NBDC Research ID: hum0114.v3
SUMMARY
Aims: Analysis of statistical genetics using cell line genotype data of Japanese ancestry
Methods: Genome-wide association study for psoriasis, Target capture sequence for HLA regioin, Construction of imputation reference panel of the KIR region
Participants/Materials: Cell line genotype data of Japanese ancestry
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0114.v1.gwas.v1 | GWAS for psoriasis | Unrestricted-access | 2017/12/18 |
| DRA007411 | NGS (Target Capture) | Unrestricted-access | 2019/04/12 |
| JGAS000314 | NGS (WGS + Target Capture, Target Capture) | Controlled-access (Type I) | 2021/08/10 |
*Data users need to apply an application 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 |
282 psoriasis patients (ICD10: L400) 426 healthy controls |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HumanCoreExome BeadChip] |
| Library Source | DNA extracted from B cell lines of Japanese ancestry |
| Cell Lines | - |
| Reagents (Kit, Version) | Illumina HumanCoreExome BeadChip kit |
| Genotype Call Methods (software) | GenCall software（GenomeStudio） |
| Filtering Methods | sample call rate < 0.99, SNP call rate < 0.99, HWE-P < 1x10^-7 |
| Marker Number (after QC) | 255,632 SNPs (on autosomal chromosomes、hg19) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 6 MB (txt.zip) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | Cell lines of the Japanese population: 560 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods |
HLA region (HLA-A, -B, -C, -DMA, -DMB, -DOA, -DOB, -DPA1, -DPB1, -DQA1, -DQB1, -DRA, -DRB1, -DRB2, -DRB3, -DRB4, -DRB5, -DRB6, -DRB7, -DRB8, -DRB9, -E, -F, -G, -H, -J, -L, -V, MICA, MICB, TAP1, TAP2) |
| Platform | Illumina [MiSeq] |
| Library Source | DNA extracted from cell lines of Japanese population |
| Cell Lines | - |
| Library Construction (kit name) | KAPA Hyper Prep Plus, SeqCap EZ choice |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 602 bp |
| DDBJ Sequence Read Archive ID | DRA007411 |
| Total Data Volume | about 215 GB (fastq) |
| Comments (Policies) | NBDC policy |
JGAS0000314: WGS + Target Capture
| Participants/Materials | Cell lines of the Japanese population: 689 samples |
| Targets | WGS, Target Capture |
| Target Loci for Capture Methods | KIR gene |
| Platform |
WGS: Illumina [HiSeq X Ten, NovaSeq] Target Capture: Illumina [MiSeq] |
| Library Source | DNA extracted from cell lines of Japanese population |
| Cell Lines | - |
| Library Construction (kit name) | KAPA Hyper Prep Plus, SeqCap EZ choice |
| Fragmentation Methods |
WGS: Ultrasonic fragmentation Target Capture: Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
WGS: 151 bp Target 350/250 bp |
| Mapping Methods | bwa |
| Reference Genome Sequence | GRCh37 |
| Variant Numbers in reference panel | 1,959 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000425 |
| Total Data Volume | 1.1 MB (vcf) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | Cell lines of the Japanese population: 1,173 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods | KIR gene |
| Platform | Illumina [MiSeq] |
| Library Source | DNA extracted from cell lines of Japanese population |
| Cell Lines | - |
| Library Construction (kit name) | KAPA Hyper Prep Plus, SeqCap EZ choice |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 350/250 bp |
| Mapping Methods | bwa |
| Reference Genome Sequence | GRCh37 |
| Coverage (Depth) | 140.6 |
| Variant Numbers in reference panel | 118 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000425 |
| Total Data Volume | 0.3 MB (txt) |
| 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 |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas | Cancer drug discovery based on statistical genetics and big data | 15H05911 |
| KAKENHI Grant-in-Aid for Young Scientists (A) | Identification of autoimmune disease biomarkers using HLA imputation | 15H05670 |
| Advanced Genome Research and Bioinformatics Study to Facilitate Medical Innovation (GRIFIN), Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED) | Implementation of genomic prediction medicine based on statistical genetics | JP21km0405211 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Variants at HLA-A, HLA-C, and HLA-DQB1 confer risk of psoriasis vulgaris in Japanese | doi: 10.1016/j.jid.2017.10.001 | hum0114.v1.gwas.v1 |
| 2 | Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population. | doi: 10.1038/s41588-018-0336-0 | DRA007411 |
| 3 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Koya Fukunaga | Division of Medical Safety Science, National Institute of Health Sciences | Japan | Research on the biomarkers associated with drug-induced interstitial pneumonia | JGAD000425 | 2023/02/05-2026/03/31 |
| Koya Fukunaga | Division of Medical Safety Science, National Institute of Health Sciences | Japan | Research on the biomarkers associated with drug-induced liver injury | JGAD000425 | 2023/02/05-2024/03/31 |
| Koya Fukunaga | Division of Medical Safety Science, National Institute of Health Sciences | Japan | Research on the biomarkers associated with drug-induced myopathy | JGAD000425 | 2023/02/05-2026/03/31 |
| Koya Fukunaga | Division of Medical Safety Science, National Institute of Health Sciences | Japan | Research on the diagnosis, treatment, and biomarkers for severe cutaneous adverse reactions | JGAD000425 | 2023/02/08-2026/03/31 |
| Kouya Shiraishi | Department of Clinical Genomics, National Cancer Center Research Institute | Japan | Search for genes involved in susceptibility to lung cancer | JGAD000425 | 2024/06/24-2025/12/31 |
| Nobuhisa Mizuki | Department of Ophthalmology, School of Medicine, Yokohama City University | Japan | Mapping of susceptibility genes for Behcet's disease | JGAD000425 | 2024/08/01-2027/03/31 |
| Taisei Mushiroda | Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences | Japan | Search of genomic biomarkers associated with drug-induced eruptions | JGAD000425 | 2024/08/01-2028/03/31 |
| Taisei Mushiroda | Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences | Japan | SNP analysis of wheat allergy | JGAD000425 | 2025/10/02-2026/03/31 |
