case study
Simplifying Genetic Research
Necessary information /
Context / Client information
The Institute of Molecular and Translational Medicine (IMTM) aimed to create a comprehensive database of the Czech genome as part of the ENIGMA project. This involved processing 700 sequenced genomes from Czech donors to compute population-specific characteristics of genetic variants.
However, they faced significant challenges:
- Data Volume: Traditional methods could not handle the massive amount of data.
- Storage and Accessibility: Existing solutions could not efficiently store, query, and retrieve such vast genomic data.
- Resource Constraints: Developing the database in-house would require substantial computational resources and personnel.
How we solved the problem /
Solution /
DNAi's Floxgen Aggregation offered a multifaceted solution to IMTM's challenges. Floxgen automates genomic data processing, transforming raw variants into actionable insights using Apache Hail and ElasticSearch for rapid exploration and efficient storage. Its unique one-click recalculation feature allows instant updates whenever new samples are added or specific populations need to be analyzed.
The workflow starts with uploading VCF files, followed by ingestion into a big data database and essential pre-processing. Specialized plugins annotate variants for clinical context, and then aggregation and statistical calculations reveal patterns and associations. Scientists can access information through ElasticSearch, a relational database, or the GraphQL API.
Finally, a user-friendly web portal empowers scientific exploration through powerful search capabilities.
Used technologies /
Technologies /
Floxgen automates genomic data processing using Apache Hail and ElasticSearch, with VCF ingestion, preprocessing, clinical variant annotation, aggregation, statistical calculations, and access through ElasticSearch, a relational database, or the GraphQL API.
The platform also includes a user-friendly web portal and a one-click recalculation feature for new samples and population analyses.
Direct outcome /
RESULT /
Floxgen Aggregation has proven to improve the process in quantifiable areas.
- Efficiency Gains: Development time was reduced by up to 90% compared to traditional methods.
- Cost Savings: The solution significantly lowered database creation costs.
- Barrier Removal: By lowering technological and personnel barriers, Floxgen simplified the creation of the population database.
The Czech Genome Portal, powered by Floxgen, serves as a valuable resource for researchers and clinicians. Insights from the database contribute to personalized healthcare decisions.
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