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MedGen: Harmonizing phenotypic information into an online, computer-readable resource of medical genetics

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MedGen: Harmonizing phenotypic information into an online, computer-readable resource of medical genetics

What is MedGen? A portal to information and terminology related to human disorders and phenotypes having a genetic component. It serves as the phenotype backbone of Genetic Testing Registry (GTR) test descriptions and ClinVar variant interpretations. Supports the interactive and computational needs of the genetic community. https://www.ncbi.nlm.nih.gov/medgen

MedGen: Fills a Gap

Specificity of information about phenotype is critical to precision medicine as it is needed for ordering genetic tests, interpreting variants, and discovery in medical genetics

-Phenotype vocabularies and ontologies have grown organically to suit various needs of our community

-There is much overlap, but no lingua franca that serves all contexts (rare disease, oncology, pharmacogenomics)

MedGen: Facilitates Data Sharing

Sharing computationally accessible information globally and across the continuum of care is critical. Laboratories, manufacturers, hospital systems and databases can no longer operate in isolation.

Why does MedGen harmonize genetic nomenclatures?

-enable accurate interpretation of the clinical significance of sequence variation
-enable deep phenotyping of sequenced individuals to inform variant interpretation
-facilitate integration of valuable information into electronic health records (EHR)
-streamline the billing process

How does MedGen facilitate data sharing?

-uses SNOMED CT for preferred terms when available
-to support EHR data mining
-makes mapping of MedGen, HPO and OMIM concepts freely available on the ftp site

MedGen: Easily Accessible Data

Interpretation of user-generated variant files (e.g. vcf) is supported by connecting NCBI reports of clinical significance of variants in ClinVar, gene-condition relationships, modes of inheritance, features of a disorder, and literature resources.

Use the web, programming tools such as NCBI’s API, E-Utilities (esearch and summary) or Entrez Direct, or our FTP site to access data in MedGen: ftp://ftp.ncbi.nlm.nih.gov/pub/medgen

The FTP site is updated weekly every Wednesday.

Hospital systems can use NCBI's API to tailor views of genetic information for their users at point of care. e.g., import GTR test menu based on state and CLIA certifications, panel size and gene content, condition descriptions, and practice guidelines (https://www.ncbi.nlm.nih.gov/medgen/docs/help/)

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