Welcome to the April issue of the GHIF newsletter! This month we're covering Variant Curation, Discovery, and Exchange, with spotlights on efforts underway at ClinGen, Australian Genomics, and BigMed. Maximizing the personal, public, research, and clinical value of genomic information will require that clinicians, researchers, and testing laboratories exchange genetic variation data reliably. Here, we present a selection of efforts working to enable sharing of variant data.
As a reminder, recordings and materials from the GHIF meeting on March 9 and 10 are accessible on the event website. Follow-up workshops covering topics introduced at the meeting will take place in May and June. You can find details at the links below. We are also still inviting contributors interested in quality control guidelines for whole genome sequencing results to please connect with us.
Featured Topic: Variant Curation, Discovery & Exchange
Variation Representation
Genomic knowledge informing the clinical classification of variants is currently non-interoperable across resources
The GA4GH Genomic Knowledge Standards (GKS) Work Stream is developing standards for the representation and exchange of genomic variation and annotation to improve interoperability between resources
The GKS Variation Representation Specification (VRS; vrs.ga4gh.org) and Variant Annotation specification provide a standard approach to the exchange of genomic knowledge for use in the clinical evaluation of genomic variants
Community Spotlight
The Variant Interpretation for Cancer Consortium (VICC) has developed a harmonized knowledgebase of clinical classification evidence that uses the VRS specification and the VRSATILE variant description framework. This implementation will also serve as a reference implementation of the Variant Annotation specification once finalized.
Decoding the clinical significance of DNA variants is complex and challenging, and is impeded when clinical laboratories operate as data silos.
It is currently difficult for one laboratory to know if others hold evidence to support or refute the clinical impact of a variant they have assessed. Failure to share information leads to the risk of missing a diagnosis or misclassifying a variant.
Variant exchange platforms can unite data silos, and provide key variant information to laboratories, helping them better interpret genomic tests and improve the outcomes of testing for patients.
Member Spotlight
BigMed, in collaboration with DNV GL and partners in the Nordic Alliance for Clinical Genomics, have developed the Variant eXchange, a platform that facilitates sharing of quality assured variant classifications with trusted partners of choice.
Member Spotlight
Australian Genomics has developed Shariant, a controlled access platform designed to allow Australian laboratories and clinical services to automate sharing of detailed and structured scientific evidence about clinically curated variants; communicate in real-time to resolve variant interpretation differences; and access gene- and disease-focused expertise.
Member Spotlight
Genomics England has developed Clinical Variant Ark (CVA), a knowledge base for clinically relevant variants and their association to phenotypes. CVA holds the interpretation results of the 100K Genomes Project and in the future it will hold the results of the National Genomic Informatics System.
The GHIF Toolbox
The GHIF toolbox serves as a central clearinghouse for GHIF members to share documents and resources with one another as well as with the broader community. The GHIF toolbox is currently under construction, but you are welcome to access the current resources using the link below.
Next month, we will focus on quality control of whole genome sequence data. If you have innovative ways of tackling these challenges in your initiative, we'd love to hear about it!
