Poster Number
33
Poster Title
Individual-Centric Genomics Platform JPN: A 2025 Implementation Progress Report
Authors
Senkei Umehara, Ken Yagi (GENEX, Inc.)
Abstract
Genomic medicine holds great promise, but challenges such as scattered data, difficult interpretation, and ethical concerns persist. To empower individuals to utilize their own genomic data for autonomous health management in the future, we serve as an integrated hub, supporting two key areas of endeavor: (1) "individual-led genomic data management and FAIRification," and (2) "reliable interpretation and utilization of genomic information."
We obtain proper consent from individuals, collect samples, and conduct whole genome sequencing. Based on the raw data obtained, we then create appropriately structured variant data, which we securely store, entrusted by the individual. In this structuring process, we standardize the use of VRS for unique variant identification and are piloting VA-Spec to build a foundation for annotated genomic data that is less prone to hallucinations (erroneous information generation) and has clear evidence. This enhances data interoperability and reusability, establishing a robust foundation for AI agents to perform reliable interpretations.
One visible application of this data utilization is the exploration of pathogenic variants in rare diseases. We began offering whole genome sequencing in 2022 and have continuously pursued this theme. To date, we have provided technical cooperation for Japan's health insurance-covered testing for mitochondrial diseases, offering clues that could lead to definitive diagnoses for multiple undiagnosed patients. This means we are already contributing to shortening the diagnostic odyssey of patients and facilitating their access to appropriate medical care. Furthermore, our ongoing efforts to advance our data structuring foundation hold the potential to further streamline this diagnostic support and expand its scope to a wider range of diseases. This data foundation also paves the way for the FAIR utilization of appropriately de-identified aggregate data.
We will continue to pursue transparency and scientific integrity, aiming to realize the FAIRification of genomic data and its utilization for reliable personal genomic medicine.
We obtain proper consent from individuals, collect samples, and conduct whole genome sequencing. Based on the raw data obtained, we then create appropriately structured variant data, which we securely store, entrusted by the individual. In this structuring process, we standardize the use of VRS for unique variant identification and are piloting VA-Spec to build a foundation for annotated genomic data that is less prone to hallucinations (erroneous information generation) and has clear evidence. This enhances data interoperability and reusability, establishing a robust foundation for AI agents to perform reliable interpretations.
One visible application of this data utilization is the exploration of pathogenic variants in rare diseases. We began offering whole genome sequencing in 2022 and have continuously pursued this theme. To date, we have provided technical cooperation for Japan's health insurance-covered testing for mitochondrial diseases, offering clues that could lead to definitive diagnoses for multiple undiagnosed patients. This means we are already contributing to shortening the diagnostic odyssey of patients and facilitating their access to appropriate medical care. Furthermore, our ongoing efforts to advance our data structuring foundation hold the potential to further streamline this diagnostic support and expand its scope to a wider range of diseases. This data foundation also paves the way for the FAIR utilization of appropriately de-identified aggregate data.
We will continue to pursue transparency and scientific integrity, aiming to realize the FAIRification of genomic data and its utilization for reliable personal genomic medicine.
Digital Poster