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

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000035
NGS (Exome) Controlled Access (Type I) 2015/09/24

*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

 

MOLECULAR DATA

JGAS00000000035

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 Data set ID JGAD00000000035 (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):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research (C) Exome sequencing for disease gene discovery in rheumatoid arthritis 22510213

 

PUBLICATIONS

TitleDOIData Set 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. JGAD00000000035
2 Exome sequencing identifies novel rheumatoid arthritis-susceptible variants in the BTNL2. doi: 10.1038/jhg.2013.2. JGAD00000000035

 

USERS (Controlled-Access Data)

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