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Nguyen TK, Vu GM, Duong VC, Pham TL, Nguyen NT, Tran TTH, Tran MH, Nguyen DT, Vo NS, Phung HT, Hoang TH. The therapeutic landscape for COVID-19 and post-COVID-19 medications from genetic profiling of the Vietnamese population and a predictive model of drug-drug interaction for comorbid COVID-19 patients. Heliyon 2024; 10:e27043. [PMID: 38509882 PMCID: PMC10950508 DOI: 10.1016/j.heliyon.2024.e27043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 12/13/2023] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
Despite the raised awareness of the role of pharmacogenomic (PGx) in personalized medicines for COVID-19, data for COVID-19 drugs is extremely scarce and not even a publication on this topic for post-COVID-19 medications to date. In the current study, we investigated the genetic variations associated with COVID-19 and post-COVID-19 therapies by using whole genome sequencing data of the 1000 Vietnamese Genomes Project (1KVG) in comparison with other populations retrieved from the 1000 Genomes Project Phase 3 (1KGP3) and the Genome Aggregation Database (gnomAD). Moreover, we also evaluated the risk of drug interactions in comorbid COVID-19 and post-COVID-19 patients based on pharmacogenomic profiles of drugs using a computational approach. For COVID-19 therapies, variants related to the response of two causal treatment agents (tolicizumab and ritonavir) and antithrombotic drugs are common in the Vietnamese cohort. Regarding post-COVID-19, drugs for mental manipulations possess the highest number of clinical annotated variants carried by Vietnamese individuals. Among the superpopulations, East Asian populations shared the most similar genetic structure with the Vietnamese population, whereas the African population showed the most difference. Comorbid patients are at an increased drug-drug interaction (DDI) risk when suffering from COVID-19 and after recovering as well due to a large number of potential DDIs which have been identified. Our results presented the population-specific understanding of the pharmacogenomic aspect of COVID-19 and post-COVID-19 therapy to optimize therapeutic outcomes and promote personalized medicine strategy. We also partly clarified the higher risk in COVID-19 patients with underlying conditions by assessing the potential drug interactions.
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Affiliation(s)
| | - Giang Minh Vu
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Viet Nam
- GeneStory JSC, Hanoi, Viet Nam
| | - Vinh Chi Duong
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Viet Nam
- GeneStory JSC, Hanoi, Viet Nam
| | | | | | - Trang Thi Ha Tran
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Viet Nam
- GeneStory JSC, Hanoi, Viet Nam
| | - Mai Hoang Tran
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Viet Nam
- GeneStory JSC, Hanoi, Viet Nam
| | - Duong Thuy Nguyen
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Viet Nam
- GeneStory JSC, Hanoi, Viet Nam
| | - Nam S. Vo
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Viet Nam
- GeneStory JSC, Hanoi, Viet Nam
| | - Huong Thanh Phung
- Faculty of Biotechnology, Hanoi University of Pharmacy, Hanoi, Viet Nam
| | - Tham Hong Hoang
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Viet Nam
- GeneStory JSC, Hanoi, Viet Nam
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Hoang TH, Vu DM, Vu GM, Nguyen TK, Do NM, Duong VC, Pham TL, Tran MH, Khanh Nguyen LT, Han HTT, Can TT, Pham TH, Pham TD, Nguyen TH, Do HP, Vo NS, Nguyen XH. A study of genetic variants associated with skin traits in the Vietnamese population. BMC Genomics 2024; 25:52. [PMID: 38212682 PMCID: PMC10785522 DOI: 10.1186/s12864-023-09932-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/20/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Most skin-related traits have been studied in Caucasian genetic backgrounds. A comprehensive study on skin-associated genetic effects on underrepresented populations such as Vietnam is needed to fill the gaps in the field. OBJECTIVES We aimed to develop a computational pipeline to predict the effect of genetic factors on skin traits using public data (GWAS catalogs and whole-genome sequencing (WGS) data from the 1000 Genomes Project-1KGP) and in-house Vietnamese data (WGS and genotyping by SNP array). Also, we compared the genetic predispositions of 25 skin-related traits of Vietnamese population to others to acquire population-specific insights regarding skin health. METHODS Vietnamese cohorts of whole-genome sequencing (WGS) of 1008 healthy individuals for the reference and 96 genotyping samples (which do not have any skin cutaneous issues) by Infinium Asian Screening Array-24 v1.0 BeadChip were employed to predict skin-associated genetic variants of 25 skin-related and micronutrient requirement traits in population analysis and correlation analysis. Simultaneously, we compared the landscape of cutaneous issues of Vietnamese people with other populations by assessing their genetic profiles. RESULTS The skin-related genetic profile of Vietnamese cohorts was similar at most to East Asian cohorts (JPT: Fst = 0.036, CHB: Fst = 0.031, CHS: Fst = 0.027, CDX: Fst = 0.025) in the population study. In addition, we identified pairs of skin traits at high risk of frequent co-occurrence (such as skin aging and wrinkles (r = 0.45, p = 1.50e-5) or collagen degradation and moisturizing (r = 0.35, p = 1.1e-3)). CONCLUSION This is the first investigation in Vietnam to explore genetic variants of facial skin. These findings could improve inadequate skin-related genetic diversity in the currently published database.
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Affiliation(s)
- Tham Hong Hoang
- GeneStory JSC, Hanoi, Vietnam
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam
| | - Duc Minh Vu
- Hi-Tech Center and Vinmec-VinUni Institute of Immunology, Vinmec Healthcare System, Hanoi, Vietnam
| | - Giang Minh Vu
- GeneStory JSC, Hanoi, Vietnam
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam
| | | | | | - Vinh Chi Duong
- GeneStory JSC, Hanoi, Vietnam
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam
| | | | - Mai Hoang Tran
- GeneStory JSC, Hanoi, Vietnam
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam
| | | | | | - Thu-Thuy Can
- Vinmec Times City International Hospital, Vinmec Healthcare System, Hanoi, Vietnam
| | | | - Tho Duc Pham
- View Plastic Surgery Center, Vinmec, Hanoi, Vietnam
| | - Thanh Hong Nguyen
- Hi-Tech Center and Vinmec-VinUni Institute of Immunology, Vinmec Healthcare System, Hanoi, Vietnam
| | | | - Nam S Vo
- GeneStory JSC, Hanoi, Vietnam.
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam.
| | - Xuan-Hung Nguyen
- Hi-Tech Center and Vinmec-VinUni Institute of Immunology, Vinmec Healthcare System, Hanoi, Vietnam.
- College of Health Sciences, VinUniversity, Hanoi, Vietnam.
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Chi Duong V, Minh Vu G, Khac Nguyen T, Tran The Nguyen H, Luong Pham T, S Vo N, Hong Hoang T. A rapid and reference-free imputation method for low-cost genotyping platforms. Sci Rep 2023; 13:23083. [PMID: 38155188 PMCID: PMC10754833 DOI: 10.1038/s41598-023-50086-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 12/15/2023] [Indexed: 12/30/2023] Open
Abstract
Most current genotype imputation methods are reference-based, which posed several challenges to users, such as high computational costs and reference panel inaccessibility. Thus, deep learning models are expected to create reference-free imputation methods performing with higher accuracy and shortening the running time. We proposed a imputation method using recurrent neural networks integrating with an additional discriminator network, namely GRUD. This method was applied to datasets from genotyping chips and Low-Pass Whole Genome Sequencing (LP-WGS) with the reference panels from The 1000 Genomes Project (1KGP) phase 3, the dataset of 4810 Singaporeans (SG10K), and The 1000 Vietnamese Genome Project (VN1K). Our model performed more accurately than other existing methods on multiple datasets, especially with common variants with large minor allele frequency, and shrank running time and memory usage. In summary, these results indicated that GRUD can be implemented in genomic analyses to improve the accuracy and running-time of genotype imputation.
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Affiliation(s)
- Vinh Chi Duong
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam
- GeneStory Joint Stock Company, Hanoi, Vietnam
| | - Giang Minh Vu
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam
- GeneStory Joint Stock Company, Hanoi, Vietnam
| | | | - Hung Tran The Nguyen
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam
- Nanyang Technological University, Singapore, Singapore
| | | | - Nam S Vo
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam.
- GeneStory Joint Stock Company, Hanoi, Vietnam.
| | - Tham Hong Hoang
- Center for Biomedical Informatics, Vingroup Big Data Institute, Hanoi, Vietnam.
- GeneStory Joint Stock Company, Hanoi, Vietnam.
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