Medical Variation and Phenotypes at NCBI: GTR, MedGen, and ClinVar

Presented During:   Poster Presentations - Even Numbered
03/22/2013: 10:30 AM  - 11:30 AM 
Phoenix Convention Center North Building  
Room: Exhibit Halls B-D  

Abstract Number:

374 

Authors:

Wendy Rubinstein1, Donna Maglott2, Adriana Malheiro3, Brandi Kattman3, Jennifer Lee3, George Riley2, Melissa Landrum3, Douglas Hoffman3, Shanmuga Chitipiralla3, Michael Ovetsky3, Viatcheslav Gorelenkov3, Vichet Hem3, Guangfeng Song3, Craig Wallin3, Kenneth Katz3, Wonhee Jang3, Maryam Halavi3, Cathy Fomous4, Deanna Church5, James Ostell2

Institutions:

1National Institutes of Health, Bethesda, MD, 2NCBI/NLM/NIH, Bethesda, MD, 3NIH/NLM/NCBI, Bethesda, MD, 4National Institutes of Health, Office of Biotechnology Activities, Bethesda, MD, 5NIH, Bethesda, MD

Abstract:

Genetics professionals need to access and synthesize information about sequence variation and phenotypes in order to translate advances in genomic technology into medical practice. The mission of the National Center for Biotechnology Information (NCBI) is to advance science and health by providing access to biomedical and genomic information. NCBI has recently launched three new, interoperable resources - ClinVar, MedGen, and GTR - to enable genetics professionals to locate information about variation, phenotypes, and genetic tests in a centralized location.

The Genetic Testing Registry (GTR; www.ncbi.nlm.nih.gov/gtr/) maintains comprehensive information about testing offered worldwide for disorders with a genetic basis. GTR has been seeded with data pulled from GeneTests which will be phased out on June 4, 2013. GTR provides an explicit description of tests for Mendelian disorders and pharmacogenetic responses, includes quality measures such as analytical validity and proficiency testing, assembles practice guidelines, and is integrated with other NCBI databases. While GTR offers information about conditions and phenotypes, more comprehensive information about both is provided through MedGen. Laboratories that submit to GTR assert that relationships exist between tested variation and medical conditions (clinical validity); the aggregation of assertions about variation-to-condition relationships is the focus of ClinVar.

MedGen (www.ncbi.nlm.nih.gov/medgen/) is NCBI's portal to Medical Genetics. MedGen starts with defined medical concepts, and centralizes access to a wealth of related information such as clinical features, related genes, practice guidelines, ontologies, GeneReviews, OMIM, research literature, consumer resources, and genetic tests registered in GTR. Features of interest to geneticists such as synonyms and term hierarchies are presented. Advanced searches can be conducted for combinations of clinical features and other concepts such as chromosome, mode of inheritance, and keyword.

ClinVar (www.ncbi.nlm.nih.gov/clinvar/) aggregates information about sequence variation and assertions made about clinical significance. ClinVar then presents the data for individual users, laboratories that want to incorporate it in their daily workflow, and organizations that want to incorporate it into their own applications. For example, clinicians and researchers may search a DNA or protein location to learn what is known about the clinical significance of a sequence variation. Expert evaluations of assertions about pathogenicity will be reported. Data are assembled from diverse sources, including testing laboratories, researchers, OMIM, GeneReviews, PharmGKB, locus-specific databases (LSDB), and UniProtKB/Swiss-Prot, in order to reduce the burden on professionals to collate this information independently and to enable them to perform an informed and comprehensive assessment which can be repeated when new information is available.

Topic Focus:

Clinical Genetics

Keywords:

Bioinformatics
Databases
Phenotype
Phenotypic delineation of disorders
Public, Patient and Professional Education