C01: Computer Demo 1 NCBI Variation Portal: Databases and Tools for Genetic Variation Discovery, Analysis, and Interpretation

NCBI Variation Portal: Databases and Tools for Genetic Variation Discovery, Analysis, and Interpretation Lon Phan, NIH/NLM/NCBI, Bethesda, MD The Variation Portal site (http://www.ncbi.nlm.nih.gov/variation/) at NCBI is a gateway for users to access databases and tools that can be used in the fields of genomics, genetics, and management of variation data for human and over 300 organisms. There are five NCBI databases that archive, analyze, display, and report information about germline and somatic variants and the relationship of these variants to phenotype and clinical significance. dbSNP houses short variations; dbVar houses large scale genomic variants; the database of Genotypes and Phenotypes (dbGaP) houses genotypes and phenotypes associations; ClinVar houses reported relationships between human variation and phenotypes; and the Genetic Testing Registry (GTR) provides a central location for accessing inherited and somatic genetic variations that are being tested for a specific trait or disorder. The Variation Portal site also includes tools to explore and expedite the analysis of submitted variant and NCBI annotated information. The Variation Viewer allows users to search, navigate, and view variations in genomic and gene context. The Variation Reporter accepts uploaded VCF files and generates a comprehensive report that includes molecular consequences, allele novel to NCBI, and information from NCBI’s databases. NCBI Remap is a tool that allows users to project annotation data from one coordinate system to another. In addition, dbSNP, dbVar, and ClinVar provides a VCF report that can be used for filtering large sets of variation. This presentation will provide demonstrations to navigate, search, view, and retrieve the large volume of data from these public NCBI databases and tools.