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Project title: Development of an information technology infrastructure for the Latvian residents’ reference genome storage and provision of access

Project No.:

Period: 14.12.2023. – 31.05.2026.

Project costs: 832 300,00 EUR

Principal Investigator: Dr.biol. Jānis Kloviņš

Project summary:

The objective of the project corresponds to the provisions of Cabinet Regulation No. 435 of July 14, 2022, “Procedures for the Implementation of the 2nd Component of the European Union Recovery and Resilience Mechanism Plan ‘Digital Transformation,’ Direction 2.1 ‘Digital Transformation of Public Administration, Including Local Governments,'” specified in subparagraph 4.2 – to ensure the storage and availability of the genome reference data of the residents of Latvia for the purposes of healthcare(prevention, diagnosis, and treatment), research, and innovation. The aim is to establish a national ICT infrastructure and data processing framework to ensure secure storage and access to genome reference data obtained from 3500 residents of Latvia in the reform project 4.1.1.r. “Creation of the Genome Reference for the Residents of Latvia”.

Latvia has joined the European Commission’s declaration “1+ Million Genomes Declaration” (hereinafter referred to as 1+MG), which aims to create a cohort of at least one million European residents’ whole genome sequences. The objective is to ensure the availability of genetic and related health data in a secure and protected manner for healthcare purposes (prevention, diagnosis, and treatment), as well as for research and innovation. Researchers and medical professionals will be able to analyze and compare individuals’ genetic and clinical information. This will aid in earlier disease detection, prediction of their development/progression, and determination of the best ways to improve health. To achieve this goal, a data processing framework is being established among the 1+MG countries. A federal data infrastructure is planned to be created to ensure the secure storage of national genome data collections in respective countries and cross-border access to them. Within the 1+MG initiative, it is planned to implement the European Genome Project (The Genome of Europe Project (GoE))  to create a representative genome reference cohort of 500,000 European residents. The State Resident Genome Data System established within the project will contain the genome reference of Latvian residents, which has not been available in Latvia until now. This will enable precise genetic diagnostics for oncology and inherited disease patients and, in the long term, promote precision medicine in Latvia.

The number and format of data stored in the State Resident Genome Data System corresponds to the recommendations developed within the framework of the GoE project. Additionally, the total number of participants aligns with calculations made for each country, determining the minimum volume of genome sequences needed to create a representative sample. An infrastructure for data storage will be established, encompassing approved information systems and analytical solutions to fully ensure the functionalities of data acquisition, receipt, and storage, as well as access and processing solutions for Latvian users. This includes protocols suitable for optimizing the use of high-performance computing resources.

The created genome data access platform and the associated data processing tools will provide access to registered users (such as doctors, healthcare system administrators, and researchers).

The funding recipient is the Latvian Biomedical Research and Study Center (BMC), which serves as the main processor of the State Resident Genome Database. BMC will ensure efficient and rapid implementation of activities, as many planned activities will be organized in accordance with data processing procedures developed in international projects, ensuring compliance with existing legislation and ethical standards. Since 2005, the Genomics Center, a structural unit of BMC, has been responsible for the procedures of biobank formation and has been part of the Biobanking and Biomolecular Resources Research Infrastructure – European Research Infrastructure Consortium (BBMRI-ERIC) since 2016, participating in international quality control procedures.

Since 2015, BMC has been providing next-generation sequencing and has demonstrated high-throughput sequencing of samples in both scientific projects and within the context of COVID-19 monitoring. Since 2015, a Bioinformatics unit has been established within BMC, responsible for genome data processing. Unfortunately, up to the present moment, a unified and standardized data processing system has not been established to facilitate genome data processing and utilization for end-users. The project involves personnel with extensive experience in project management, data processing, and bioinformatics. BMC and its staff are members of various international organizations, including the European Molecular Biology Laboratory (EMBL), 1+ Million Genomes Declaration, BBMRI-ERIC infrastructure, etc.  ensuring the transfer of expertise and the latest technologies to Latvia.

Information published 15.12.2023.

Progress of the project:

1 December 2023 – 30 April 2024

  1. An analysis of user needs has been conducted, and user stories and portal usage scenarios have been prepared. Currently, the user stories and portal usage scenarios are being reviewed with the portal users – doctors and researchers;
  2. The environment has been configured, and genome sequence files are being uploaded to the LNB object repository. The LNB object repository for data management and utilization will be integrated with the LNB DOM system;
  3. The description of genome file metadata has been prepared and is currently being reviewed with the portal users – doctors and researchers;
  4. A collaboration agreement with the LNB is being finalized to utilize the resources of the national data centre for the storage of the Latvian population’s genome reference data;
  5. Alternatives for project implementation have been evaluated.

Information published 30.04.2024.