Report from the Global Alliance for Genomics and Health 3rd Plenary Meeting

The Global Alliance for Genomics and Health (GA4GH) 3rd Plenary Meeting in Leiden, the Netherlands, recognised and celebrated the promising progress made over the last two years.

The day got off to a rousing start with a keynote from Ewan Birney (EMBL-EBI) which begun by acknowledging how genomics and healthcare come from very different cultures. A striking example showed how a high dimensional phenotype of a human heart study can be correlated with a genome-wide association study (GWAS). The long game was held up as being really important for success. The consortium would benefit from greater global diversity of membership, including stronger relationships with industry, mentioning the GSK-Sanger-EMBL-EBI Centre for Therapeutic Target Validation, as a specific example. Birney stressed how data access such as I/O bottlenecks must be tackled. He finished by stressing the importance of implementation to demonstrate value and thereby, develop a compelling “pitch” to funders in health care institutions and hospitals, which was developed during the question session.

The current mechanisms to access data via Beacons and Matchmaker Exchange (MME) were presented by David Haussler (UCSC) and Heidi Rehm (Broad Institute). Beacons enable access to gene variants with minimal detail and authentication whereas MME matches genotype and phenotype for pairs if individual patient cases. In future, it is expected that these two mechanisms will converge. They both include the necessary authentication of users with appropriate levels of access which is important to protect patient confidentiality. Policies to define the security of access to personal data is being clarified through the activities of the security working group.

The eHealth group, led by John Mattison (Kaiser Permanente), expressed the opinion that there are too many ontologies; an issue which is being tackled through the Pistoia Alliance Ontologies Mapping Project. He also mentioned that capture of structured data (e.g. selection from pick lists) by busy physicians is often inaccurate and meaningless, whereas extraction of assertions through natural language processing can give much better results.

Numerous national initiatives from the Netherlands, United Kingdom, Canada, Australia, Brazil and Singapore were presented during the afternoon session to show how they fit in with the global alliance. Interesting presentations were given by the charity, Autism Speaks, Baylor College of Medicine and the Centre for Genomic regulation. We also heard from the commercial vendors BGI and Amazon.

The day finished with David Altshuler (Vertex Pharmaceuticals and retiring Chair of the Steering Committee of GA4GH), who described how federation, through cloud services, has replaced a centralised approach to storage of genotype and phenotype data since inception of the consortium, only two years ago. While federated storage has many advantages it affects how analytical tools for interpretation are designed and deployed. More of such applications, which exploit the numerous APIs, are required to achieve wider adoption by users, especially in healthcare institutions such as hospitals. One issue that remains to be tackled is the inconsistent format for describing gene variants which hinders interoperability. Altshuler finished with the point that more engagement with industry would be mutually beneficial, which is an opportunity for the Pistoia Alliance.

Posted in Pistoia Alliance Blog.

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