AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance.

We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a single command line. The analysis results in a report showing the genome structure, genome annotations, antibiotic resistance and virulence profile for each sample. The pan-genome of all samples of the collection is analyzed to identify core- and accessory-genes. Phylogenies of the whole genome as well as all gene clusters are also generated. The toolkit provides a web-based visualization dashboard allowing researchers to interactively examine various aspects of the analysis results. Availability: AMRViz is implemented in Python and NodeJS, and is publicly available under open source MIT license at https://github.com/amromics/amrviz .

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.

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.

A study of genetic variants associated with skin traits in the Vietnamese population.

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.

Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies.

Whole genome sequencing has increasingly become the essential method for studying the genetic mechanisms of antimicrobial resistance and for surveillance of drug-resistant bacterial pathogens. The majority of bacterial genomes sequenced to date have been sequenced with Illumina sequencing technology, owing to its high-throughput, excellent sequence accuracy, and low cost. However, because of the short-read nature of the technology, these assemblies are fragmented into large numbers of contigs, hindering the obtaining of full information of the genome. We develop Pasa, a graph-based algorithm that utilizes the pangenome graph and the assembly graph information to improve scaffolding quality. By leveraging the population information of the bacteria species, Pasa is able to utilize the linkage information of the gene families of the species to resolve the contig graph of the assembly. We show that our method outperforms the current state of the arts in terms of accuracy, and at the same time, is computationally efficient to be applied to a large number of existing draft assemblies.

Classroom aerosol dispersion modeling: experimental assessment of a low-cost flow simulation tool.

The purpose of this study was to assess the utility of a low-cost flow simulation tool for an indoor air modeling application by comparing its outputs with the results of a physical experiment, as well as those from a more advanced computational fluid dynamics (CFD) software package. Five aerosol dispersion tests were performed in two different classrooms by releasing a CO2 tracer gas from six student locations. Resultant steady-state concentrations were monitored at 13 locations around the periphery of the room. Subsequently, the experiments were modeled using both a low-cost tool (SolidWorks Flow Simulation) and a more sophisticated tool (STAR-CCM+). Models were evaluated based on their ability to predict the experimentally measured concentrations at the 13 monitoring locations by calculating four performance parameters commonly used in the evaluation of dispersion models: fractional mean bias (FB), normalized mean-square error (NMSE), fraction of predicted value within a factor of two (FAC2), and normalized absolute difference (NAD). The more sophisticated model performed better in 15 of the 20 possible cases (five tests at four parameters each), with parameters meeting acceptance criteria in 19 of 20 cases. However, the lower-cost tool was only slightly worse, with parameters meeting acceptance criteria in 18 of 20 cases, and it performed better than the other tool in 3 of 20 cases. Because it provides useful results at a fraction of the monetary and training cost and is already widely accessible to many institutions, such a tool may be worthwhile for many indoor aerosol dispersion applications, especially for students or researchers just beginning CFD modeling.

A superconducting nanowire single-photon camera with 400,000 pixels.

For the past 50 years, superconducting detectors have offered exceptional sensitivity and speed for detecting faint electromagnetic signals in a wide range of applications. These detectors operate at very low temperatures and generate a minimum of excess noise, making them ideal for testing the non-local nature of reality1,2, investigating dark matter3,4, mapping the early universe5-7 and performing quantum computation8-10 and communication11-14. Despite their appealing properties, however, there are at present no large-scale superconducting cameras-even the largest demonstrations have never exceeded 20,000 pixels15. This is especially true for superconducting nanowire single-photon detectors (SNSPDs)16-18. These detectors have been demonstrated with system detection efficiencies of 98.0% (ref. 19), sub-3-ps timing jitter20, sensitivity from the ultraviolet21 to the mid-infrared22 and microhertz dark-count rates3, but have never achieved an array size larger than a kilopixel23,24. Here we report on the development of a 400,000-pixel SNSPD camera, a factor of 400 improvement over the state of the art. The array spanned an area of 4 × 2.5 mm with 5 × 5-µm resolution, reached unity quantum efficiency at wavelengths of 370 nm and 635 nm, counted at a rate of 1.1 × 105 counts per second (cps) and had a dark-count rate of 1.0 × 10-4 cps per detector (corresponding to 0.13 cps over the whole array). The imaging area contains no ancillary circuitry and the architecture is scalable well beyond the present demonstration, paving the way for large-format superconducting cameras with near-unity detection efficiencies across a wide range of the electromagnetic spectrum.

EVALUATION OF THE ANTI-CARIES EFFECT OF LESPEDEZA CUNEATA EXTRACT AGAINST STREPTOCOCCUS MUTANS.

The purpose of this study was to identify the antimicrobial activity of Lespedeza cuneata extract, a natural medicine, against a main causative bacterium of dental caries, Streptococcus mutans (S. mutans). Lespedeza cuneata purchased from Hwalim Natural Drug Co., Ltd. (Busan, South Korea) was immersed in 70% ethanol for 12 h, and concentrated Lespedeza cuneata extract was applied to S. mutans diluted to 6×105 CFU/mL at the concentrations of 0, 1.25, 2.5, 5, 10, 20, and 40 mg/ml. Then the colony-forming units (CFUs) were checked at 6 and 24 h to evaluate the antimicrobial activity of the extract. The CFUs and survival rate of S. mutans according to the concentration showed a higher mortality rate as the concentration of Lespedeza cuneata extract increased. In the time-dependent changes, the minimal inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) were 1.25 and 40 mg/mL or more, respectively, at 6 h, but they were 1.25 and 5 mg/mL, respectively, at 24 h. Therefore, Lespedeza cuneata extract is considered an excellent natural antibiotic for the prevention and treatment of dental caries, a typical oral disease, because it has excellent dental caries development suppression and bacteria extermination effects.

Rotational thromboelastometry during Cesarean section as a predictive evaluation for the progression of persistent postpartum hemorrhage in parturients with placenta previa: A prospective observational study.

Background: The rotational thromboelastogram (ROTEM) has been used in the management of massive bleeding and transfusion strategy. This study investigated ROTEM parameters measured during Cesarean section as predictors for the progression of persistent postpartum hemorrhage (PPH) in parturients with placenta previa. Methods: This prospective observational study recruited 100 women scheduled for elective Cesarean section after being diagnosed with placenta previa. Recruited women were divided into two groups according to the amount of estimated blood loss: the PPH group (PPH > 1500 ml) vs. the non-PPH group. ROTEM with laboratory tests was performed three times, preoperative, intraoperative, and postoperative time, which were compared between the two groups. Results: The PPH and non-PPH groups included 57 and 41 women, respectively. The area under the receiver-operating characteristic curve of postoperative FIBTEM A5 to detect PPH was 0.76 (95% CI = 0.64 to 0.87; P < 0.001). When postoperative FIBTEM A5 was 9.5, the sensitivity and specificity were 0.74 (95% CI = 0.55 to 0.88) and 0.73 (95% CI = 0.57 to 0.86), respectively. When subgrouping the PPH group based on the postoperative FIBTEM A5 value of 9.5, intraoperative cEBL was similar between the two subgroups; however, postoperative RBC was transfused more in the subgroup with FIBTEM A5 < 9.5 than the subgroup with FIBTEM A5 ≥ 9.5 (7.4 ± 3.0 vs 5.1 ± 2.3 units, respectively; P = 0.003). Conclusion: Postoperative FIBTEM A5, with appropriate selection of the cut-off value, can be a biomarker for more prolonged PPH and massive transfusion following Cesarean section by placenta previa.

Assessing polygenic risk score models for applications in populations with under-represented genomics data: an example of Vietnam.

Most polygenic risk score (PRS)models have been based on data from populations of European origins (accounting for the majority of the large genomics datasets, e.g. >78% in the UK Biobank and >85% in the GTEx project). Although several large-scale Asian biobanks were initiated (e.g. Japanese, Korean, Han Chinese biobanks), most other Asian countries have little or near-zero genomics data. To implement PRS models for under-represented populations, we explored transfer learning approaches, assuming that information from existing large datasets can compensate for the small sample size that can be feasibly obtained in developing countries, like Vietnam. Here, we benchmark 13 common PRS methods in meta-population strategy (combining individual genotype data from multiple populations) and multi-population strategy (combining summary statistics from multiple populations). Our results highlight the complementarity of different populations and the choice of methods should depend on the target population. Based on these results, we discussed a set of guidelines to help users select the best method for their datasets. We developed a robust and comprehensive software to allow for benchmarking comparisons between methods and proposed a computational framework for improving PRS performance in a dataset with a small sample size. This work is expected to inform the development of genomics applications in under-represented populations. PRSUP framework is available at: https://github.com/BiomedicalMachineLearning/VGP.

A comprehensive evaluation of polygenic score and genotype imputation performances of human SNP arrays in diverse populations.

Regardless of the overwhelming use of next-generation sequencing technologies, microarray-based genotyping combined with the imputation of untyped variants remains a cost-effective means to interrogate genetic variations across the human genome. This technology is widely used in genome-wide association studies (GWAS) at bio-bank scales, and more recently, in polygenic score (PGS) analysis to predict and stratify disease risk. Over the last decade, human genotyping arrays have undergone a tremendous growth in both number and content making a comprehensive evaluation of their performances became more important. Here, we performed a comprehensive performance assessment for 23 available human genotyping arrays in 6 ancestry groups using diverse public and in-house datasets. The analyses focus on performance estimation of derived imputation (in terms of accuracy and coverage) and PGS (in terms of concordance to PGS estimated from whole-genome sequencing data) in three different traits and diseases. We found that the arrays with a higher number of SNPs are not necessarily the ones with higher imputation performance, but the arrays that are well-optimized for the targeted population could provide very good imputation performance. In addition, PGS estimated by imputed SNP array data is highly correlated to PGS estimated by whole-genome sequencing data in most cases. When optimal arrays are used, the correlations of PGS between two types of data are higher than 0.97, but interestingly, arrays with high density can result in lower PGS performance. Our results suggest the importance of properly selecting a suitable genotyping array for PGS applications. Finally, we developed a web tool that provides interactive analyses of tag SNP contents and imputation performance based on population and genomic regions of interest. This study would act as a practical guide for researchers to design their genotyping arrays-based studies. The tool is available at: https://genome.vinbigdata.org/tools/saa/ .

LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays.

Despite the rapid development of sequencing technology, single-nucleotide polymorphism (SNP) arrays are still the most cost-effective genotyping solutions for large-scale genomic research and applications. Recent years have witnessed the rapid development of numerous genotyping platforms of different sizes and designs, but population-specific platforms are still lacking, especially for those in developing countries. SNP arrays designed for these countries should be cost-effective (small size), yet incorporate key information needed to associate genotypes with traits. A key design principle for most current platforms is to improve genome-wide imputation so that more SNPs not included in the array (imputed SNPs) can be predicted. However, current tag SNP selection methods mostly focus on imputation accuracy and coverage, but not the functional content of the array. It is those functional SNPs that are most likely associated with traits. Here, we propose LmTag, a novel method for tag SNP selection that not only improves imputation performance but also prioritizes highly functional SNP markers. We apply LmTag on a wide range of populations using both public and in-house whole-genome sequencing databases. Our results show that LmTag improved both functional marker prioritization and genome-wide imputation accuracy compared to existing methods. This novel approach could contribute to the next generation genotyping arrays that provide excellent imputation capability as well as facilitate array-based functional genetic studies. Such arrays are particularly suitable for under-represented populations in developing countries or non-model species, where little genomics data are available while investment in genome sequencing or high-density SNP arrays is limited. $\textrm{LmTag}$ is available at: https://github.com/datngu/LmTag.