Poster ID
P-05
Poster Title
Beaconize Thai Genomic Reference Database
Authors
Worawich Phornsiricharoenphant
University of Zurich, Zurich, Switzerland
Swiss Institute of Bioinformatics, Zurich, Switzerland
National Center for Genetic Engineering and Biotechnology, Thailand
National Science and Technology Development Agency, Thailand
Watcharapot Janpoung
National Center for Genetic Engineering and Biotechnology, Thailand
National Science and Technology Development Agency, Thailand
Chumpol Ngamphiw
National Center for Genetic Engineering and Biotechnology, Thailand
National Science and Technology Development Agency, Thailand
Sissades Tongsima
National Center for Genetic Engineering and Biotechnology, Thailand
National Science and Technology Development Agency, Thailand
Michael Baudis
University of Zurich, Zurich, Switzerland
Swiss Institute of Bioinformatics, Zurich, Switzerland
University of Zurich, Zurich, Switzerland
Swiss Institute of Bioinformatics, Zurich, Switzerland
National Center for Genetic Engineering and Biotechnology, Thailand
National Science and Technology Development Agency, Thailand
Watcharapot Janpoung
National Center for Genetic Engineering and Biotechnology, Thailand
National Science and Technology Development Agency, Thailand
Chumpol Ngamphiw
National Center for Genetic Engineering and Biotechnology, Thailand
National Science and Technology Development Agency, Thailand
Sissades Tongsima
National Center for Genetic Engineering and Biotechnology, Thailand
National Science and Technology Development Agency, Thailand
Michael Baudis
University of Zurich, Zurich, Switzerland
Swiss Institute of Bioinformatics, Zurich, Switzerland
Abstract
Genomic reference databases of population-level allele frequencies are essential for variant interpretation, distinguishing rare pathogenic variants from common polymorphisms. However, most large-scale resources are drawn predominantly from European and East Asian populations, leaving Southeast Asian groups, including Thai individuals, underrepresented. This limits interpretation accuracy for these populations and drives the need for Thai population resources that contribute to the global genomic reference pool while remaining interoperable with international standards. To address this gap, the Genomic Thailand project was initiated to sequence the genomes of 50,000 Thai individuals while addressing research topics related to five areas of interest - rare diseases, cancer, non-communicable diseases, pharmacogenomics, and infectious diseases.
As one output of this project, we built the Thai Genomic Reference Database, which currently includes 14,000 unrelated individuals from the planned 50,000 samples, and will grow to nearly that target after related samples are excluded. The database provides variant-level frequencies across multiple population contexts, including global references (e.g. gnomAD), the general Thai population, and specific disease subgroups. For interoperability with international genomic standards we adopted the GA4GH Beacon API, the leading protocol for programmatic discovery of genomic variant data. Beacon defines a common query interface and response format, allowing users to search for variants and retrieve standardized information about their frequency and population context in federated data discovery scenarios.
We implemented the GA4GH Beacon v2 API for the Thai Genomic Reference Database using bycon, an open-source Python-based Beacon implementation. We containerized bycon with Docker and deployed it on our institutional server and built a custom conversion script to map our database data onto the Beacon v2 data model.
Here we present our implementation architecture, the Beacon API endpoints currently available, and example queries and responses. Our goal is to show the genomics community that the Thai Genomic Reference Database now conforms to the GA4GH Beacon standard enables standardized, potentially federated queries to integrate Thai-specific allele frequency data into variant interpretation and research applications.
ThaiGeR : https://thaiger.genomicsthailand.com/
Bycon : https://bycon.progenetix.org/
As one output of this project, we built the Thai Genomic Reference Database, which currently includes 14,000 unrelated individuals from the planned 50,000 samples, and will grow to nearly that target after related samples are excluded. The database provides variant-level frequencies across multiple population contexts, including global references (e.g. gnomAD), the general Thai population, and specific disease subgroups. For interoperability with international genomic standards we adopted the GA4GH Beacon API, the leading protocol for programmatic discovery of genomic variant data. Beacon defines a common query interface and response format, allowing users to search for variants and retrieve standardized information about their frequency and population context in federated data discovery scenarios.
We implemented the GA4GH Beacon v2 API for the Thai Genomic Reference Database using bycon, an open-source Python-based Beacon implementation. We containerized bycon with Docker and deployed it on our institutional server and built a custom conversion script to map our database data onto the Beacon v2 data model.
Here we present our implementation architecture, the Beacon API endpoints currently available, and example queries and responses. Our goal is to show the genomics community that the Thai Genomic Reference Database now conforms to the GA4GH Beacon standard enables standardized, potentially federated queries to integrate Thai-specific allele frequency data into variant interpretation and research applications.
ThaiGeR : https://thaiger.genomicsthailand.com/
Bycon : https://bycon.progenetix.org/
Digital Poster