First publication of data on 1,000 Vietnamese genomes

The Vietnamese gene decoding project is led by Dr. Vo Sy Nam and Professor Vu Ha Van at VinUni University, including more than 40 Vietnamese scientists from VinUni, Hanoi University of Science and Technology, Hanoi National University, Hanoi Medical University, Ho Chi Minh City National University, Vietnam Academy of Science and Technology, Vinmec Health System, University of Queensland (Australia), Houston Methodist Research Institute (USA), Cornell University (USA). show. Study “VN1K is a pangenome-informed multi-omics and phenomics resource for the Vietnamese population” was announced on July 22 above Nature Communications.

Professor Vu Ha Van, the initiator of the project, said that VN1K was built on the basis of data analysis of 1,011 Vietnamese people from 53/63 provinces and cities (according to the old administrative boundaries at the time of sampling), recording more than 42 million genetic variations, of which about 8.5 million variations have never been recorded in popular international databases. From this data source, the research team developed Vietnamese PanGenome Reference (VPR), Vietnam’s first large-scale population reference genome.

According to the research team, currently there is very limited data on Vietnamese people on popular databases, making the characteristics of Vietnamese people in terms of disease risk and drug response not fully understood. But now the data set will be the basis for detecting gene variants that pose a risk of causing disease in the Vietnamese population, increasing the accuracy of biomedical analysis, building models to predict drug effectiveness and disease diagnosis, and genetic analysis.

For example, data from VN1K shows that the HLA-B*15:02 genotype, which is closely related to serious side effects with the epilepsy drug carbamazepine, appears in 23.24% of Vietnamese individuals. This discovery has been applied in the project “The right medicine for children”, helping thousands of children with epilepsy in difficult circumstances receive genetic testing before treatment, reducing the risk of serious drug reactions.

The data also recorded many variations in the PMFBP1 and GCNT2 genes related to a number of specific diseases that appear at a fairly high rate in Vietnamese people, 14.84%, but are rare in Europe, less than 0.5%. In contrast, variants belonging to HNRNPUL2 and BSCL2, which are associated with congenital systemic lipodystrophy and breast cancer, have a prevalence of less than 10% in Vietnamese but are more common in other populations, 28.93% in Europe and 28.12% in South Asia.

In the near future, the team will use VN1K to conduct research “predicting the risk of common cancer, metabolic and aging diseases in Vietnamese people and the ability to respond to commonly used drugs”, Dr. Nam said.

Professor Vu Ha Van said that applications in the future will include preventive health testing, predicting disease risk for lifestyle changes, determining drug responsiveness to select imported pharmaceuticals suitable for the Vietnamese population.

One of the outstanding applications of VN1K to date is VinGenChip, developed by GeneStory, a company co-founded by some members of the research team with investment from Vingroup and a number of other investors, based on the built data set. The chip is capable of simultaneously analyzing tens of thousands of unique genetic variations of Vietnamese people to help identify individuals, predict drug response, screen for disease risk and research population genetics. The product is being used experimentally in the Gene Bank Project for martyrs and their relatives, as well as the 500-day and night campaign to find martyrs’ graves. With optimization on the Vietnamese genome, the chip has high accuracy when matching DNA data of relatives and remains and is many times cheaper than imported solutions.

According to Professor Van, VN1K is a platform that opens application solutions of great value and can be measured, through improving community health, reducing the burden of disease, and increasing treatment effectiveness. These solutions will not be feasible or effective if “imported”, because they are not based on Vietnamese genetic data.

“Personalized medicine based on this research has great potential, however commercialization is still a challenge in the context that the concept of preventive medicine in Vietnam is not yet popular,” he assessed.

According to the research team, the biggest limitation of VN1K currently is that the sample size is relatively small compared to the population size as well as compared to similar data sets in the world. The group hopes to continue to have long-term investment and state participation, similar to major gene decoding projects in the world, to continue expanding research and record more information about the Vietnamese genome.

VN1K is expected not only to be a foundation for large-scale research on genetics and AI in biomedicine in general, but also for many new applications in precision medicine, preventive medicine and personalized health care, contributing to bringing the achievements of genetics, statistics and AI closer to the Vietnamese health system and people.