VN1K is a pangenome-informed multi-omics and phenomics resource for the Vietnamese population
The population of Vietnam remains underrepresented in global genomic databases. Here, we present VN1K, a resource of multi-omics and phenotypic information for 1011 unrelated Vietnamese individuals. We present high-depth short-read whole-genome sequencing data for all samples along with various -omics datasets. Using a high-sensitivity variant detection pipeline, which includes a pangenome graph reference and a deep-learning framework, we identify approximately 42 million variants with 7 million short insertions/deletions and 90 thousand structural variants. VN1K also features a whole-genome methylation profile based on long read sequencing. We create a genotype imputation panel with high accuracy on the Vietnamese population, allowing us to identify variants with significantly different allele frequencies in the Vietnamese population compared to other populations. We establish the functional relevance of some of these variants, particularly those in genes associated with genetic disorders, immune diseases, and drug responses, by integrating the allele frequency differences with known genotype–phenotype associations and clinical annotations. Further, we map various loci related to hepatitis B virus infection, triglyceride levels, LDL-C levels, serum glucose levels, HbA1c levels, and levels of two liver enzymes (ALT and AST). The VN1K dataset is accessible via genome.vinbigdata.org, an integrated platform with both linear and graph-based genome browsers. The population of Vietnam remains underrepresented in global genomic databases. Here, the authors launch VN1K, a pangenome-informed multi-omics resource for the Vietnamese population.
Authors
- Vinh Duong
- Y Hoang (ORCID: https://orcid.org/0000-0001-8804-534X)
- Duc Vu (ORCID: https://orcid.org/0000-0001-8932-2142)
- Quang‐Huy Nguyen (ORCID: https://orcid.org/0000-0002-9978-8920)
- Trang T. H. Tran (ORCID: https://orcid.org/0000-0002-3605-3193)
- Nam Q. Le (ORCID: https://orcid.org/0000-0001-9266-0054)
- Duc‐Hau Le (ORCID: https://orcid.org/0000-0002-4951-5916)
- Nam S. Vo (ORCID: https://orcid.org/0000-0002-5454-9176)
- Vu Gt
- Chi Trung Ha (ORCID: https://orcid.org/0000-0001-8413-7263)
- Tuan Do (ORCID: https://orcid.org/0000-0001-9554-6062)
- Vu Quoc Hien (ORCID: https://orcid.org/0000-0002-9259-8382)
- Tien M. Pham (ORCID: https://orcid.org/0000-0002-3517-1876)
- Hung Nguyen (ORCID: https://orcid.org/0000-0003-0174-6659)
- Quang Tran (ORCID: https://orcid.org/0009-0004-6314-3903)
- Huong Le (ORCID: https://orcid.org/0009-0005-8854-900X)
- Nguyen Minh Trang (ORCID: https://orcid.org/0000-0002-0438-8538)
- Sang Van Nguyen (ORCID: https://orcid.org/0000-0002-5252-3386)
- Mai H. Tran
- Thien K. Nguyen
- Liem T. Nguyen
- Quan Nguyen
- Hung N. Luu
- Nguyen Thuy Duong
- Ly Le
- Giang H. Phan (ORCID: https://orcid.org/0009-0005-2068-2840)
- Linh T. Le
- Thinh Tran
- Nam N. Nguyen (ORCID: https://orcid.org/0000-0002-6329-585X)
- Tho D. Ngo
- Quang T. Vu
- Tham H. Hoang
- Thang Pham
- Loan Nguyen
- Minh Dao
- Cuong Le
- Nguyen T. Nguyen
- Vinh S. Le
- Van Vu
- Hoang Nguyen
- Dat T. Nguyen
- Toan Dang
- Dat X. Dao
Institutions
- Houston Methodist (US)
- The University of Texas MD Anderson Cancer Center (US)
- The University of Queensland (AU)
- Vietnam National University, Hanoi (VN)
- Hanoi Medical University (VN)
- Cornell University (US)
- Vinmec Times City International Hospital (VN)
- Agriculture and Food (AU)
- VinUniversity (VN)
- Hanoi University (VN)
- Vietnam Academy of Science and Technology (VN)
- Hanoi University of Science and Technology (VN)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-07-22
- DOI
- https://doi.org/10.1038/s41467-026-75375-0
- Primary Topic
- Genetic Associations and Epidemiology
- Type
- article
- Field-Weighted Citation Impact
- 0.00