Just over five years ago, a Consortium of 29 partners, from widely different scientific fields, was brought together to simply gather samples, sequence samples, share the sequence data and metadata, and analyze/visualize the data, all within a secure ‘playground’. Each area came with their own perspective, vocabulary, ways of working and prejudices. At the end of this grand experiment called ‘COMPARE’, we have now demonstrated, not only within the Consortium, but beyond its confines as well, that, at least to some degree, a common sample and laboratory prep can be determined, a secure data hub with multiple ways of uploading sequences as well as metadata can be created and used by several types of users, and that the mix of data can be visualized into information of action and used for detection, surveillance and tracking of clinical infections, foodborne outbreaks and emerging infectious diseases.
During the initial phases of COMPARE, major efforts were put into preparing, evaluating and comparing protocols for sampling and generating sequencing data, as well as creating IT-infrastructures and bioinformatics workflows allowing for secure storage and analyses of sequencing data. These infrastructures were piloted using different real-life studies focusing on clinical microbiology, foodborne infections and emerging infectious diseases. Most pilot studies involved only a single organism, but some fulfilled the end goal of combining all domains of life.
In addition, we have explored the economical potentials of including next-generation sequencing in diagnostic, surveillance and outbreak detection, as well as the political, legal, ethical and other barriers for rapid sharing of sequencing data, and we have also been a global voice and advocate for sharing data for the benefit of public health.
Besides a huge number of scientific conquests, documented by many scientific publications, COMPARE has established standard workflows, protocols, ring-tests, data-sharing hubs and bioinformatics pipelines that both during the project, but also in the years to come have been and will be used by other scientists involved in next-generation sequencing. A key component of the project has been the deep exploration of barriers to data sharing, as seen by scientists and end-users of data, and has led to an agreed code of conduct and governance models that have been brought forward far beyond COMPARE.
The COMPARE project, and the solutions established, have thus, made a change in the landscape, and we see great demand for taking tools, infrastructure and data hubs further.
