) | mach2dat（ver. 1.0.19） |
| Filtering Methods |
Genotyping QC: sample call rate < 0.98, SNV call rate < 0.99, HWE P < 1 x 10^-6 QC for reference panel: After excluding 11 closely related individuals, variants with HWE P < 1.0 x 10^-6, MAF < 0.01 were excluded. QC after imputation: Variants with imputation quality of Rsq < 0.7 were excluded. We also excluded variants with |beta| > 4 in the uploaded files. |
| Marker Number (after QC) |
autosomes：5,961,428 SNPs（hg19） male X-chromosome：147,351 SNPs（hg19） female X-chromosome：147,353 SNPs（hg19） |
| NBDC Data Set ID |
(Click the Data Set ID to download the file) |
| Total Data Volume | 113 MB（txt.zip） |
| Comments (Policies) | NBDC policy |
JGAS000114 / hum0014.v8.58qt.v1
hum0014.v9.Men.v1 / hum0014.v9.MP.v1
| Participants/Materials |
67,029 females with information on age at menarche 43,861 females with information on age at menopause |
| Targets | genome wide SNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HumanOmniExpress / HumanExome / OmniExpressExome BeadChip] |
| Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | HumanOmniExpress / HumanExome / OmniExpressExome BeadChip kit |
| Genotype Call Methods (software) |
minimac [imputation (1000 genomes Phase I v3)] GenCall software (GenomeStudio) |
| Association Analysis (software) | mach2qtl (v1.1.3) |
| Filtering Methods |
Genotyping QC: sample call rate < 0.98, SNV call rate < 0.99, HWE P < 1 x 10^-6 QC for reference panel: After excluding 11 closely related individuals, variants with HWE P < 1.0 x 10^-6, MAF < 0.01 were excluded. QC after imputation: Variants with imputation quality of Rsq < 0.7 were excluded. We also excluded variants with |beta| > 4 in the uploaded files. |
| Marker Number (after QC) | 9,296,729 SNPs (hg19) |
| NBDC Data Set ID |
menarche: hum0014.v9.Men.v1 menopause: hum0014.v9.MP.v1 (Click the Data Set ID to download the file) menarche: Dictionary file menopause: Dictionary file |
| Total Data Volume |
menarche: 181 MB（txt.gz） menopause: 186 MB（txt.gz） |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Michiaki Kubo
Affiliation: RIKEN Center for Integrative Medical Sciences
Project / Group Name: Tailor-made Medical Treatment Program (Bio Bank Japan: BBJ)
Funds / Grants (Research Project Number) :
| Name | Title | Project Number |
|---|---|---|
| Ministry of Education, Culture, Sports, Science and Technology in Japan | Tailor-made Medical Treatment Program (the 3rd phase) | - |
PUBLICATIONS
| Title | DOI | Data Set ID | |
|---|---|---|---|
| 1 | A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese. | doi:10.1038/ejhg.2014.110 | hum0014.v1.freq.v1 |
| 2 | A functional variant in ZNF512B is associated with susceptibility to amyotrophic lateral sclerosis in Japanese. | doi:10.1093/hmg/ddr268 | hum0014.v2.jsnp.92als.v1 |
| 3 | Functional variants in ADH1B and ALDH2 coupled with alcohol and smoking synergistically enhance esophageal cancer risk. | doi: 10.1053/j.gastro.2009.07.070 | hum0014.v2.jsnp.182ec.v1 |
| 4 | SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations. | doi: 10.1038/ng.208 | T2DM (JSNP) |
| 5 | Common variants in a novel gene, FONG on chromosome 2q33.1 confer risk of osteoporosis in Japanese. | doi: 10.1371/journal.pone.0019641 | Osteoporosis (JSNP) |
| 6 | Genome-wide association studies in the Japanese population identify seven novel loci for type 2 diabetes. | doi: 10.1038/ncomms10531 | |
| 7 | Multi-ancestry genome-wide association study of 21,000 cases and 95,000 controls identifies new risk loci for atopic dermatitis. | doi: 10.1038/ng.3424 | hum0014.v4.AD.v1 |
| 8 | Genome-wide association study identifies eight new susceptibility loci for atopic dermatitis in the Japanese population. | doi: 10.1038/ng.2438 | hum0014.v4.AD.v1 |
| 9 | Identification of six new genetic loci associated with atrial fibrillation in the Japanese population. | doi: 10.1038/ng.3842 | hum0014.v5.AF.v1 |
| 10 | Genome-wide association study identifies 112 new loci for body mass index in the Japanese population. | doi:10.1038/ng.3951 | |
| 11 | Genome-wide association study identifies seven novel susceptibility loci for primary open-angle glaucoma. | doi: 10.1093/hmg/ddy053 | hum0014.v7.POAG.v1 |
| 12 | Genetic analysis of quantitative traits in the Japanese population links cell types to complex human diseases. | doi:10.1038/s41588-018-0047-6 | |
| 13 | Elucidating the genetic architecture of reproductive ageing in the Japanese population | doi: 10.1038/s41467-018-04398-z |
USRES (Controlled-Access Data)
| Principal Investigator: | Affiliation: | Data in Use (Data Set ID) | Period of Data Use |
|---|---|---|---|
