VaDE

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VaDE version 1.7(2016-9-20 released)

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What's VaDE?

OUTLINE OF VaDE

A VarySysDB Disease Edition (VaDE) is a database of human genome polymorphisms involved in traits such as various disease susceptibilities or drug responses, which have been collected from a number of academic papers.

Most of the data that has been registered in VaDE is a genome polymorphisms associated with disease or drug responses. Besides, it contains a number of genome polymorphisms associated with general traits such as height or weight. VaDE provides a wealth of information about these genome polymorphisms such as odds ratio, β value, sample population, p value and so on. Furthermore, VaDE evaluates reproducibility of associations in multiple independent studies.

By using VaDE, you can easily search and get the reliable information of genome polymorphisms associated with disease susceptibility. This information can be used in researches for predicting disease risks, which lead to application to preventive medicine in the future. In addition, data registered in VaDE is available in a wide range of fields such as drug discovery, forensic medicine, and anthropology, so the role of this database will become increasingly important in the future.

DETAILED INFORMATION OF PAGES AND UTILIZATION

Please refer to the following VaDE manual.

VaDE Manual verion 1.1 released.

Database construction

DETAILED INFORMATION OF DATABASE CONSTRUCTION

Collection of SNP-trait association data

There are two kinds of SNP-trait association data in VaDE database; 1. One was collected from The NHGRI-EBI Catalog of published genome-wide association studies (NHGRI-EBI GWAS catalog) http://www.ebi.ac.uk/gwas/, 2. The other was a VaDE original comprehensive manual curation data.

1. We did manual curation for the data from a NHGRI-EBI GWAS catalog to check and modify the data, add the items, and change the format. 2. Comprehensive manual curation is currently underway by the VaDE team. Some data provided from collaborators have been imported through a confirmation process by the VaDE team. Details of each data can be found in the following RELEASE HISTOY.

Because the association results in articles use variety of genetic models, we integrated associations of allelic or additive models and excluded results of dominant and recessive models.

Standardize ontology of population, disease, and gene

In addition to an association analysis result, VaDE provides information of ancestral population, ethnicity, and nationality for a subject used in each study. Vocabulary of nation and population were standardized by referring to the World Factbook of CIA and Composition of regions of United Nations Statistics Division.

Subject population information was classified into the following eleven populations.

Trait and disease were classified into the following three categories; disease, trait, and pharmacogenomics (PGx). Disease was further sub-categorized based on ICD10 by automatic linking and manual curation using Unified Medical Language System (UMLS).

SNP locations were based on dbSNP137. Reported genes were those reported in original articles.

Reproducibility assessment of SNP-trait association

For reproducibility assessment if SNP-trait association, we used only SNP-association data on single-population samples with significant p-value (GWAS: p ≤ 1.0 × 10-5, replication study: p ≤ 0.05).

We counted total number of significant results for each stages when multi-studies were conducted with independent samples such as a two-stage design GWAS. For each combination of population, trait, SNP, and risk allele, total number of significant studies was counted between independent articles to confirm reproducibility. SNP-trait associations which reproducibility was confirmed by more than one independent studies within or between literatures were summarized in Reproduced Associations page.

Collection of functional genomic data

Experimental data such as ChIP-seq, DNase I hypersensitivity experiments, regulatory motifs data from ENCODE project, chromatin state segmentation from ENCODE/Broad, chromatin state segmentation from NIH Roadmap Epigenomics Mapping Consortium, and RefSeq gene annotation were downloaded from Haploreg v2. Annotation of H-InvDB transcript to SNP was based on VarySysDB. Linkage disequilibrium (LD) between SNP and upstream and downstream 3000 SNPs based on 1000 Genomes Project were provided by Center for Statistical Genetics, University of Michigan. Detailed information of method is described at http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G.2012-02-14.html. To visualize location and relation between SNPs and functional genomic region, we developed Genome Browser based on UCSC Genome Browser.

Download files

In "Reproduced Associations" page and "All Associations" page, the displayed records can be downloaded by pressing "CSV" or "TSV" button at the lower right corner of the window. Please refer to the document below about the column description.

VaDE download file column description

RELEASE HISTORY

2016-9-20 VaDE version 1.7

Items of data
Category# of kinds# of records# of original articles
Disease 554 11,176 1,188
Trait 1,040 13,719 814
PGx 105 987 105
All 1,699 25,882 2,107
Information of data source
Data source# of recordsDescription
NHGRI-EBI GWAS catalog18,634 Association data were collected from NHGRI-EBI GWAS catalog download file. Detailed curation method is provided by web site of NHGRI-EBI GWAS catalog. Sample population (ancestry), country and ethnicity were added by VaDE team. The duplicated data were excluded after data of NHGRI-EBI GWAS catalog and VaDE were merged.
NHGRI-EBI GWAS caralog (uncurated)5,867 Association data were collected from NHGRI-EBI GWAS catalog download file. Correction of trait names in accordance with VaDE's nomenclature rules and classification of sample populations were carried out. Not yet finished detailed investigation by VaDE team.
VaDE1,381
  1. 1) Extract all significant and non-significant associations that have been reported from original article. Currently, association data of hypertension and rheumatoid arthritis were included.
  2. 2) Association analysis data of Type 2 diabetes in Japanese based on Sato N et al.(PMID:25069673) that have been provided from Tokyo Medical and Dental University.

2016-1-20 VaDE version 1.6

2015-9-17 VaDE version 1.6

Items of data
Category# of kinds# of records# of original articles
Disease 434 15,202 1,101
Trait 877 10,066 673
PGx 84 753 87
All 1,395 26,021 1,861
Information of data source
Data source# of recordsDescription
NHGRI GWAS catalog18,494 Extract association results which p-value is smaller than 1E-5. Detailed curation method is provided by web site of NHGRI GWAS catalog. Sample population (ancestry), country and ethnicity were added by VaDE team. The duplicated data were excluded after data of NHGRI GWAS catalog and VaDE were merged.
VaDE7,527
  1. 1) Extract all significant and non-significant associations that have been reported from original article. Currently, association data of hypertension and rheumatoid arthritis were included.
  2. 2) Association analysis data of Type 2 diabetes in Japanese based on Sato N et al.(PMID:25069673) that have been provided from Tokyo Medical and Dental University.

2015-6-16

2015-3-27 VaDE version 1.5

Items of data
Category# of kinds# of records# of original articles
Disease 420 15,017 1,079
Trait 889 9,967 675
PGx 84 775 86
All 1,393 25,759 1,840
Information of data source
Data source# of recordsDescription
NHGRI GWAS catalog18,232 Extract association results which p-value is smaller than 1E-5. Detailed curation method is provided by web site of NHGRI GWAS catalog. Sample population (ancestry), country and ethnicity were added by VaDE team. The duplicated data were excluded after data of NHGRI GWAS catalog and VaDE were merged.
VaDE7,527
  1. 1) Extract all significant and non-significant associations that have been reported from original article. Currently, association data of hypertension and rheumatoid arthritis were included.
  2. 2) Association analysis data of Type 2 diabetes in Japanese based on Sato N et al.(PMID:25069673) that have been provided from Tokyo Medical and Dental University.

2014-12-16

2014-11-20 VaDE version 1.4

Items of data
Category# of kinds# of records# of original articles
Disease 344 13,873 965
Trait 455 8,118 648
PGx 64 588 68
Others 218 1,967 84
All 1,081 24,546 1,722
Information of data source
Data source# of recordsDescription
NHGRI GWAS catalog17,019 Extract association results which p-value is smaller than 1E-5. Detailed curation method is provided by web site of NHGRI GWAS catalog. Sample population (ancestry), country and ethnicity were added by VaDE team. The duplicated data were excluded after data of NHGRI GWAS catalog and VaDE were merged.
VaDE7,527
  1. 1) Extract all significant and non-significant associations that have been reported from original article. Currently, association data of hypertension and rheumatoid arthritis were included.
  2. 2) Association analysis data of Type 2 diabetes in Japanese based on Sato N et al.(PMID:25069673) that have been provided from Tokyo Medical and Dental University.

2014-08-21 VaDE version 1.3

Information of data source
Data source# of recordsDescription
NHGRI GWAS catalog15,283

Extract association results which p-value is smaller than 1E-5. Detailed curation method is provided by web site of NHGRI GWAS catalog. Sample population (ancestry), country and ethnicity were added by VaDE team. The duplicated data were excluded after data of NHGRI GWAS catalog and VaDE were merged.

VaDE7,530
  1. 1) Extract all significant and non-significant associations that have been reported from original article. Currently, association data of hypertension and rheumatoid arthritis were included.
  2. 2) Association analysis data of Type 2 diabetes in Japanese based on Sato N et al.(PMID:25069673) that have been provided from Tokyo Medical and Dental University.

2014-06-26 VaDE version 1.2

Information of data source
Data source# of recordsDescription
NHGRI GWAS catalog15,448

Extract association results which p-value is smaller than 1E-5. Detailed curation method is provided by web site of NHGRI GWAS catalog.Sample population (ancestry), country and ethnicity were added by VaDE team. The association data overlapped to VaDE's manually curated data were excluded.

VaDE7,464

Extract all significant and non-significant associations that have been reported from original article. Currently, association data of hypertension and rheumatoid arthritis were included.

2014-06-06 VaDE version 1.1

2014-04-24 VaDE version 1.0

Site policy

DISCLAIMER

The information on VarySysDB Disease Edition (VaDE) is presented for the purpose of academic researches. It is 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.

Every effort is taken to ensure that the information contained in this website is accurate and complete. However, accuracy cannot be guaranteed, because rapid advances in medicine may cause information contained here to become outdated, invalid or subject to debate.

TERMS OF USE

All of the pages in this database can be freely viewed at no charge. You are also free to establish links to all of the pages.

However, download and use of all data is limited for academic researches and non-commercial use. For commercial use, please contact us from the following CONTACT.

This database has set Attribution-NonCommercial 2.1 Japan based on Creative Commons. Summary is as follows.

For more details, please see this site.

https://creativecommons.org/licenses/by-nc/2.1/jp/deed.en

COPYRIGHT

The copyright of this database belongs to Biomedical Informatics Laboratory (Imanishi Laboratory), Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine.

REFERENCE

If you publish your work as a research paper using the data in this database, please refer to the following paper.

Nagai Y, Takahashi Y, and Imanishi T (2014) VaDE: a manually-curated database of reproducible associations between various traits and human genomic polymorphisms. Nucleic Acids Research, Database Issue 2014;doi:10.1093/nar/gku1037.

About us

VaDE DEVELOPMENT TEAM

Biomedical Informatics Laboratory (Imanishi Laboratory), Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine

  • Tadashi Imanishi, Professor
  • Takuya Habara, technical assistant
  • Kentarou Mamiya, technical assistant
  • Miho Sera, technical assistant

(Former Members)

  • Yoko Nagai, Postdoctoral Research Fellow
  • Yasuko Takahashi, Technical Assistant

PRESENTATION

CONTACT

Comments, suggestions, ideas, and bug reports are welcome. Your feedback is highly appreciated and will help us to improve our database in the future. Additionally, we are looking for research institutions and private companies wish to support the development of this database. Please contact us by email to the below address.

vade[@]ml.u-tokai.ac.jp

ACKNOWLEDGMENT

We express our greatest thanks to Drs. Noriko Sato, Nay Chi Htun, and Masaaki Muramatsu of Tokyo Medical and Dental University for providing us with curated data of type-2 diabetes. We also thank Dr. Takato Matsui, Dr. Junichi Takeda and members of Support Center for Medical Research and Education, Tokai University for manual curation of literatures, and Kensuke Numakura for valuable discussion and disease classification.

FUNDING

This database project is partially supported by JSPS KAKENHI, Grant-in-Aid for Publication of Scientific Research Results (Grant Number 16HP8044) in 2016.

CREDIT

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