Connecting GA4GH standards to community practice through unconferences

16 Jul 2024

In this guest blog post, GA4GH active contributor Alex Wagner explores how “unconferences” have supported standards development for the GA4GH Genomic Knowledge Standards Work Stream. Wagner invites the community to attend the Cancer Variant Curation and Coding Unconference at the Cancer Genome Consortium (CGC) meeting this August.

By Alex Wagner, Co-Lead of the Variation Representation Specification (VRS) and Driver Project Champion of the Variant Interpretation for Cancer Consortium (VICC)

Eight years ago, a small gathering of cancer knowledgebase maintainers assembled for a working meeting at the American Association for Cancer Research (AACR) annual conference. The individuals present, representing research groups with an interest in the exchange of cancer variant knowledge, had assembled to discuss the challenges of genomic knowledge representation and the interpretation bottleneck. Through the shared experiences and ideas of that meeting, it became clear that a consortium effort was needed to understand and address the challenges of harmonizing data across publicly available cancer variant knowledgebases. These investigators went on to establish the Variant Interpretation for Cancer Consortium (VICC) to evaluate and advance the interoperability of cancer variant interpretation knowledge.

Today, the VICC is a Global Alliance for Genomics and Health (GA4GH) Driver Project, and remains dedicated to advancing the interoperability of data generated and shared across cancer knowledgebases worldwide. The ongoing research efforts of the VICC have driven development of multiple clinical standards for representing and integrating genomic evidence in cancer variant evaluation, providing a foundation for the technical standards development of the GA4GH Genomic Knowledge Standards (GKS) Work Stream. The VICC anchors standards development through collaborative activities with many partner consortia, including projects with the Cancer Genome Consortium (CGC), the Clinical Genome Resource (ClinGen) Somatic Cancer work group, the American Medical Informatics Association (AMIA), the Association for Molecular Pathology (AMP), and the Human Genome Organization (HUGO).

The VICC vision for success stems from the roots of our organization: the VICC continues to find opportunities to host focused satellite meetings in conjunction with major conferences where the community is already congregating. We co-hosted a one-day meet-up with the HemOnc.org knowledgebase ahead of the American Association for Cancer Research (AACR) Advancing Precision Medicine Drug Development meeting in 2020, and on multiple occasions with the Clinical Interpretation of Variants in Cancer (CIViC) platform and ClinGen Somatic Cancer working group ahead of the CGC annual conference. 

These satellite, in-person events, typically held as “unconferences,” have facilitated the development and evaluation of significant efforts, such as oncogenicity classification standards, the VICC/ClinGen virtual molecular tumor board seminar series with the American College of Medical Genetics (ACMG), and the cross-community specification for gene fusion representation involving ClinGen, CGC, HUGO, and AMP. The wide reach of these resulting efforts, grounded in clinical laboratory practice, have provided the foundation for our contributions to GKS standards development. And since the unconference format allows us to share and select the topics of broadest value to the event participants on the day of the meeting, topics are always timely and of broad relevance to the community. These events also provide ample time to explore these topics in depth, in a format that is much more engaging than what can be accomplished on a monthly, one hour community call. As a result, these events have nucleated interdisciplinary working groups that can continue advancing clinical cancer variant interpretation standards well beyond the unconference event. 

This August, VICC, ClinGen, and CIViC are hosting another Cancer Variant Curation and Coding Unconference as a pre-conference activity of the 2024 CGC annual meeting in St. Louis, Missouri, USA. As an in-person event at CGC, it enables us to engage a wider cross-section of the clinical oncology community. We will focus on identifying and exploring common areas of interest in cancer genomics and health data sharing. One potential discussion topic is the computational representation of cytogenomics data in clinical cancer practice, a crucial yet under-discussed area in GA4GH that has global relevance to clinical genomics practice. Previous unconferences have covered topics like data representation, clinical reporting, and variant curation.

The unconference provides an ideal opportunity to introduce GA4GH products and projects to a relevant audience of clinical scientists and pathologists. As with that initial meetup of GA4GH investigators at AACR that established the VICC, this unconference is an opportunity for the GA4GH Cancer Community to engage in a structured setting to identify and discuss contemporary challenges in the use of cancer community resources in clinical genomics. It is our hope that this unconference is the first of a series of such events held to facilitate engagement between GA4GH Communities of Interest (in this case, the GA4GH Cancer Community) with practicing clinical genomics communities.

Please consider joining us for this community event at the CGC 2024 Annual Meeting, taking place 4 to 7 August at the Hyatt Regency St. Louis at the Arch. Registration details can be found here. To attend the unconference on 3 August at the same venue (and I hope that you will!), indicate ‘Unconference participation’ when you register for the CGC meeting. The event agenda can be accessed here.