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1.
Heliyon ; 10(6): e27043, 2024 Mar 30.
Article in English | MEDLINE | ID: mdl-38509882

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.

2.
BMC Genomics ; 25(1): 52, 2024 Jan 11.
Article in English | MEDLINE | ID: mdl-38212682

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.


Subject(s)
Genetic Predisposition to Disease , Polymorphism, Single Nucleotide , Skin , Southeast Asian People , Humans , Genome-Wide Association Study , Phenotype , Vietnam
3.
Sci Rep ; 13(1): 23083, 2023 12 27.
Article in English | MEDLINE | ID: mdl-38155188

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.


Subject(s)
Genome , Polymorphism, Single Nucleotide , Humans , Genotype , Gene Frequency , Genome-Wide Association Study/methods , Genotyping Techniques/methods
4.
Pediatr Infect Dis J ; 42(10): e366-e368, 2023 10 01.
Article in English | MEDLINE | ID: mdl-37729666

ABSTRACT

A cross-sectional study was conducted on 205 pediatric patients, including 150 post-COVID-19 patients and 55 noninfected patients. The study identified 10 common respiratory symptoms in post-COVID-19 patients, with significant differences in clinical symptoms between the 2 groups. Post-COVID-19 pediatric patients had a lower lymphocyte count and a higher rate of pneumonia diagnosis, which can persist for up to 16 weeks after discharge. The study's findings can help monitor and manage the clinical burden of post-COVID-19 symptoms in the pediatric population.


Subject(s)
COVID-19 , Child, Hospitalized , Humans , Child , Post-Acute COVID-19 Syndrome , Vietnam/epidemiology , Cross-Sectional Studies , COVID-19/epidemiology
5.
IEEE Trans Image Process ; 32: 1215-1230, 2023.
Article in English | MEDLINE | ID: mdl-37022797

ABSTRACT

Plenoptic images and videos bearing rich information demand a tremendous amount of data storage and high transmission cost. While there has been much study on plenoptic image coding, investigations into plenoptic video coding have been very limited. We investigate the motion compensation (or so-called temporal prediction) for plenoptic video coding from a slightly different perspective by looking at the problem in the ray-space domain instead of in the conventional pixel domain. Here, we develop a novel motion compensation scheme for lenslet video under two sub-cases of ray-space motion, that is, integer ray-space motion and fractional ray-space motion. The proposed new scheme of light field motion-compensated prediction is designed such that it can be easily integrated into well-known video coding techniques such as HEVC. Experimental results compared to relevant existing methods have shown remarkable compression efficiency with an average gain of 20.03% and 21.76% respectively under "Low delayed B " and "Random Access" configurations of HEVC.

6.
PeerJ ; 9: e12413, 2021.
Article in English | MEDLINE | ID: mdl-34760393

ABSTRACT

This study aims to understand the spatial distribution of coral reefs in the central region of Viet Nam. We classified live coral cover in Son Tra Peninsula (ST) and Cu Lao Cham Island (CLC) in the South-Central Coast Region of Viet Nam using the Maximum Likelihood Classifier on 3 m Planetscope imagery. Confusion matrices and the accuracy of the classifier were assessed using field data (1,543 and 1,560 photographs in ST and CLC, respectively). The results showed that the reef's width ranged from 30 to 300 m across the study site, and we were able to detect live coral cover across a depth gradient of 2 to 6 m below the sea surface. The overall accuracies of the classifier (the Kappa coefficient) were 76.78% (0.76) and 78.08% (0.78) for ST and CLC, respectively. We found that 60.25% of coral reefs in ST were unhealthy and the live coral cover was less than 50%, while 25.75% and 11.46% of those in CLC were in good and excellent conditions, respectively. This study demonstrates the feasibility of utilizing Planetscope imagery to monitor shallow coral reefs of small islands at a high spatial resolution of 3 m. The results of this study provide valuable information for coral reef protection and conservation.

8.
J Biol Chem ; 285(40): 30918-30, 2010 Oct 01.
Article in English | MEDLINE | ID: mdl-20663866

ABSTRACT

The catalytic domain of metalloelastase (matrix metalloproteinase-12 or MMP-12) is unique among MMPs in exerting high proteolytic activity upon fibrils that resist hydrolysis, especially elastin from lungs afflicted with chronic obstructive pulmonary disease or arteries with aneurysms. How does the MMP-12 catalytic domain achieve this specificity? NMR interface mapping suggests that α-elastin species cover the primed subsites, a strip across the ß-sheet from ß-strand IV to the II-III loop, and a broad bowl from helix A to helix C. The many contacts may account for the comparatively high affinity, as well as embedding of MMP-12 in damaged elastin fibrils in vivo. We developed a strategy called BINDSIght, for bioinformatics and NMR discovery of specificity of interactions, to evaluate MMP-12 specificity without a structure of a complex. BINDSIght integration of the interface mapping with other ambiguous information from sequences guided choice mutations in binding regions nearer the active site. Single substitutions at each of ten locations impair specific activity toward solubilized elastin. Five of them impair release of peptides from intact elastin fibrils. Eight lesions also impair specific activity toward triple helices from collagen IV or V. Eight sites map to the "primed" side in the III-IV, V-B, and S1' specificity loops. Two map to the "unprimed" side in the IV-V and B-C loops. The ten key residues circumscribe the catalytic cleft, form an exosite, and are distinctive features available for targeting by new diagnostics or therapeutics.


Subject(s)
Collagen/chemistry , Elastin/chemistry , Matrix Metalloproteinase 12/chemistry , Amino Acid Substitution , Collagen/genetics , Collagen/metabolism , Computational Biology , Elastin/genetics , Elastin/metabolism , Humans , Matrix Metalloproteinase 12/genetics , Matrix Metalloproteinase 12/metabolism , Mutation, Missense , Nuclear Magnetic Resonance, Biomolecular , Protein Structure, Secondary , Solubility , Substrate Specificity/physiology
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