NCBI has three relatively new online resources for information about genetic tests, genetic conditions, and genetic variations:
- The Genetic Testing Registry, or GTR – a registry of genetic tests for heritable and somatic changes in humans
- MedGen – a medical genetics portal that focuses on information about medical conditions with a genetic component
- ClinVar – an archival database that contains reported assertions about the relationship between genetic variations and phenotypes
This blog will provide a very brief overview of the three resources by outlining some of their content features. For a more thorough introduction to the three resources, including the types of information available in each and how to use them, we recommend viewing this approximately hour-long webinar that we conducted in June 2014.
The GTR, MedGen and ClinVar databases are all integrated, making it simple to navigate between them to find related information. They are also integrated with a number of other databases, such as OMIM, GeneReviews, PubMed, Genetics Home Reference, and others. This integration provides a rich information space for exploration, but it is nonetheless helpful to know where you might want to start based on the type of information you are seeking.
GTR is intended for health care providers, researchers, and others interested in detailed information about genetic tests. As of June 2014, GTR included information on approximately 19,000 genetic tests, about 2,000 of which test for two or more targets. Twenty-seven of the laboratories in GTR offer whole exome sequencing, while seven provide whole genome sequencing.
Among the things you can do in GTR:
- Find genetic tests that are available for a given condition
- Search tests by a variety of parameters, including gene or condition name, number of genes tested, and test methodologies
- View test-specific information, including how to order the test, the indication, the methodology used, and performance characteristics
- View lab-specific information, including the lab’s procedures for reporting results and variants of unknown significance, and the laboratory contact
- Find curated articles of interest related to the condition being tested, as well as associated practice guidelines
If you are looking for information about genetic conditions, MedGen is an excellent starting point. The database integrates information from many sources, including OMIM, GeneReviews, PubMed, Genetics Home Reference, and others.
Among the things you can do in MedGen:
- Search by condition or by clinical features (a search by clinical features might be useful, for example, if you want to learn about the conditions in which that feature is typically seen)
- Obtain information on features that distinguish a syndrome/condition from other conditions
- Get links to recent related clinical studies
- Obtain available professional guidelines that are related to the condition you are researching
- Link to a variety of related information, including tests listed in GTR, the OMIM gene record, detailed gene information in RefSeqGene, genetic variations in ClinVar and NCBI’s variation viewer, as well as consumer resources
ClinVar integrates four domains of information: variation, phenotype, the interpretation of how a variation relates to a phenotype, and the evidence that supports that interpretation. ClinVar is integrated with many other resources, such as dbSNP, dbVar, Gene, and MedGen.
Among the ways you might use ClinVar:
- Find information about a specific variant, for example to learn more about a variant found in a genetic test of a patient
- Find the variants that have been associated with a particular gene
- Obtain general information about the allele and the phenotype
- View a clinical summary of all the assertions that have been submitted for a phenotype/variant pair
- View a graphical representation of the variant in its genomic context on the chromosome using NCBI’s sequence viewer,
- Find information about the evidence provided to support the submitter’s clinical assertions
ClinVar was launched in 2013 and is still in the early stages of gathering data. As of June 2014 there were more than 117,000 submissions representing over 104,000 variants in 18,908 genes.