GSI Lab is the second largest sequencing facility in Indonesia started through the social entrepreneurship initiative to support the Government and society in accelerating the handling of COVID-19. They are registered as the Laboratory of the COVID-19 Examination and SARS-CoV-2 Whole Genome Surveillance Network and affiliated with the Ministry of Health's integrated NAR system & PeduliLindungi.
In order to manage infectious diseases like COVID-19 in Indonesia, pathogen genomic data need to be queryable across the country, in real-time, and accessible to downstream analyses for the Ministry of Health. The data needs to be uploaded to GISAID to enable analysis, querying, and searching of genomic variants within COVID-19 genomic sequences generated in Indonesia, while maintaining data sovereignty.
As the number of generated sequences increases, it is important to summarize the datasets using appropriate tables and visualizations. Additionally, efficient surveillance requires the ability to find specific mutations within entire genomic cohorts and characterizing these mutations based on their similarity to identified variants of concern (VOC). This approach can help identify potential risks and serve as a proactive measure against the spread of COVID-19.
Improve public health and well-being by providing fast, high-capacity, high-quality genomic and molecular services linked to epidemiological data and digital information systems. - GSI Lab's vision
To manage genomic data on a sovereign platform and gain clinical-insights from real-time analyses, GSI lab partnered with CSIRO in a DFAT funded project.
CSIRO developed a purpose-built viral-variation exchange platform, PathsBeacon. Based on the Global Alliance for Genomic Health developed and well-established Beacon protocol, PathsBeacon is a versatile tool for viral genomic data management that can be quickly deployed by organizations using Infrastructure As A Code (IAAC) via terraform. With PathsBeacon, researchers can quickly set up the required infrastructure within their own cloud account to enable efficient sharing of genomic variant data.
The Bioinformatics Products team also realised the importance of producing datasets that allows easy exchange of genomic information. The team developed a customised genomic analysis pipeline to process GSI Lab's sequencing data and associated metadata to produce VCF output files making the dataset queryable.
CSIRO was able to contribute to GSI Lab's vision by enabling:
- Data Sovereignty - Genomic analysis pipeline and PathsBeacon are deployed within AWS's Jakarta region empowering the researchers to perform powerful analytics without moving any data.
- Visualisations - PathsBeacon's authenticated webpage allows users with dynamic tables and visualisations to summarise searched variant queries.
- Extensibility - GSI Lab aims to extend this beacon for the surveillance of other pathogens.
- Similarity search - Searched variant profiles can be compared with similarity search algorithm which allows users to identify closeness of a profile to become Variant of Concern (VOC)
CSIRO has helped us become the first Indonesian health initative to operate in the cloud Dr. Meutia Kumaheri (Head of Laboratory)
CSIRO is also leveraging the group's machine learning expertise to develop algorithms to correlate genomic variants with associated metadata and generate further downstream insights with the data. This will further help GSI Lab make meaningful, data-backed, suggestions to MoH.