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Journal articles on the topic 'HTS sequencing'

Author: Grafiati

Published: 9 March 2023

Last updated: 31 July 2025

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1

Vuorio, Kristiina, Anita Mäki, Pauliina Salmi, Sanni Aalto, Marja Tiirola, and Marko Järvinen. "Consistency between high throughput sequencing and microscopy-based morphological characterization of phytoplankton communities." ARPHA Conference Abstracts 4 (March 4, 2021): e64972. https://doi.org/10.3897/aca.4.e64972.

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Thus far, the phytoplankton community composition analyses, used e.g. monitoring and assessment of the ecological status of water bodies, are based on time-consuming and expertise-demanding light microscopy analyses. Currently, DNA-based molecular tools are being developed to replace microscopy-based analyses. Although most of the DNA is expected to be found in living cells, long-lasting DNA in damaged cells or soluble extracellular or relic DNA can make up a large proportion of the total DNA in water samples. DNA-based phytoplankton analysis has been shown to be affected by the huge variation

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Komarova, Natalia, Daria Barkova, and Alexander Kuznetsov. "Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology." International Journal of Molecular Sciences 21, no. 22 (2020): 8774. http://dx.doi.org/10.3390/ijms21228774.

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Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HT

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3

Pérez-Losada, Marcos, Miguel Arenas, Juan Carlos Galán, et al. "High-throughput sequencing (HTS) for the analysis of viral populations." Infection, Genetics and Evolution 80 (June 2020): 104208. http://dx.doi.org/10.1016/j.meegid.2020.104208.

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He, Xuejun, Ningzhi Zhang, Wenye Cao, Yiqiao Xing, and Ning Yang. "Application Progress of High-Throughput Sequencing in Ocular Diseases." Journal of Clinical Medicine 11, no. 12 (2022): 3485. http://dx.doi.org/10.3390/jcm11123485.

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Ocular diseases affect multiple eye parts and can be caused by pathogenic infections, complications of systemic diseases, genetics, environment, and old age. Understanding the etiology and pathogenesis of eye diseases and improving their diagnosis and treatment are critical for preventing any adverse consequences of these diseases. Recently, the advancement of high-throughput sequencing (HTS) technology has paved wide prospects for identifying the pathogenesis, signaling pathways, and biomarkers involved in eye diseases. Due to the advantages of HTS in nucleic acid sequence recognition, HTS ha

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GIZA, ALEKSANDRA, EWELINA IWAN, ARKADIUSZ BOMBA, and DARIUSZ WASYL. "Basics of high throughput sequencing Summary." Medycyna Weterynaryjna 77, no. 11 (2025): 6589–2025. http://dx.doi.org/10.21521/mw.6594.

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Sequencing can provide genomic characterisation of a specific organism, as well as of a whole environmental or clinical sample. High Throughput Sequencing (HTS) makes it possible to generate an enormous amount of genomic data at gradually decreasing costs and almost in real-time. HTS is used, among others, in medicine, veterinary medicine, microbiology, virology and epidemiology. The paper presents practical aspects of the HTS technology. It describes generations of sequencing, which vary in throughput, read length, accuracy and costs ̶ and thus are used for different applications. The stages

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Aronesty, Erik. "Comparison of Sequencing Utility Programs." Open Bioinformatics Journal 7, no. 1 (2013): 1–8. http://dx.doi.org/10.2174/1875036201307010001.

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High throughput sequencing (HTS) has resulted in extreme growth rates of sequencing data. At our lab, we generate terabytes of data every day. It is usually seen as required for data output to be “cleaned” and processed in various ways prior to use for common tasks such as variant calling, expression quantification and assembly. Two common tasks associated with HTS are adapter trimming and paired-end joining. I have developed two tools at Expression Analysis, Inc. to address these common tasks. The names of these programs are fastq-mcf and fastq-join. I compared the performance of these tools

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Pu, Dan, and Pengfeng Xiao. "A real-time decoding sequencing technology—new possibility for high throughput sequencing." RSC Advances 7, no. 64 (2017): 40141–51. http://dx.doi.org/10.1039/c7ra06202h.

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Malapi-Wight, Martha, Bishwo Adhikari, Jing Zhou, et al. "HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection." Viruses 13, no. 8 (2021): 1627. http://dx.doi.org/10.3390/v13081627.

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Rapid global germplasm trade has increased concern about the spread of plant pathogens and pests across borders that could become established, affecting agriculture and environment systems. Viral pathogens are of particular concern due to their difficulty to control once established. A comprehensive diagnostic platform that accurately detects both known and unknown virus species, as well as unreported variants, is playing a pivotal role across plant germplasm quarantine programs. Here we propose the addition of high-throughput sequencing (HTS) from total RNA to the routine quarantine diagnosti

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Ma, Hailun, Trent J. Bosma, and Arifa S. Khan. "Long-Read High-Throughput Sequencing (HTS) Revealed That the Sf-Rhabdovirus X+ Genome Contains a 3.7 kb Internal Duplication." Viruses 15, no. 10 (2023): 1998. http://dx.doi.org/10.3390/v15101998.

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We previously reported a novel rhabdovirus produced from the Spodoptera frugiperda Sf9 cell line, designated as Sf-rhabdovirus X+ since it contained a unique accessory gene X. The Sf-rhabdovirus X+ genome sequence was generated using Sanger sequencing and short-read high-throughput sequencing (HTS). In this study, we have used long-read HTS technologies, PacBio’s single-molecule real-time sequencing and Oxford’s Nanopore RNA direct sequencing, to analyze the parent Sf9 cell line transcriptome and the virus RNA produced from an X+ cell clone, respectively. A unique 3.7 kb duplication was identi

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Bester, Rachelle, Chanel Steyn, Johannes H. J. Breytenbach, Rochelle de Bruyn, Glynnis Cook, and Hans J. Maree. "Reproducibility and Sensitivity of High-Throughput Sequencing (HTS)-Based Detection of Citrus Tristeza Virus and Three Citrus Viroids." Plants 11, no. 15 (2022): 1939. http://dx.doi.org/10.3390/plants11151939.

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The credibility of a pathogen detection assay is measured using specific parameters including repeatability, specificity, sensitivity, and reproducibility. The use of high-throughput sequencing (HTS) as a routine detection assay for viruses and viroids in citrus was previously evaluated and, in this study, the reproducibility and sensitivity of the HTS assay were assessed. To evaluate the reproducibility of HTS, the same plants assayed in a previous study were sampled again, one year later, and assessed in triplicate using the same analyses to construct the virome profile. The sensitivity of t

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Droege, Gabriele, Jonas Zimmermann, Tim Fulcher, der Linde Sietse Van, and Walter Berendsohn. "Environmental samples, eDNA and HTS libraries – data standard proposals from the Global Genome Biodiversity Network (GGBN)." Biodiversity Information Science and Standards 1 (August 21, 2017): e20483. https://doi.org/10.3897/tdwgproceedings.1.20483.

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The GGBN Data Portal (http://www.ggbn.org, Droege et al. 2014) has established standardised data flows for genomic DNA samples, including voucher specimens, tissue samples, DNA samples as well as resulting sequences and publications. Dealing with different types of DNA (aDNA, gDNA, eDNA) is essential and closely related to user-friendly search and display functionalities. GGBN aims both at preserving voucher specimens of all kinds of DNA as well as making these important data accessible on the Internet. In addition to genomic DNA, the development and use of high-throughput-/next-generation-seq

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Bester, Rachelle, Glynnis Cook, and Hans J. Maree. "Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing." Viruses 13, no. 2 (2021): 168. http://dx.doi.org/10.3390/v13020168.

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The application of high-throughput sequencing (HTS) has successfully been used for virus discovery to resolve disease etiology in many agricultural crops. The greatest advantage of HTS is that it can provide a complete viral status of a plant, including information on mixed infections of viral species or virus variants. This provides insight into the virus population structure, ecology, or evolution and can be used to differentiate among virus variants that may contribute differently toward disease etiology. In this study, the use of HTS for citrus tristeza virus (CTV) genotype detection was e

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Kunej, Urban, Aida Dervishi, Valérie Laucou, Jernej Jakše, and Nataša Štajner. "The Potential of HTS Approaches for Accurate Genotyping in Grapevine (Vitis vinifera L.)." Genes 11, no. 8 (2020): 917. http://dx.doi.org/10.3390/genes11080917.

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The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electrophoresis (CE) approaches limit the information to the length polymorphism and do not allow the determination of a complete marker sequence. As an alternative, high-throughput sequencing (HTS) offers complete information regarding marker sequences and their flanking regions. In this work, we investigated the suitability of a semi-quantitative seque

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WANG, MINGBANG, XIAOMEI FAN, TAO WANG, and JINYU WU. "High-throughput sequencing of autism spectrum disorders comes of age." Genetics Research 95, no. 4 (2013): 121–29. http://dx.doi.org/10.1017/s0016672313000153.

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SummaryAutism spectrum disorders (ASDs) are lifelong neurodevelopmental disabilities that affect 1 in 88 children in the USA. Despite the high heritability, the genetic basis for a majority of the ASDs remains elusive. The considerable clinical and genetic heterogeneity pose a significant challenge technically. State-of-the-art high-throughput sequencing (HTS), which makes the analyses of any specific single/multiple genes or whole exomes feasible, has shown a promising perspective in disease gene discovery. To date, numerous genetic studies using HTS have been reported and many rare inherited

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Fuentes, Azahara, Alicia Serrano, Blanca Ferrer Lores, et al. "Ighv Mutational Status By Deep Next Generation Sequencing Refines Ighv Sanger Sequencing Classification in Patients with Chronic Lymphocytic Leukaemia." Blood 134, Supplement_1 (2019): 3028. http://dx.doi.org/10.1182/blood-2019-129145.

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Introduction: Determination of the mutational status of rearranged immunoglobulin heavy chain variable (IgHV) genes in patients with Chronic Lymphocytic Leukaemia (CLL), is considered one of the most important prognostic factors: patients with unmutated IgHV (UM; ≥98% of identity to the germline) genes have a more aggressive disease course and develop more frequently unfavourable genetic deletions or mutations than patients with mutated IgHV (M; ≤98%). Mutational status, is currently determined by Sanger sequencing (Sseq) that allows the analysis of the major clone, however, international guid

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GIZA, ALEKSANDRA, EWELINA IWAN, and DARIUSZ WASYL. "Application of high throughput sequencing in veterinary science." Medycyna Weterynaryjna 78, no. 02 (2022): 6622–2022. http://dx.doi.org/10.21521/mw.6622.

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High throughput sequencing (HTS) creates an opportunity for comprehensive genomic studies. It can be applied in veterinary science, bacteriology and virology, diagnostics of animal diseases, food safety, examinations of the composition of environmental samples, and even in veterinary vaccinology. Thus HTS a wide-ranging method that can be applied in different areas of the One Health approach. In particular, the whole genome sequencing (WGS) of bacteria is routinely used in food hygiene and outbreak investigations for phylogenetic analysis of pathogenic bacteria isolated from various sources ac

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Ness, Tara E., Andrew DiNardo, and Maha R. Farhat. "High Throughput Sequencing for Clinical Tuberculosis: An Overview." Pathogens 11, no. 11 (2022): 1343. http://dx.doi.org/10.3390/pathogens11111343.

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High throughput sequencing (HTS) can identify the presence of Mycobacterium tuberculosis DNA in a clinical sample while also providing information on drug susceptibility. Multiple studies have provided a context for exploring the clinical application of HTS for TB diagnosis. The workflow challenges, strengths and limitations of the various sequencing platforms, and tools used for analysis are presented to provide a framework for further innovations in the field.

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Xu, Chonghe, Dangui Zhou, and Mei Zhu. "High throughput sequencing technology and its clinical application in circulating tumor DNA detection in patients with tumors." Investigación Clínica 65, no. 4 (2024): 476–94. https://doi.org/10.54817/ic.v65n4a09.

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The high-throughput sequencing (HTS) is now a highly favoured technology in the field of genome research. A distinctive feature of this sequenc-ing method is its data-yielding capability, which is capable of generating more than 100 times than the first-generation Sanger sequencing platform. HTS technology has been widely adopted for its advantages, including high through-put, sensitivity, automaticity, information density and cost-effectiveness. Not only does it help in the treatment and diagnosis of multiple diseases, but it also provides new insights into the research in molecular biology o

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Boegel, Sebastian, John C. Castle, and Andreas Schwarting. "Current status of use of high throughput nucleotide sequencing in rheumatology." RMD Open 7, no. 1 (2021): e001324. http://dx.doi.org/10.1136/rmdopen-2020-001324.

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ObjectiveHere, we assess the usage of high throughput sequencing (HTS) in rheumatic research and the availability of public HTS data of rheumatic samples.MethodsWe performed a semiautomated literature review on PubMed, consisting of an R-script and manual curation as well as a manual search on the Sequence Read Archive for public available HTS data.ResultsOf the 699 identified articles, rheumatoid arthritis (n=182 publications, 26%), systemic lupus erythematous (n=161, 23%) and osteoarthritis (n=152, 22%) are among the rheumatic diseases with the most reported use of HTS assays. The most repre

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Villamor, D. E. V., T. Ho, M. Al Rwahnih, R. R. Martin, and I. E. Tzanetakis. "High Throughput Sequencing For Plant Virus Detection and Discovery." Phytopathology® 109, no. 5 (2019): 716–25. http://dx.doi.org/10.1094/phyto-07-18-0257-rvw.

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Over the last decade, virologists have discovered an unprecedented number of viruses using high throughput sequencing (HTS), which led to the advancement of our knowledge on the diversity of viruses in nature, particularly unraveling the virome of many agricultural crops. However, these new virus discoveries have often widened the gaps in our understanding of virus biology; the forefront of which is the actual role of a new virus in disease, if any. Yet, when used critically in etiological studies, HTS is a powerful tool to establish disease causality between the virus and its host. Conversely

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Kurtz, David M., Michael R. Green, Scott V. Bratman, et al. "Noninvasive monitoring of diffuse large B-cell lymphoma by immunoglobulin high-throughput sequencing." Blood 125, no. 24 (2015): 3679–87. http://dx.doi.org/10.1182/blood-2015-03-635169.

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Key Points DLBCL can be detected in the blood by immunoglobulin high-throughput sequencing (Ig-HTS) with high specificity. Although DLBCL can be detected in leukocytes or plasma by Ig-HTS, plasma has greater sensitivity and more accurately reflects disease.

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Glasa, Miroslav, Katarína Šoltys, Lukáš Predajňa, et al. "High-throughput sequencing of Potato virus M from tomato in Slovakia reveals a divergent variant of the virus." Plant Protection Science 55, No. 3 (2019): 159–66. http://dx.doi.org/10.17221/144/2018-pps.

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High-throughput sequencing (HTS) analysis of tomato (Solanum lycopersicum) samples revealed the presence of Potato virus M (PVM) in this crop in Slovakia. Full-length genomes of three PVM isolates were obtained using both HTS and Sanger sequencing validation. While two isolates (T40 and T50) were shown to belong to major Group I, a divergent T20 isolate was phylogenetically unrelated to any known PVM variant, potentially representing a new phylogenetic group. Despite a relatively high intraspecies diversity (17.3 ± 0.3%), no evidence of recombination was detected in the dataset of available co

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Wu, David, Ryan O. Emerson, Anna Sherwood, et al. "Robust Detection Of Minimal Residual Disease In Unselected Patients With B-Cell Precursor Acute Lymphoblastic Leukemia By High-Throughput Sequencing Of IGH." Blood 122, no. 21 (2013): 2550. http://dx.doi.org/10.1182/blood.v122.21.2550.2550.

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Abstract High-throughput sequencing (HTS) of immunoglobulin heavy chain genes (IGH) may be useful for detecting minimal residual disease (MRD) in acute lymphoblastic leukemia. We previously demonstrated the first application of high-throughput sequencing for the detection of minimal residual disease in T-cell precursor acute lymphoblastic leukemia (TPC-ALL) (Sci. Transl. Med. 4(134):134ra63. 2012). Recently, Faham and colleagues considered deep sequencing for MRD detection in B-cell precursor acute lymphoblastic leukemia (BPC-ALL) (Blood 120(26):5173-80, 2012). As this prior analysis in BPC-AL

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Javaran, Vahid Jalali, Peter Moffett, Pierre Lemoyne, Dong Xu, Charith Raj Adkar-Purushothama, and Mamadou Lamine Fall. "Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics." Plants 10, no. 11 (2021): 2355. http://dx.doi.org/10.3390/plants10112355.

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Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facing outbreaks of known and emerging viral diseases across the world. Although high-throughput sequencing (HTS) has been used extensively in grapevine virology, the application and potential of third-generation sequencing have not been explored in understanding grapevine viruses and their impact on the

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Espindola, Andres S., and Kitty F. Cardwell. "Microbe Finder (MiFi®): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data." Plants 10, no. 2 (2021): 250. http://dx.doi.org/10.3390/plants10020250.

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Agricultural high throughput diagnostics need to be fast, accurate and have multiplexing capacity. Metagenomic sequencing is being widely evaluated for plant and animal diagnostics. Bioinformatic analysis of metagenomic sequence data has been a bottleneck for diagnostic analysis due to the size of the data files. Most available tools for analyzing high-throughput sequencing (HTS) data require that the user have computer coding skills and access to high-performance computing. To overcome constraints to most sequencing-based diagnostic pipelines today, we have developed Microbe Finder (MiFi®). M

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Nellimarla, Srinivas, and Prasad Kesanakurti. "Next-Generation Sequencing: A Promising Tool for Vaccines and Other Biological Products." Vaccines 11, no. 3 (2023): 527. http://dx.doi.org/10.3390/vaccines11030527.

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Next-generation sequencing (NGS), also known as high-throughput sequencing (HTS), is a commonly used term to represent a set of DNA sequencing technologies that have been in use for almost two decades [...]

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Soltani, Nourolah, Kristian A. Stevens, Vicki Klaassen, Min-Sook Hwang, Deborah A. Golino, and Maher Al Rwahnih. "Quality Assessment and Validation of High-Throughput Sequencing for Grapevine Virus Diagnostics." Viruses 13, no. 6 (2021): 1130. http://dx.doi.org/10.3390/v13061130.

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Development of High-Throughput Sequencing (HTS), also known as next generation sequencing, revolutionized diagnostic research of plant viruses. HTS outperforms bioassays and molecular diagnostic assays that are used to screen domestic and quarantine grapevine materials in data throughput, cost, scalability, and detection of novel and highly variant virus species. However, before HTS-based assays can be routinely used for plant virus diagnostics, performance specifications need to be developed and assessed. In this study, we selected 18 virus-infected grapevines as a test panel for measuring pe

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Bai, Ling, Liu He, Penghao Yu, et al. "Molecular Characterization of Mycobiota and Aspergillus Species from Eupolyphaga sinensis Walker Based on High-Throughput Sequencing of ITS1 and CaM." Journal of Food Quality 2020 (May 7, 2020): 1–7. http://dx.doi.org/10.1155/2020/1752415.

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Eupolyphaga sinensis Walker is a valuable traditional Chinese animal medicine first recorded in Shennong Bencao. Previous research has shown that E. sinensis is easily contaminated by aflatoxins (AFs), which are highly toxic mycotoxins, during harvest, storage, and transport, thereby posing a considerable threat to consumer health. Most often, these AFs are produced by Aspergillus species. In this study, we contrast the traditional culture-based dilution plating method to the high-throughput sequencing (HTS) technology for fungal identification in TCM E. sinensis. Both of the methods used inte

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Feijoo, M., and A. Parada. "Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage." Molecular Phylogenetics and Evolution 113 (June 12, 2017): 76–83. https://doi.org/10.5281/zenodo.13482191.

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(Uploaded by Plazi for the Bat Literature Project) In the last few years high-throughput sequencing technologies have permitted significant advances in mammalian phylogenetic studies from a genomic perspective. However, these studies have been restricted to a sparse number of species with available reference genomes. Thus, several issues inside the eutherian mammals phylogeny remain unresolved. This may be due in part to limited taxon sampling, as taxonomic density is known to affect phylogenetic resolution. In this context, we present a protocol to increase taxon coverage using high-throughpu

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Feijoo, M., and A. Parada. "Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage." Molecular Phylogenetics and Evolution 113 (June 7, 2017): 76–83. https://doi.org/10.5281/zenodo.13482191.

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(Uploaded by Plazi for the Bat Literature Project) In the last few years high-throughput sequencing technologies have permitted significant advances in mammalian phylogenetic studies from a genomic perspective. However, these studies have been restricted to a sparse number of species with available reference genomes. Thus, several issues inside the eutherian mammals phylogeny remain unresolved. This may be due in part to limited taxon sampling, as taxonomic density is known to affect phylogenetic resolution. In this context, we present a protocol to increase taxon coverage using high-throughpu

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Feijoo, M., and A. Parada. "Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage." Molecular Phylogenetics and Evolution 113 (July 3, 2017): 76–83. https://doi.org/10.5281/zenodo.13482191.

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(Uploaded by Plazi for the Bat Literature Project) In the last few years high-throughput sequencing technologies have permitted significant advances in mammalian phylogenetic studies from a genomic perspective. However, these studies have been restricted to a sparse number of species with available reference genomes. Thus, several issues inside the eutherian mammals phylogeny remain unresolved. This may be due in part to limited taxon sampling, as taxonomic density is known to affect phylogenetic resolution. In this context, we present a protocol to increase taxon coverage using high-throughpu

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Feijoo, M., and A. Parada. "Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage." Molecular Phylogenetics and Evolution 113 (July 10, 2017): 76–83. https://doi.org/10.5281/zenodo.13482191.

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(Uploaded by Plazi for the Bat Literature Project) In the last few years high-throughput sequencing technologies have permitted significant advances in mammalian phylogenetic studies from a genomic perspective. However, these studies have been restricted to a sparse number of species with available reference genomes. Thus, several issues inside the eutherian mammals phylogeny remain unresolved. This may be due in part to limited taxon sampling, as taxonomic density is known to affect phylogenetic resolution. In this context, we present a protocol to increase taxon coverage using high-throughpu

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Feijoo, M., and A. Parada. "Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage." Molecular Phylogenetics and Evolution 113 (July 17, 2017): 76–83. https://doi.org/10.5281/zenodo.13482191.

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(Uploaded by Plazi for the Bat Literature Project) In the last few years high-throughput sequencing technologies have permitted significant advances in mammalian phylogenetic studies from a genomic perspective. However, these studies have been restricted to a sparse number of species with available reference genomes. Thus, several issues inside the eutherian mammals phylogeny remain unresolved. This may be due in part to limited taxon sampling, as taxonomic density is known to affect phylogenetic resolution. In this context, we present a protocol to increase taxon coverage using high-throughpu

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Rajter, Ľubomír, and Micah Dunthorn. "Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data." Metabarcoding and Metagenomics 5 (August 30, 2021): e69602. https://doi.org/10.3897/mbmg.5.69602.

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Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental metabarcoding data. Here we fill this gap by providing reference alignments and trees for those ciliates taxa with available SSU-rDNA sequences derived from identified species. Each alignment contains 478 ciliate and six outgroup taxa, and they were made using different masking strategies for alignment positions (unmasked, masked and masked except the

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Espindola, Andres S. "Simulated High Throughput Sequencing Datasets: A Crucial Tool for Validating Bioinformatic Pathogen Detection Pipelines." Biology 13, no. 9 (2024): 700. http://dx.doi.org/10.3390/biology13090700.

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The validation of diagnostic assays in plant pathogen detection is a critical area of research. It requires the use of both negative and positive controls containing a known quantity of the target pathogen, which are crucial elements when calculating analytical sensitivity and specificity, among other diagnostic performance metrics. High Throughput Sequencing (HTS) is a method that allows the simultaneous detection of a theoretically unlimited number of plant pathogens. However, accurately identifying the pathogen from HTS data is directly related to the bioinformatic pipeline utilized and its

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Ruiz-García, Ana Belén, Celia Canales, Félix Morán, Manuel Ruiz-Torres, Magdalena Herrera-Mármol, and Antonio Olmos. "Characterization of Spanish Olive Virome by High Throughput Sequencing Opens New Insights and Uncertainties." Viruses 13, no. 11 (2021): 2233. http://dx.doi.org/10.3390/v13112233.

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The use of high throughput sequencing (HTS) for the analysis of Spanish olive trees showing leaf yellowing discoloration, defoliation, and/or decline has provided new insights into the olive viruses present in Spain and has opened discussions about the pros and cons of these technologies for diagnostic purposes. In this study, we report for the first time in Spanish orchards the presence of olive leaf yellowing-associated virus (OLYaV), for which the second full coding sequence has been determined. This virus has also been detected in a putative vector, the psyllid Euphyllura olivina. In addit

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Krehenwinkel, Pomerantz, and Prost. "Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions." Genes 10, no. 11 (2019): 858. http://dx.doi.org/10.3390/genes10110858.

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We live in an era of unprecedented biodiversity loss, affecting the taxonomic composition of ecosystems worldwide. The immense task of quantifying human imprints on global ecosystems has been greatly simplified by developments in high-throughput DNA sequencing technology (HTS). Approaches like DNA metabarcoding enable the study of biological communities at unparalleled detail. However, current protocols for HTS-based biodiversity exploration have several drawbacks. They are usually based on short sequences, with limited taxonomic and phylogenetic information content. Access to expensive HTS te

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Bastida, José María, Rocío Benito, María Luisa Lozano, et al. "Molecular Diagnosis of Inherited Coagulation and Bleeding Disorders." Seminars in Thrombosis and Hemostasis 45, no. 07 (2019): 695–707. http://dx.doi.org/10.1055/s-0039-1687889.

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AbstractDiagnosis of inherited bleeding disorders (IBDs) remains challenging, especially in the case of inherited platelet disorders, due to the heterogeneity of the clinical and laboratory phenotype, the limited specificity of platelet function tests, and the large number of potential culprit genes. Unraveling the underlying molecular defect provides the definitive diagnosis of IBDs, facilitating prognosis and clinical care, which are especially important for severe clinical syndromes and those that may be associated with an increased risk of malignancy. Until recently, Sanger sequencing of c

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Scherer, Florian, David M. Kurtz, Maximilian Diehn, and Ash A. Alizadeh. "High-throughput sequencing for noninvasive disease detection in hematologic malignancies." Blood 130, no. 4 (2017): 440–52. http://dx.doi.org/10.1182/blood-2017-03-735639.

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Abstract Noninvasive monitoring of minimal residual disease (MRD) has led to significant advances in personalized management of patients with hematologic malignancies. Improved therapeutic options and prolonged survival have further increased the need for sensitive tumor assessment that can inform treatment decisions and patient outcomes. At diagnosis or relapse of most hematologic neoplasms, malignant cells are often easily accessible in the blood as circulating tumor cells (CTCs), making them ideal targets to noninvasively profile the molecular features of each patient. In other cancer types

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Yin, Mengxue, and Wenxing Xu. "Special Issue: “Evolution, Ecology and Diversity of Plant Virus”." Viruses 15, no. 2 (2023): 487. http://dx.doi.org/10.3390/v15020487.

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Siddique, Abu Bakar, Anis Mahmud Khokon, and Martin Unterseher. "What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions." MycoKeys 20 (February 21, 2017): 1–16. https://doi.org/10.3897/mycokeys.20.11265.

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Comparative simultaneous studies of environmental high-throughput sequencing (HTS) and cultivation of plant-associated fungi have rarely been conducted in the past years. For the present contribution, HTS and extinction culturing were applied for the same leaf samples of European beech (Fagus sylvatica) in order to trace both "real" environmental drivers as well as method-dependent signals of the observed mycobiomes. Both approaches resulted in non-overlapping community composition and pronounced differences in taxonomic classification and trophic stages. However, both methods revealed similar

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Kenzhebekova, Roza, Pozharskiy A.S.,, Kostyukova V.S, and Gritsenko D.A.,. "HIGH-THROUGHPUT SEQUENCING FOR DETECTION OF POTATO VIRUSES IN NORTHERN KAZAKHSTAN." Ġylym ža̋ne bìlìm 2, no. 3(76) (2024): 3–14. https://doi.org/10.52578/2305-9397-2024-3-2-3-14.

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This study explores the use of high-throughput sequencing (HTS) technologies to identify and analyze potato viruses in Northern Kazakhstan, enhancing our understanding of viral impacts on agriculture. Focusing on viruses like Potato virus X (PVX), Potato virus Y (PVY), Potato virus M (PVM), and Potato virus S (PVS), the research demonstrates HTS's effectiveness in detecting and detailing these pathogens. The study's goal is to apply HTS for a comprehensive examination of viral populations that affect potato crops in Northern Kazakhstan, an area where potato production is crucial but faces chal

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Choi, Jiyeong, Anya Clara Osatuke, Griffin Erich, et al. "High-Throughput Sequencing Reveals Tobacco and Tomato Ringspot Viruses in Pawpaw." Plants 11, no. 24 (2022): 3565. http://dx.doi.org/10.3390/plants11243565.

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Pawpaw (Asimina triloba) trees exhibiting stunting and foliar mosaic, chlorosis, or distortions were observed in New York. In 2021, leaf samples from two symptomatic trees and a sapling, as well as two asymptomatic trees, were tested for the presence of viruses and viroids by high-throughput sequencing (HTS) using total RNA after ribosomal RNA depletion. HTS sequence information revealed tobacco ringspot virus (TRSV) and tomato ringspot virus (ToRSV) in symptomatic but not in asymptomatic leaves. HTS reads and de novo-assembled contigs covering the genomes of both viruses were obtained, with a

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Lightbody, Gaye, Valeriia Haberland, Fiona Browne, et al. "Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application." Briefings in Bioinformatics 20, no. 5 (2019): 1795–811. http://dx.doi.org/10.1093/bib/bby051.

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Abstract There has been an exponential growth in the performance and output of sequencing technologies (omics data) with full genome sequencing now producing gigabases of reads on a daily basis. These data may hold the promise of personalized medicine, leading to routinely available sequencing tests that can guide patient treatment decisions. In the era of high-throughput sequencing (HTS), computational considerations, data governance and clinical translation are the greatest rate-limiting steps. To ensure that the analysis, management and interpretation of such extensive omics data is exploit

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Bérubé, Jean A., Patrick N. Gagné, Julien P. Ponchart, J. Phelan, A. Varga, and D. James. "Heterobasidion species detected using High Throughput Sequencing (HTS) methods on British Columbia nursery plants." Canadian Journal of Plant Pathology 41, no. 4 (2019): 560–65. http://dx.doi.org/10.1080/07060661.2019.1611665.

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Giner, Caterina R., Irene Forn, Sarah Romac, Ramiro Logares, Colomban de Vargas, and Ramon Massana. "Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes." Applied and Environmental Microbiology 82, no. 15 (2016): 4757–66. http://dx.doi.org/10.1128/aem.00560-16.

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ABSTRACTHigh-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescencein situhybridization preparations. These relative ab

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Lynch, Tarah, Aaron Petkau, Natalie Knox, Morag Graham, and Gary Van Domselaar. "A Primer on Infectious Disease Bacterial Genomics." Clinical Microbiology Reviews 29, no. 4 (2016): 881–913. http://dx.doi.org/10.1128/cmr.00001-16.

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SUMMARYThe number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies. The use of HTS for bacterial infectious disease research is attractive because one whole-genome sequencing (WGS) run can replace multiple assays for bacterial typing, molecular epidemiology investigations, and more in-depth pathogenomic studies. The computational resources and bioinformatics expertise required to accommodate and analyze the large amounts of data pose new challenges for researchers embarking on genomics projects for the first time

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Kutnjak, Denis, Lucie Tamisier, Ian Adams, et al. "A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses." Microorganisms 9, no. 4 (2021): 841. http://dx.doi.org/10.3390/microorganisms9040841.

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High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus d

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Anslan, Sten, R. Henrik Nilsson, Christian Wurzbacher, Petr Baldrian, Leho Tedersoo, and Mohammad Bahram. "Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding." MycoKeys 39 (September 10, 2018): 29–40. https://doi.org/10.3897/mycokeys.39.28109.

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Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data se

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Fabiańska, Izabela, Stefan Borutzki, Benjamin Richter, Hon Q. Tran, Andreas Neubert, and Dietmar Mayer. "LABRADOR—A Computational Workflow for Virus Detection in High-Throughput Sequencing Data." Viruses 13, no. 12 (2021): 2541. http://dx.doi.org/10.3390/v13122541.

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High-throughput sequencing (HTS) allows detection of known and unknown viruses in samples of broad origin. This makes HTS a perfect technology to determine whether or not the biological products, such as vaccines are free from the adventitious agents, which could support or replace extensive testing using various in vitro and in vivo assays. Due to bioinformatics complexities, there is a need for standardized and reliable methods to manage HTS generated data in this field. Thus, we developed LABRADOR—an analysis pipeline for adventitious virus detection. The pipeline consists of several third-

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