title: VaDE: a manually curated database of reproducible associations between various traits and human genomic polymorphisms.
abstract: Genome-wide association studies (GWASs) have identified numerous single nucleotide polymorphisms (SNPs) associated with the development of common diseases. However, it is clear that genetic risk factors of common diseases are heterogeneous among human populations. Therefore, we developed a database of genomic polymorphisms that are reproducibly associated with disease susceptibilities, drug responses and other traits for each human population: 'VarySysDB Disease Edition' (VaDE; http://bmi-tokai.jp/VaDE/). SNP-trait association data were obtained from the National Human Genome Research Institute GWAS (NHGRI GWAS) catalog and RAvariome, and we added detailed information of sample populations by curating original papers. In addition, we collected and curated original papers, and registered the detailed information of SNP-trait associations in VaDE. Then, we evaluated reproducibility of associations in each population by counting the number of significantly associated studies. VaDE provides literature-based SNP-trait association data and functional genomic region annotation for SNP functional research. SNP functional annotation data included experimental data of the ENCODE project, H-InvDB transcripts and the 1000 Genome Project. A user-friendly web interface was developed to assist quick search, easy download and fast swapping among viewers. We believe that our database will contribute to the future establishment of personalized medicine and increase our understanding of genetic factors underlying diseases.
authors.affiliation: Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan.
authors.forename: Yoko
authors.initials: Y
authors.lastname: Nagai
authors.affiliation: Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan.
authors.forename: Yasuko
authors.initials: Y
authors.lastname: Takahashi
authors.affiliation: Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan Data Management and Integration Team, Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan imanishi@tokai-u.jp.
authors.forename: Tadashi
authors.initials: T
authors.lastname: Imanishi
mesh_terms: D030561:Databases, Nucleic Acid; D020022:Genetic Predisposition to Disease; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D020407:Internet; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results