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 IDType of DataCriteriaRelease 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

*Release Note

*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

hum0114.v1.gwas.v1

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

hum0114.v1.gwas.v1

(Click the Dataset ID to download the file)

Dictionary file

Total Data Volume 6 MB (txt.zip)
Comments (Policies) NBDC policy

 

DRA007411

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 Shearing
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 shearing

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

 

JGAS000314: Target Capture

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 shearing
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):

NameTitleProject 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

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData 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