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NCBI Resources: Genetic Variation

Contains information about the NCBI databases to be used as a teaching tool.

Genetic Variation

Over time, genomes acquire changes by genetic mutation. The resulting variety of DNA changes are known as genetic variation. These changes come in a variety that make up two general categories: single base pair changes (single nucleotide polymorphisms or SNPs) or structural variation (like chromosomal rearrangements, large deletions or insertions). 

These variations can result in changes in phenotypes, including causing diseases known as genetic disorders. A vast amount of data is being generated to probe relationships between genetic variation and phenotypes. The NCBI collects and presents some of this data in the Variation databases

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Variation Databases

The NCBI Variation databases can be divided into two categories:

The Archival Databases (dbSNP and dbVar​) contain records of variation submitted by investigators all over the world and how common they are in specific populations. They do not directly contain information about the consequences of these variations but they link to medical genetic databases that do.

  • dbSNP contains information about single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants.
  • dbVar contains records of larger (>50 bp) genomic structural variation, including insertions, deletions, duplications, inversions, multinucleotide substitutions, mobile element insertions, translocations, and complex chromosomal rearrangements.

The Medical Genetics Databases (dbGaP, ClinVar, GTR, MedGen and OMIM) contain clinical information about the results of these variants.

  • dbGaP (the database of genotypes and phenotypes) contains data regarding  the interaction of genotype and phenotype in Humans.
  • ClinVar aggregates information about genomic variation and its link to human health.
  • GTR contains information about genetic tests
  • MedGen Organizes information related to human medical genetics, such as attributes of conditions with a genetic contribution.
  • OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily.

See the figure below for a diagram of the databases and how they relate to biological concepts.  

Variation Tools

The NCBI also provides a suite of tools to search and visualize the variation data. Here are a few: 

  • Phenotype-Genotype Integrator (PheGenI), combines genome-wide association study (GWAS) data from dbGAP and an NHGRI project with genetic, phenotype, expression, and polymorphism data from the NCBI databases
  • Variation Viewer visualizes all of the variation data in a genomic region from a variety of data sources
  • Variation Reporter takes variant calls from your experiment and searches for known variations that match your data

See the following diagram for how these tools relate to the variation databases.

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