GENSAM - Joint national management of clinical microbial sequencing data

Purpose and goal

The project´s objective is to develop and establish a national database and web-based platform for the collection, analysis and sharing of genomic sequencing data of infectious agents to authorized parties. During stage 2, the platform has been developed, partially launched in production and is available for testing and development with users involved as project partners. The existing platform offers the necessary functionality for a complete workflow that includes uploading, automated bioinformatic analysis and report of results.

Expected results and effects

During the UDI step-2 collaboration phase, the need for sequencing data analysis has increased further because all regions in Sweden, due to the Covid-19 pandemic, have established some capacity for WGS of microbial agents. The local capacity was made possible as the GENSAM platform offers a standardized bioinformatic analysis of sequencing data that does not need to be done by local staff. The effect is that the infrastructure has improved, and the equality in access to technology regarding the generation and analysis of sequencing data of infectious agents in Sweden has increased.

Planned approach and implementation

The Covid-19 pandemic has affected the project in several ways. The initial plan involved the primary users in workshops, surveys and user tests to a greater extent. However, these elements had to be adapted due to challenges in allocating time for the collaborators in clinical microbiology. On the other hand, the prioritization of the infectious agent SARS-CoV-2 has delivered precise requirements on GENSAM and its design in many ways. In this way, the development of the platform has genuinely been challenge-driven.