#AGBTPH – Jonathan Berg, ClinGen and Clinvar: Approaches to variant curation and dissemination for genomic medicine.

Jonathan Berg, University of North Carolina, Chapel Hill

Views himself as an ambassador for ClinGen – What can clinGen do for you?  What can you do for ClinGen?

The Problem:  Ability to detect variants has outpaced our ability to interpret their clinical impact. 

Data is fragmented into many different academic databases, or held in clinical testing databases.  Want all this to be freely available and rich for use in medicine and research.

Many partners who are involved.

Building a genomic knowledge base to improve patient care.  Includes clinical domain working groups to curate the clinical genome.  Cover lots of different areas that are clinically relevant: cancer, mendelian, etc.

Engaging communities directly to encourage variant deposition.  

Clinvar:  Global, Archival, aggregates information.  Takes assertions about a specific variant.  NCBI  maintains providence so you know about the origin of who, what, why, etc.  Submissions continues to climb for clinvar.

Also worth noting that data has a rating system, so you can rapidly work out the reliability of the data.  Discussion of rating system, including “Expert Panels” who have brought together many different sources to collaborate on a single variant classification scheme.

GenomeConnect – another way to get the data into the public domain.

Is a gene associated with a disease:

Set out to define qualitative descriptors.  Six categories of gene-disease assertions:  definitive, strong, moderate, limited, disputed, refuted.  Based on strength of genetic evidence, strength of function evidence, replication, test of time, strength of curation.  Have a expert classification system to work through the rating.

ACMG standards and guidelines have been adopted as framework, as well.   Expert groups are using them as well.  There is a huge amount of work that goes into interpreting it, and it may be slightly different gene by gene.

Building a Genomic Knowledge base:

Website for ClinGen.  You can follow along with the working groups there,. Would love feedback on website and usability.

Major focus not Electronic Health Records

Need ways to integrate Genoics into EHR.  eg. Open Infobutton system for links to external resources.


Big group of people doing many many different things – working hard to make the data accessible.


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