NBDC Research ID: hum0014.v11

 

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. A whole-genome sequencing analysis for 1,026 patients, who were registered Bio Bank Japan from 2003 - 2007 was performed with Illumina HiSeq2500. A target sequencing of 11 hereditary breast cancer genes in 7,104 breast cancer patients and 23,731 controls was also performed with Illumina HiSeq2500.

Participants/Materials: Participants for the Tailor-made Medical Treatment Program (BioBank Japan: BBJ)

URL: https://biobankjp.org/cohort_3rd/english/index.html

 

Data Set IDType of DataCriteriaRelease 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
JGAS00000000101 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
JGAS00000000114

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
JGAS00000000114 58 quantitative traits data for 200,849 individuals Controlled Access (Type I) 2018/05/01

hum0014.v9.Men.v1

hum0014.v9.MP.v1

GWAS for age at menarche and menopause Un-restricted Access 2018/08/07
JGAS00000000114 WGS for 1,026 individuals Controlled Access (Type I) 2018/08/13
JGAS00000000140 target sequencing of 11 hereditary breast cancer genes in 7,104 breast cancer patients and 23,731 controls Controlled Access (Type I) 2018/10/16

* Release Note

* 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

hum0014.v1.freq.v1

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

hum0014.v1.freq.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 71.3 MB (xlsx)
Comments (Policies) NBDC policy

 

hum0014.v2.jsnp.934ctrl.v1

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

hum0014.v2.jsnp.934ctrl.v1

(Click the Data Set ID to download the file)

Dictionary 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)

Dictionary 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.

 

hum0014.v2.jsnp.182ec.v1

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

hum0014.v2.jsnp.182ec.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 6.6 MB (zip [txt])
Comments (Policies) NBDC policy

 

hum0014.v2.jsnp.92als.v1

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

hum0014.v2.jsnp.92als.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 3.2 MB (zip [txt])
Comments (Policies) NBDC policy

 

hum0014.v3.T2DM-1.v1

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

hum0014.v3.T2DM-1.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 84.0 MB (xlsx)
Comments (Policies) NBDC policy

 

hum0014.v3.T2DM-2.v1

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

hum0014.v3.T2DM-2.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 72.6 MB (xlsx)
Comments (Policies) NBDC policy

 

hum0014.v4.AD.v1

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

hum0014.v4.AD.v1

(Click the Data Set ID to download the file)

Dictionary 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

 

JGAS00000000101 / hum0014.v5.AF.v1

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]

hum0014.v5.AF.v1

(Click the Data Set ID to download the file)

Dictionary file

[Individual data sets]

Phenotype: JGAD00000000101

Genotype: JGAD00000000102

Total Data Volume

GWAS: 473 MB (txt)

Individual phenotype-genotype data: 1 GB (txt)

Comments (Policies) NBDC policy

 

JGAS00000000114 / 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]

hum0014.v6.158k.v1

(Click the Data Set ID to download the file)

Dictionary file

[Individual data sets]

Phenotype data (BMI): JGAD00000000124

Genotype data: JGAD00000000123

Detailed information on genotyping array

Probe information (BLAST)

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

 

hum0014.v7.POAG.v1

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

hum0014.v7.POAG.v1

(Click the Data Set ID to download the file)

Dictionary file

Total Data Volume 113 MB(txt.zip)
Comments (Policies) NBDC policy

 

JGAS00000000114 / hum0014.v7.58qt.v1

Participants/Materials 162,255 individuals for 58 quantitative traits
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) 5,961,600 and 147,353 SNVs on autosomes and X-chromosome, respectively.

NBDC Data Set ID /

Japanese Genotype-phenotype

Archive Data set ID

Metabolic Total cholesterol JGAD00000000144
High density lipoprotein cholesterol JGAD00000000145
Low density lipoprotein cholesterol JGAD00000000146
Triglyceride JGAD00000000147
Blood sugar JGAD00000000148
Hemoglobin A1c JGAD00000000149
Protein Total protein JGAD00000000150
Albumin JGAD00000000151
Non-albumin protein JGAD00000000152
Albumin/globulin ratio JGAD00000000153
Kidney-related Blood urea nitrogen JGAD00000000154
Serum creatinine JGAD00000000155
Estimated glomerular filtration rate JGAD00000000156
Uric acid JGAD00000000157
Electrolyte Sodium JGAD00000000158
Potassium JGAD00000000159
Chlorine JGAD00000000160
Calcium JGAD00000000161
Phosphorus JGAD00000000162
Liver-related Total bilirubin JGAD00000000163
Zinc sulfate turbidity test JGAD00000000164
Aspartate aminotransferase JGAD00000000165
Alanine aminotransferase JGAD00000000166
Alkaline phosphatase JGAD00000000167
Gamma-glutamyl transferase JGAD00000000168
Other biochemical Activated partial thromboplastin time JGAD00000000169
Prothrombin time JGAD00000000170
Fibrinogen JGAD00000000171
Creatine kinase JGAD00000000172
Lactate dehydrogenase JGAD00000000173
C-reactive protein JGAD00000000174
Hematological White blood cell count JGAD00000000175
Neutrophil count JGAD00000000176
Eosinophil count JGAD00000000177
Basophil count JGAD00000000178
Monocyte count JGAD00000000179
Lymphocyte count JGAD00000000180
Red blood cell count JGAD00000000181
Hemoglobin JGAD00000000182
Hematocrit JGAD00000000183
Mean corpuscular volume JGAD00000000184
Mean corpuscular hemoglobin JGAD00000000185
Mean corpuscular hemoglobin concentration JGAD00000000186
Platelet count JGAD00000000187
Blood pressure Systolic blood pressure JGAD00000000188
Diastolic blood pressure JGAD00000000189
Mean arterial pressure JGAD00000000190
Pulse pressure JGAD00000000191
Echocardiographic Interventricular septum thickness JGAD00000000192
Posterior wall thickness JGAD00000000193
Left ventricular internal dimension in diastole JGAD00000000194
Left ventricular internal dimension in systole JGAD00000000195
Left ventricular mass JGAD00000000196
Left ventricular mass index JGAD00000000197
Relative wall thickness JGAD00000000198
Fractional shortening JGAD00000000199
Ejection fraction JGAD00000000200
E/A ratio JGAD00000000201

(Click the trait names to download the gwas summary statistics)

Dictionary file

Total Data Volume

GWAS: 123 MB (zip) on average

Phenotype data (58 quantitative traits): 2.4 MB (txt.gz) on average

Comments (Policies) NBDC policy

 

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

 

JGAS00000000114 / JGAD00000000220

Participants/Materials 1,026 individuals
Targets WGS
Target Loci for Capture Methods -
Platform Illumina [HiSeq2500]
Library Source DNA extracted from peripheral blood cells
Cell Lines -
Library Construction (kit name) TruSeq Nano DNA Library Preparation Kit
Fragmentation Methods Ultrasonic fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 160 bp
Japanese Genotype-phenotype Archive Data set ID JGAD00000000220
Total Data Volume 73 TB (fastq)
Comments (Policies) NBDC policy

* Summarized data is available at JENGER site.

 

JGAS00000000140

Participants/Materials 7,104 breast cancer patients and 23,731 controls
Targets Target Capture
Target Loci for Capture Methods 11 hereditary breast cancer genes (ATM, BRCA1, BRCA2, CDH1, CHEK2, NBN, NF1, PALB2, PTEN, STK11, TP53)
Platform Illumina [HiSeq2500]
Library Source DNA extracted from peripheral blood cells
Cell Lines -
Library Construction (kit name) 1st PCR was performed with 2X Platinum Multiplex PCR Master Mix (Thermo Fisher Scientific) to amplify the target region, followed by the 2nd PCR with 8-bp barcode and adapter sequences added using KAPA HiFi HotStart DNA Polymerase (KAPA) *1
Fragmentation Methods -
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp x 2
Japanese Genotype-phenotype Archive Data set ID JGAD00000000209
Total Data Volume 1 TB (fastq)
Comments (Policies) NBDC policy

*1 Hum Mol Genet. 25,:5027-5034 (2016)

 

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)

URL: https://biobankjp.org/english/index.html

Funds / Grants (Research Project Number) :

NameTitleProject Number
Ministry of Education, Culture, Sports, Science and Technology in Japan Tailor-made Medical Treatment Program (the 3rd phase) -

 

PUBLICATIONS

TitleDOIData 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

hum0014.v3.T2DM-1.v1

hum0014.v3.T2DM-2.v1

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

hum0014.v6.158k.v1

JGAD00000000123

JGAD00000000124

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

hum0014.v8.58qt.v1

JGAD00000000144-JGAD00000000201

13 Elucidating the genetic architecture of reproductive ageing in the Japanese population doi: 10.1038/s41467-018-04398-z

hum0014.v9.Men.v1

hum0014.v9.MP.v1

14 Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese. doi: 10.1038/s41467-018-03274-0 JGAD00000000220
15 Germline pathogenic variants of 11 breast cancer genes in 7,051 Japanese patients and 11,241 controls. doi: 10.1038/s41467-018-06581-8 JGAD00000000209

 

USRES (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use