The advent of cost-effective, high-throughput genomic sequencing technologies represents an important point of inflection in global public health and the prevention and control of infectious diseases. Public health departments throughout the world have significant experience in the development and standardization of new laboratory techniques and protocols. Unlike many precedent technologies, high-throughput pathogen sequencing, has significant data management, information technology and bioinformatics requirements, requiring significant new investments in infrastructure and workforce.
As microbial sequencing becomes more routine, access to flexible, sustainable bioinformatics capacity has increasingly become one of the most critical emerging needs for public health laboratories throughout the world. We see a tremendous opportunity to advance global public health through the development of an open source, community-supported ecosystem for bioinformatic software development, implementation, validation and support. Current models for public health bioinformatic software development are heavily fragmented, and rely heavily on government platforms and academic software development, often to the exclusion of interested contributors. Openness will help reduce many of the current barriers to sustainable bioinformatics capacity in public health by enabling broader participation, defining key gaps and shared priorities, improving modularity, scalability and interoperability of existing software, and developing a mechanism to help fund critical software and development gaps, and ensuring the sustainability of core software, databases and tools.
At present, there is no organized effort to champion the development of open source, reproducible bioinformatics, or to support the development of bioinformatic and data standards, architectures and methods for public health. A global, community-driven effort is desperately needed to help build consensus on technical solutions, to drive the establishment of best practices and reference models, and to provide a forum to debate and develop new standards for data exchange and bioinformatic development. In addressing these challenges, we see an incredible opportunity to advance global public health.
In March of 2019, we convened an international group of experts to explore this problem, and one of the key conclusions was the need for a new organization to help develop consensus standards and best practices. The Public Health Alliance for Genomic Epidemiology (PHA4GE) was established as a result of these key bioinformatics stakeholders recognizing the need to combine global efforts, and we have already begun to take some critical formative steps with the establishment of technical resources, an organizational charter, a code of conduct and a handful of focused working groups.
The Public Health Alliance for Genomic Epidemiology (PHA4GE) is a global coalition that is actively working to establish consensus standards; document and share best practices; improve the availability of critical bioinformatic tools and resources; and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics.
The Public Health Alliance for Genomic Epidemiology has the following objectives:
PHA4GE is working to: