NBDC Research ID: hum0037.v1
SUMMARY
Aims: Searching for rare/low frequency variants in rheumatoid arthritis (RA)
Methods: Obtaining of susceptible candidate genes for RA by exome sequencing and validation methods
Participants/Materials: Patients with RA as cases and healthy individuals as controls
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000035 |
NGS (Exome) | Controlled-access (Type I) | 2015/09/24 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
39 RAs One pooled DNA of 5 healthy men One pooled DNA of 5 healthy women |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000] |
| Library Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon 50 Mb Kit (Agilent) |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000035 (GRCh37_decoy) |
| Total Data Volume | 680 GB (BAM format files), 143 MB (vcf format files) *1 |
| Comments (Policies) | NBDC policy |
*1：BAM files for 39 RAs. Vcf files for 2 pooled DNAs.
This study was supported by “Genome Science”. “Genome Science” is a part of the “Support Programs for Three Fields in Life Sciences (cancer, genome and brain sciences)” established by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) under the Grant-in-Aid for Scientific Research on Innovative Areas.
DATA PROVIDER
Principal Investigator: Shigeki Mitsunaga
Affiliation: Department of Molecular Life Sciences Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine
Project / Group Name:
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Exome sequencing for disease gene discovery in rheumatoid arthritis | 22510213 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Aggregation of rare/low-frequency variants of the mitochondria respiratory chain-related proteins in rheumatoid arthritis patients. | doi: 10.1038/jhg.2015.50 | JGAD000035 |
| 2 | Exome sequencing identifies novel rheumatoid arthritis-susceptible variants in the BTNL2. | doi: 10.1038/jhg.2013.2 | JGAD000035 |
USERS (Controlled-access Data)
| Principal Investigator: | Affiliation: | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|
