hum0014 Release Note
| Research ID | Release Date | Type of Data |
|---|---|---|
| hum0014.v36 | 2024/11/28 | reference panel by using of WGS data of the biobank Japan project (N=3,256) and 1KGP p3v5 ALL (N=2,504) |
| hum0014.v35 | 2024/10/25 | reference panel by using of WGS data of the biobank Japan project (N=7,472) and 1KGP p3v5 ALL (N=2,504) |
| hum0014.v34 | 2024/09/19 |
Processed data of JGAD000220 (WGS for 1,026 individuals) by JGA (data for the use of TogoImputation) Processed data of JGAD000495 (WGS for 1,964 individuals) by JGA (data for the use of TogoImputation) |
| hum0014.v33 | 2024/05/27 |
WGS for 256 gastric cancer patients SNP array for 269,000 patients (51 diseases) in BBJ 1st and 2nd cohort WGS for 617 colorectal cancer patients WGS for 2,162 diabetes patients WGS for 2,067 gastric cancer patients |
| hum0014.v32 | 2024/01/11 | WGS for 1,007 individuals |
| hum0014.v31 | 2023/09/01 |
Processed data of JGAD000220 (WGS for 1,026 individuals) by JGA (CRAM, gVCF) Processed data (joint call) of JGAD000220 (WGS for 1,026 individuals) by JGA (aggregate VCF) Processed data of JGAD000220 (reference panel) by JGA (data for the use of TogoImputation) |
| hum0014.v30 | 2023/04/20 | target sequencings of 27 cancer-predisposing genes in 1,982 lymphoma patients, 10,366 gastric cancer patients and 37,592 controls |
| hum0014.v29 | 2023/04/05 |
GWAS for 9,826 AF patients and 140,446 controls from BBJ 1st cohort GWAS meta-analysis for 77,690 AF patients and 1,167,040 controls |
| hum0014.v28 | 2023/04/05 | mobile element variations in 4,880 individuals from the BBJ 1st cohort |
| hum0014.v27 | 2022/12/31 | GWAS for survival time in 137,693 individuals from the BBJ 1st cohort |
| hum0014.v26 | 2022/04/01 | target sequencings of 27 cancer-predisposing genes and 13 renal cell carcinoma-related genes in 740 renal cell cancer patients and 5,996 controls |
| hum0014.v25 | 2022/01/25 | WGS for 1,765 myocardial infarction patients and 199 dementia patients |
| hum0014.v24 | 2021/11/26 | target sequencing of 27 cancer-predisposing genes in 1,005 pancreatic cancer patients, 12,503 colorectal cancer patients and 23,705 controls |
| hum0014.v23 | 2021/07/13 | bam/gvcf data of WGS (JGAD000220) |
| hum0014.v22 | 2021/05/21 | targeted sequencing of 23 genes related to clonal hematopoiesis and SNP-array in 11,234 subjects extracted from approximately 200,000 subjects registered in Biobank Japan between fiscal years 2003 to 2007 |
| hum0014.v21 | 2020/08/25 | GWAS for coronary artery disease |
| hum0014.v20 | 2020/08/17 | GWAS for coronary artery disease |
| hum0014.v19 | 2020/04/20 | GWAS for dietary habits |
| hum0014.v18 | 2019/11/26 | GWAS for Breast cancer |
| hum0014.v17 | 2019/10/08 | GWAS for 40 diseases |
| hum0014.v16 | 2019/10/07 | target sequencing of 8 hereditary prostate cancer genes in 7,636 prostate cancer patients and 12,366 controls |
| hum0014.v15 | 2019/09/27 |
reference panel by using of WGS data of the biobank Japan project (N=1,037) and 1KGP p3v5 ALL (N=2,504) GWAS for height |
| hum0014.v14 | 2019/03/26 | GWAS for smoking behavior |
| hum0014.v13 | 2019/01/25 | meta analysis of 4 GWASs for T2DM |
| hum0014.v12 | 2018/12/10 | meta analysis of 2 GWASs for T2DM with diabetic nephropathy |
| hum0014.v11 | 2018/10/16 | target sequencing of 11 hereditary breast cancer genes in 7,104 breast cancer patients and 23,731 controls |
| hum0014.v10 | 2018/08/13 | WGS for 1,026 individuals |
| hum0014.v9 | 2018/08/07 | GWAS for age at menarche and menopause |
| hum0014.v8 | 2018/05/01 | GWAS for 58 quantitative traits |
| hum0014.v7 | 2018/04/04 | GWAS for POAG |
| hum0014.v6 | 2017/09/08 |
GWAS for BMI Genotype data for 182,505 individuals |
| hum0014.v5 | 2017/05/18 |
GWAS for AF Genotype data for 8180 AFs |
| hum0014.v4 | 2016/02/02 | GWAS for AD |
| hum0014.v3 | 2016/01/28 | GWASs for T2DM |
| hum0014.v2 | 2015/12/28 | Genotype frequencies of 934 healthy individuals, about 190 patients from each of 35 diseases, 182 esophageal cancer patients, and 92 ALS patients. |
| hum0014.v1 | 2014/09/30 | GWAS for MI |
hum0014.v36
A new reference panel was build with WGS data of the biobank Japan project (N=3,256) and the 1KGP p3v5 ALL (N=2,504). Phased data (vcf) were provided.
hum0014.v35
A new reference panel was build with WGS data of the biobank Japan project (N=7,472) and the 1KGP p3v5 ALL (N=2,504). Phased data (vcf) were provided.
hum0014.v34
The vcf (phased) files, tbi index files, the bref3 files, and a config file processed JGAD000220 (whole genome sequencing data for a total of 1,026 patients) and JGAD000495 (whole genome sequencing data for a total of 1,964 patients) in a certain workflow were provided. These files can be used in the TogoImputation. If you plan to use the data, please indicate both original data (JGAD000220 and JGAD000495) and processed data (JGAD000867 and JGAD000868) on the application form for data use.
hum0014.v33
Whole genome sequencing analysis for 256 gastric cancer patients registered in BBJ 1st cohort was performed. Fastq files are provided.
SNP array analysis for 269,000 patients (51 diseases) registered in BBJ 1st and 2nd cohort was performed. IDAT files are provided.
Whole genome sequencing analysis for 617 colorectal cancer patients registered in BBJ 1st and 2nd cohort was performed. Fastq files are provided.
Whole genome sequencing analysis for 2,162 diabetes patients registered in BBJ 1st cohort was performed. Fastq files are provided.
Whole genome sequencing analysis for 2,067 gastric cancer patients registered in BBJ 1st cohort was performed. Fastq files are provided.
hum0014.v32
Whole genome sequencing analysis for a total of 1,007 patients, who were registered Bio Bank Japan from 2003 - 2007 was performed. Fastq and vcf files are provided.
hum0014.v31
The alignment results [CRAM], variant call results per sample [gVCF] processed JGAD000220 (whole genome sequencing data for a total of 1,026 patients, who were registered BioBank Japan from 2003 - 2007) in a certain workflow were provided. If you plan to use the data, please indicate both original data (JGAD000220) and processed data (JGAD000690) on the application form for data use.
The variant call results per dataset [aggregated VCF, tabix] processed JGAD000220 (whole genome sequencing data for a total of 1,026 patients, who were registered BioBank Japan from 2003 - 2007) in a certain workflow were provided. If you plan to use the data, please indicate both original data (JGAD000220) and processed data (JGAD000758) on the application form for data use.
The tbi index file, the bref3 file, and a config file processed JGAD000220 (JGAS000114 reference panel) in a certain workflow were provided. These files can be used in the TogoImputation. If you plan to use the data, please indicate both original data (JGAD000220) and processed data (JGAD000679) on the application form for data use.
hum0014.v30
Target capture sequencing analyses of 27 cancer-predisposing genes in 1,982 lymphoma patients, 10,366 gastric cancer patients and 37,592 controls were performed. Fastq files are provided.
hum0014.v29
GWAS summary statistics file for 9,826 AF cases and 140,446 controls from the BBJ 1st cohort was added (txt).
Summary statistics file of cross-ancestry meta-analysis for 77,690 AF cases and 1,167,040 controls and polygenic risk score file calculated from the meta-analysis were added (txt).
hum0014.v28
Files for mobile element variations in 4,880 individuals from the BBJ 1st cohort were added (txt).
hum0014.v27
GWAS analysis files for 137,693 individuals from the BBJ 1st cohort were added (txt).
Sex-stratified genome-wide association studies using a Cox proportional hazard model under the assumption of the additive genetic model were performed. Associations of genetic variants estimated by saddle point estimation using SPACox software were also evaluated.
hum0014.v26
Target capture sequencing analyses of 27 cancer-predisposing genes and 13 renal cell carcinoma-related genes in 740 renal cell cancer patients and 5,996 controls were performed. Fastq files are provided.
hum0014.v25
Whole genome sequencing analysis for 1,765 myocardial infarction patients and 199 dementia patients were performed. Whole genome sequencing analyzed data were mapped to the GRCh37 reference genome sequence, and variant detection was carried out using the GATK (Genome Analysis Toolkit) standards. This project is an initiative of the GEnome Medical alliance Japan (GEM Japan, GEM-J). Fastq files, Bam files and gvcf files were provided.
hum0014.v24
A target capture sequencing analysis of 27 cancer-predisposing genes in 1,005 pancreatic cancer patients, 12,503 colorectal cancer patients and 23,705 controls was performed. Fastq files are provided.
hum0014.v23
Whole genome sequencing analyzed data included in the JGAD000220 were mapped to the GRCh37 reference genome sequence, and variant detection was carried out using the GATK (Genome Analysis Toolkit) standards. Bam files and gvcf files were added. This project is an initiative of the GEnome Medical alliance Japan (GEM Japan, GEM-J).
hum0014.v22
Target capture sequencing of 23 genes related to clonal hematopoiesis and SNP-array in 11,234 subjects extracted from approximately 200,000 subjects registered in Biobank Japan between fiscal years 2003 to 2007 were performed. A list of somatic SNVs/indels detected by targeted sequencing (txt) and a table of somatic copy-number alterations detected by analysis of SNP-array data (csv) are provided.
hum0014.v21
GWAS analysis files for coronary artery disease patients were added.
hum0014.v20
A total of 25,892 patients with coronary artery disease and 142,336 controls were genotyped by using of Illumina HumanOminiExpress, HumanExome, or OmniExpressExome BeadChip. A genotype imputation was carried out using Minimac3 algorithm with the BBJ-CAD reference panel. Then, genome-wide association study was performed using plink2 for 20 million variants.
hum0014.v19
A total of 165,084 participants whose dietary habits status is available were genotyped by using of Illumina HumanOminiExpress BeadChip, HumanExome, or OmniExpressExome BeadChip. A genotype imputation was carried out using Minimac algorithm with the 1000 genomes Phase I v3 release as a reference. Then, a genome-wide association study (about 6,000,000 imputed SNVs) was performed (BOLT-LMM and ProbABEL program).
hum0014.v18
GWAS analysis files for breast cancer patients were added.
hum0014.v17
A total of 212,453 patients of 40 diseases were genotyped by using of HumanOmniExpress/HumanExome/OmniExpressExome BeadChip(Illumina). A genotype imputation was carried out using Minimac3 algorithm with the 1000 genomes Phase 3 v5 release as a reference. Then, genome-wide association studies (8,919,992 imputed SNVs) were performed (SAIGE v0.29.4.2).
hum0014.v16
A target capture sequencing analysis of 8 hereditary prostate cancer genes in 7,636 prostate cancer patients and 12,366 controls was performed. Fastq files are provided.
hum0014.v15
- A new reference panel was build with WGS data of the biobank Japan project (N=1,037) and the 1KGP p3v5 ALL (N=2,504) .
- A total of 159,095 individuals were genotyped by using of Illumina HumanOminiExpress BeadChip, HumanExome, or OmniExpressExome BeadChip. A genotype imputation was carried out using Minimac algorithm with the reference panel using WGS data of the biobank Japan project (N=1,037) and 1KGP p3v5 ALL (N=2,504). Then, a genome-wide association study (about 20,000,000 imputed variants) for height was performed (BOLT-LMM [ver2.2] and mach2qtl).
hum0014.v14
A total of 165,436 participants whose smoking status is available were genotyped by using of Illumina HumanOminiExpress BeadChip, HumanExome, or OmniExpressExome BeadChip. A genotype imputation was carried out using Minimac algorithm with the 1000 genomes Phase I v3 release as a reference. Then, a genome-wide association study (about 6,000,000 imputed SNVs) was performed (BOLT-LMM and ProbABEL program).
hum0014.v13
Result of meta analysis of following 4 GWASs (txt file) .
- 9,804 T2DM patients and 6,728 controls
- 5,639 T2DM patients and 19,407 controls
- 18,688 T2DM patients and 121,950 controls
- 2,483 T2DM patients and 7,065 controls
Genotypes were determined by using of Illumina [HumanOmniExpress, HumanExome, OmniExpressExome, Human610-Quad BeadChip].
hum0014.v12
Result of meta analysis of following 2 GWASs (csv file).
- 2,380 T2DM with diabetic nephropathy patients and 5,234 T2DM without diabetic nephropathy patients
- 429 T2DM with diabetic nephropathy patients and 358 T2DM without diabetic nephropathy patients
Genotypes were determined by using of OmniExpressExome Beadchip or Human610-Quad BeadChip [Illumina].
hum0014.v11
A target capture sequencing analysis of 11 hereditary breast cancer genes in 7,104 breast cancer patients and 23,731 controls was performed. Fastq files are provided.
hum0014.v10
Whole genome sequencing analysis for a total of 1,026 patients, who were registered Bio Bank Japan from 2003 - 2007 was performed. Fastq files are provided.
hum0014.v9
A total of 67,029 females with information on age at menarche and 43,861 females with information on age at menopause were genotyped by using of Illumina HumanOminiExpress BeadChip, HumanExome, or OmniExpressExome BeadChip. A genotype imputation was carried out using Minimac algorithm with the 1000 genomes Phase I v3 release as a reference. Then, a genome-wide association study (about 10,000,000 imputed SNVs) was performed (mach2dat program).
hum0014.v8
A total of 162,255 patients, who were registered Bio Bank Japan from 2003 - 2007 were genotyped by using of Illumina HumanOminiExpress-12 BeadChip, HumanExome, or OmniExpressExome BeadChip. A genotype imputation was carried out using Minimac algorithm with the 1000 genomes Phase I v3 release as a reference. Then, genome-wide association studies (about 6,000,000 imputed SNVs) were performed (mach2qtl program).
hum0014.v7
A total of 3980 patients with primary open-angle glaucoma and 18,815 controls were genotyped by using of Illumina HumanOminiExpress BeadChip, HumanExome, or OmniExpressExome BeadChip. A genotype imputation was carried out using Minimac algorithm with the 1000 genomes Phase I v3 release as a reference. Then, a genome-wide association study (about 6,000,000 imputed SNVs) was performed (mach2dat program).
hum0014.v6
A total of 158,284 patients, who were registered Bio Bank Japan from 2003 - 2007 were genotyped by using of Illumina HumanOminiExpress-12 BeadChip, HumanExome, or OmniExpressExome BeadChip. A genotype imputation was carried out using Minimac algorithm with the 1000 genomes Phase I v3 release as a reference. Then, a genome-wide association study (about 6,000,000 imputed SNVs) was performed (mach2qtl program).
hum0014.v5
A total of 8180 patients with atrial fibrillation, who were registered Bio Bank Japan from 2003 - 2007, and 28,612 controls were genotyped by using of Illumina HumanOminiExpress-12 BeadChip, HumanExome, or OmniExpressExome BeadChip (900,000 SNVs). A genotype imputation was carried out using Minimac algorithm with the 1000 genomes Phase I v3 release as a reference. Then, a genome-wide association study (5,000,000 imputed SNVs) was performed (mach2dat program).
hum0014.v4
A total of 1472 patients with atopic dermatitis and 7966 controls were genotyped by using of Illumina HumanOminiExpress-12 BeadChip (606,164 SNVs). A genotype imputation was carried out using Minimac algorithm with the 1000 genomes Phase I v3 release as a reference. Then, a genome-wide association study (7,700,000 imputed SNVs) was performed using logic regression tests with imputed SNP dosage data (mach2dat program).
hum0014.v3
GWASs for T2DM were performed using 552,915 SNPs (9817 T2DM patients vs 6763 controls) and 479,088 SNPs (5646 T2DM patients vs 19,420 controls). Allele frequencies of T2DM patients and controls were compared.
Genotypes were determined by using of OmniExpressExome Beadchip or Human610-Quad BeadChip [Illumina], respectively.
hum0014.v2
Genotype frequencies of 934 healthy individuals, about 190 patients from each of 35 diseases, 182 esophageal cancer patients, and 92 ALS patients.
35 diseases:
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)
Illumina [Human610-Quad BeadChip, HumanHap550v3 Genotyping BeadChip], Perlegen Sciences [high-density oligonucleotide arrays], or Hologic Japan [Invader] were used for the genotyping.
hum0014.v1
A Genome-Wide Association Study (GWAS) for MI was performed using 455,781 SNPs (Illumina Human610-Quad BeadChip and HumanHap550v3 Genotyping BeadChip). Allele frequencies of 1666 MI patients and 3198 controls were compared.
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