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Citation

Please acknowledge RAvariome in your publications by citing the following reference:
Nagai Y and Imanishi T*. RAvariome: a genetic risk variants database for rheumatoid arthritis based on assessment of reproducibility between or within human populations. Database (Oxford). 2013 Oct 23;2013(0):bat073.

Data resources

The data in RAvariome integrate reported human genetic variants including SNPs, HLA alleles, CNVs, and variable number of tandem repeats (VNTR) markers. Literatures of GWASs and meta-analyses were collected from the NHGRI catalog and HuGE Navigator, and an additional search was conducted using the automatic paper recommendation system PubMedScan (http://medals.jp/pubmedscan/). The association result, ethnicity of subjects, the country where subjects were recruited, the total numbers of cases and controls, the analysis platform, and the study design were extracted manually.

Significance level of associations

The results of statistical tests in original publications were re-evaluated according to following criteria. For a GWAS, if the corresponding P-value was <5.0 ÁE10∁E, the result of the statistical analysis was judged as significant evidence of strong association, and P-value between 1.0 ÁE10∁E and 5.0 ÁE10 E was judged as significant evidence of moderate association. Associations with P-value >1.0 ÁE10-5 were judged as not significant. Results of meta-analysis focusing on a specific variant was judged as “strong Efor P-value <0.01, “moderate Efor P-value between 0.01 and 0.05, and “not significant Efor P-value >0.05.

strength Study of genome-wide SNPs Study of selected SNPs
Strong P-value < 10-8 P-value < 0.01
Moderate 10-8< P-value < 10-5 0.01 < P-value < 0.05
Not significant 10-5 < P-value 0.05 < P-value
Reproducibility assessment

To assess the reproducibility of associations between RA and a genetic variant in a specific population and between different populations, associations were classified into the following nine populations; European (including European American, European Australian, European New Zealander, West European, North European, South European, and East European), East Asian (including South-East Asian), West Asian, South Asian, South American, Central American, North African, South African and African American. Because many follow-up studies were conducted about previous GWAS results, it was necessary to extract a representative association of the variants from each geographical population. Thus, the result of an association study with the largest number of case subjects was chosen as the representative association for each population. To determine intra-population reproduced variants, the number of significant (strong and moderate) associations was counted for each variant in each population. Then, the number of significant representative associations for each variant was counted to determine inter-population reproduced variants.

Calculation of risk

To calculate relative genetic risk (RGR) to the average population for each marker, an individual genotype specific risk si is estimated as:
RR
where ri is a risk factor assumed to equal the allelic OR of i-th marker. RGR of individual marker is estimated as: RR
Here pi is the risk allele frequency of i-th marker in control group. Thus, the overall RGR of an individual estimated by multi-markers is calculated as:
RR

The genetic risk score (GRS) was calculated as follows:

RR
where n is the number of markers available and Xi represents the copy number of risk allele at a marker i. If an individual carries one risk allele at i-th marker, Xi is 1, and if an individual carries two risk alleles, then Xi is 2.

Disclaimer

The information on this website is presented for the purpose of disseminating health information for the benefit of the public, but not providing professional medical advice, diagnosis, treatment or care. We does not accept any liability for any injury, loss or damage incurred by use of the information provided on this website.

The data in this database are available to download for academic researches and non-commercial use. For commercial use, please contact to us.

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Last update 2013.09.26
  • Publication: 90 published articles
  • Collection: 7,728 associations
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