scholarly journals Application of the New Generation of Sequencing Technologies for Evaluation of Genetic Consistency of Influenza A Vaccine Viruses

10.5772/64371 ◽  
2016 ◽  
Author(s):  
Ewan Peter Plant ◽  
Tatiana Zagorodnyaya ◽  
Elvira Rodionova ◽  
Alin Voskanian-Kordi ◽  
Vahan Simonyan ◽  
...  
Keyword(s):  
Influenza A ◽  
Sequencing Technologies ◽  
New Generation

scholarly journals LeafGo: Leaf to Genome, a quick workflow to produce high-quality De novo genomes with Third Generation Sequencing technology

2021 ◽  
Author(s):  
Patrick Driguez ◽  
Salim Bougouffa ◽  
Karen Carty ◽  
Alexander Putra ◽  
Kamel Jabbari ◽  
...  
Keyword(s):  
De Novo ◽  
Rapid Development ◽  
Plant Genome ◽  
Plant Genomics ◽  
High Quality ◽  
High Molecular Weight Dna ◽  
Tissue Samples ◽  
Sequencing Technologies ◽  
The Cost ◽  
New Generation

AbstractRecent years have witnessed a rapid development of sequencing technologies. Fundamental differences and limitations among various platforms impact the time, the cost and the accuracy for sequencing whole genomes. Here we designed a complete de novo plant genome generation workflow that starts from plant tissue samples and produces high-quality draft genomes with relatively modest laboratory and bioinformatic resources within seven days. To optimize our workflow we selected different species of plants which were used to extract high molecular weight DNA, to make PacBio and ONT libraries for sequencing with the Sequel I, Sequel II and GridION platforms. We assembled high-quality draft genomes of two different Eucalyptus species E. rudis, and E. camaldulensis to chromosome level without using additional scaffolding technologies. For the rapid production of de novo genome assembly of plant species we showed that our DNA extraction protocol followed by PacBio high fidelity sequencing, and assembly with new generation assemblers such as hifiasm produce excellent results. Our findings will be a valuable benchmark for groups planning wet- and dry-lab plant genomics research and for high throughput plant genomics initiatives.

Eukaryotic systematics: a user's guide for cell biologists and parasitologists

Parasitology ◽  
2011 ◽  
Vol 138 (13) ◽  
pp. 1638-1663 ◽  
Author(s):  
GISELLE WALKER ◽  
RICHARD G. DORRELL ◽  
ALEXANDER SCHLACHT ◽  
JOEL B. DACKS
Keyword(s):  
Cellular Level ◽  
Point Of View ◽  
Eukaryotic Diversity ◽  
Sequencing Technologies ◽  
Human Habitat ◽  
On Line ◽  
Supplementary Material ◽  
New Generation ◽  
Evolution Of Photosynthesis ◽  
Evolutionary Point

SUMMARYSingle-celled parasites like Entamoeba, Trypanosoma, Phytophthora and Plasmodium wreak untold havoc on human habitat and health. Understanding the position of the various protistan pathogens in the larger context of eukaryotic diversity informs our study of how these parasites operate on a cellular level, as well as how they have evolved. Here, we review the literature that has brought our understanding of eukaryotic relationships from an idea of parasites as primitive cells to a crystallized view of diversity that encompasses 6 major divisions, or supergroups, of eukaryotes. We provide an updated taxonomic scheme (for 2011), based on extensive genomic, ultrastructural and phylogenetic evidence, with three differing levels of taxonomic detail for ease of referencing and accessibility (see supplementary material at Cambridge Journals On-line). Two of the most pressing issues in cellular evolution, the root of the eukaryotic tree and the evolution of photosynthesis in complex algae, are also discussed along with ideas about what the new generation of genome sequencing technologies may contribute to the field of eukaryotic systematics. We hope that, armed with this user's guide, cell biologists and parasitologists will be encouraged about taking an increasingly evolutionary point of view in the battle against parasites representing real dangers to our livelihoods and lives.

scholarly journals Machine Learning Models for Accurate Prioritization of Variants of Uncertain Significance

2020 ◽  
Author(s):  
Daniel Mahecha ◽  
Haydemar Nuñez ◽  
Maria Lattig ◽  
Jorge Duitama
Keyword(s):  
Machine Learning ◽  
Genetic Diagnosis ◽  
Software Tool ◽  
Support Vector ◽  
Clinical Settings ◽  
Loss Of Function ◽  
Variants Of Uncertain Significance ◽  
Sequencing Technologies ◽  
Uncertain Significance ◽  
New Generation

The growing use of new generation sequencing technologies on genetic diagnosis has produced an exponential increase in the number of Variants of Uncertain Significance (VUS). In this manuscript we compare three machine learning methods to classify VUS as Pathogenic or No pathogenic, implementing a Random Forest (RF), a Support Vector Machine (SVM), and a Multilayer Perceptron (MLP). To train the models, we extracted 82,463 high quality variants from ClinVar, using 9 conservation scores, the loss of function tool and allele frequencies. For the RF and SVM models, hyperparameters were tuned using cross validation with a grid search. The three models were tested on a set of 5,537 variants that had been classified as VUS any time along the last three years but had been reclassified in august 2020. The three models yielded superior accuracy on this set compared to the benchmarked tools. The RF based model yielded the best performance across different variant types and was used to create VusPrize, an open source software tool for prioritization of variants of uncertain significance. We believe that our model can improve the process of genetic diagnosis on research and clinical settings.

scholarly journals The Dark Matter of Human Microbiota: Virobiota and Virome

2021 ◽  
Author(s):  
Gülendam Bozdayı ◽  
Işıl Fidan
Keyword(s):  
High Throughput Sequencing ◽  
Inflammatory Diseases ◽  
Human Microbiome ◽  
Endogenous Retroviruses ◽  
Therapeutic Approaches ◽  
Sequencing Technologies ◽  
Health And Disease ◽  
New Generation Sequencing ◽  
New Generation ◽  
Generation Sequencing

The viral component of the human microbiome is referred as ‘virobiota’. The virobiota is the sum of all viruses found in or on humans. The set of all genes of virobiota is referred as ‘virome’. The human virome consists of virus-derived genetic elements found in human genome constituted of viruses that infect eukaryotic cells, bacteriophages, prokaryotic cells, and, endogenous retroviruses. The development of new sequencing technologies, such as high-throughput sequencing techniques allowed the analysis of the human virome. Many new viruses have been discovered lately, using new generation sequencing technology. In recent years, there has been an increase in the studies of the human virome as changes in virome have been observed in diseases. The alterations in the human virome may be associated with infectious, inflammatory diseases, cancer and autoimmunity. The understanding of how the virome affects human health and disease can provide the development of potential therapeutic approaches that target the members of the virome.

Amyotrophic Lateral Sclerosis

2017 ◽  
Author(s):  
Matthew B. Harms ◽  
Timothy M. Miller
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Motor Neuron ◽  
Targeted Therapies ◽  
Biological Pathways ◽  
Sequencing Technologies ◽  
Risk Alleles ◽  
Number Of Genes ◽  
Multistep Process ◽  
New Generation ◽  
Lateral Sclerosis

Recent advances in sequencing technologies have dramatically expanded the number of genes associated with amyotrophic lateral sclerosis, including rare but highly penetrant causative mutations as well as common risk alleles. This chapter discusses these gene discoveries and how they have implicated a diverse array of biological pathways essential for motor neuron health and have begun to inform our understanding of ALS pathogenesis as a heterogeneous and multistep process. Insights from these discoveries are leading to a new generation of targeted therapies directed at specific genes and are poised to inform how patients with amyotrophic lateral sclerosis are evaluated and treated in the clinic.

scholarly journals A Mutated PB1 Residue 319 Synergizes with the PB2 N265S Mutation of the Live Attenuated Influenza Vaccine to Convey Temperature Sensitivity

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1246
Author(s):  
Andrew Cox ◽  
Jordana Schmierer ◽  
Josephine D’Angelo ◽  
Andrew Smith ◽  
Dustyn Levenson ◽  
...  
Keyword(s):  
Temperature Sensitivity ◽  
Genetic Background ◽  
Influenza A ◽  
Polymerase Activity ◽  
Influenza Vaccines ◽  
Potential Utility ◽  
Live Vaccines ◽  
Live Attenuated Influenza Vaccine ◽  
Complete Set ◽  
New Generation

Current influenza vaccines have modest efficacy. This is especially true for current live attenuated influenza vaccines (LAIV), which have been inferior to the inactivated versions in recent years. Therefore, a new generation of live vaccines may be needed. We previously showed that a mutation at PB1 residue 319 confers enhanced temperature sensitivity and attenuation in an LAIV constructed in the genetic background of the mouse-adapted Influenza A Virus (IAV) strain A/PR/8/34 (PR8). Here, we describe the origin/discovery of this unique mutation and demonstrate that, when combined with the PB2 N265S mutation of LAIV, it conveys an even greater level of temperature sensitivity and attenuation on PR8 than the complete set of attenuating mutations from LAIV. Furthermore, we show that the combined PB1 L319Q and PB2 N265S mutations confer temperature sensitivity on IAV polymerase activity in two different genetic backgrounds, PR8 and A/Cal/04/09. Collectively, these findings show that the PB2 LAIV mutation synergizes with a mutation in PB1 and may have potential utility for improving LAIVs.

scholarly journals Applications of Deep Mutational Scanning in Virology

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1020
Author(s):  
Thomas D. Burton ◽  
Nicholas S. Eyre
Keyword(s):  
Influenza A ◽  
Reverse Genetics ◽  
Rna Viruses ◽  
Human Gene ◽  
Viral Gene ◽  
Epigenetic Changes ◽  
Molecular Virology ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
Generation Sequencing

Several recently developed high-throughput techniques have changed the field of molecular virology. For example, proteomics studies reveal complete interactomes of a viral protein, genome-wide CRISPR knockout and activation screens probe the importance of every single human gene in aiding or fighting a virus, and ChIP-seq experiments reveal genome-wide epigenetic changes in response to infection. Deep mutational scanning is a relatively novel form of protein science which allows the in-depth functional analysis of every nucleotide within a viral gene or genome, revealing regions of importance, flexibility, and mutational potential. In this review, we discuss the application of this technique to RNA viruses including members of the Flaviviridae family, Influenza A Virus and Severe Acute Respiratory Syndrome Coronavirus 2. We also briefly discuss the reverse genetics systems which allow for analysis of viral replication cycles, next-generation sequencing technologies and the bioinformatics tools that facilitate this research.

scholarly journals Inclusion of site-specific mutations in the PB1-gene of a virulent A/WSN/33 (H1N1) strain of influenza A virus changes its phenotypic characteristics

2019 ◽  
pp. 21-29
Author(s):  
V. Yu. Kost ◽  
O. A. Sukhova ◽  
I. I. Akopova ◽  
E. O. Gorbacheva ◽  
K. V. Lisovskaya ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Crucial Importance ◽  
Phenotypic Characteristics ◽  
Site Specific ◽  
Ann Arbor ◽  
H1n1 Strain ◽  
New Generation ◽  
Ts Mutations ◽  
Functional Defects

Aim. Study of changes in the phenotypic characteristics of the virulent A/WSN/33 (H1N1) strain of influenza A virus under the influence of the inclusion of site-specific mutations in the PB1-gene of this strain.Materials and methods. Using a two-step polymerase reaction in the PB1 gene of A/ WSN/33 (H1N1) strain were included ts mutations taken from the genome of attenuated CA donors-strains: A/Ann Arbor/6/60 (H2N2), A/Leningrad 134/17/57 (H2N2) and A/ Krasnodar/101/35/59. Ts-phenotype, att-phenotype, immunogenicity, as well as weight loss in mice infected with these mutants were studied in the obtained site-specific mutants.Results. It was shown that the inclusion of ts mutations from the genome of CA donorsstrains of attenuation in the PB1 gene of the virulent A/WSN/33 (H1N1) strain leads to a change in the phenotypic characteristics of this strain to different degrees.Discussion. Analysis of the genome of CA strains- donors of attenuation of influenza virus indicates the crucial importance of the presence of functional defects in the PB1– protein for the formation of the attenuation phenotype of the virus.Conclusion. The technology of site-specific mutagenesis canbe successfully used to modify the PB1 gene of a virulent influenza A virus strain in order to construct a new generation of live influenza vaccines.

Biotechnology, Human Genome Sequencing Technologies, and the Medical, Public Health, and Wealth Creation Initiatives in the Industrialized G8 Nations

2016 ◽  
pp. 106-124 ◽  
Keyword(s):  
Public Health ◽  
Human Genome ◽  
Genome Sequencing ◽  
Economic Benefits ◽  
Genomic Research ◽  
Wealth Creation ◽  
Sequencing Project ◽  
Sequencing Technologies ◽  
Human Genome Sequencing ◽  
New Generation

This project focused on the return on investment from the Human Genome Sequencing Project, and we characterized the quality of life indices and economic resources in the G8 nations. The research team explored the existing scientific infrastructures already in place in the industrialized nations, even before the completion of the human genome sequencing by March 2003. Their authentic and well-established technological workforce developed a new generation of innovative technologies for inexpensive, spontaneous, and precise genomic sequencing. The project team not only discussed the medical, public health and economic benefits derived from genomic research, but also compiled the fledging careers in bioscience and genetics in the G8 nations.

ANALYSIS OF CONTEXT-DEPENDENT ERRORS FOR ILLUMINA SEQUENCING

2012 ◽  
Vol 10 (02) ◽  
pp. 1241005 ◽  
Author(s):  
IRINA ABNIZOVA ◽  
STEVEN LEONARD ◽  
TOM SKELLY ◽  
ANDY BROWN ◽  
DAVID JACKSON ◽  
...  
Keyword(s):  
Conditional Probability ◽  
Variant Calling ◽  
Candidate Snps ◽  
Simple Method ◽  
Second Best ◽  
Sequencing Errors ◽  
Sequencing Technologies ◽  
Nucleotide Context ◽  
Quality Value ◽  
New Generation

The new generation of short-read sequencing technologies requires reliable measures of data quality. Such measures are especially important for variant calling. However, in the particular case of SNP calling, a great number of false-positive SNPs may be obtained. One needs to distinguish putative SNPs from sequencing or other errors. We found that not only the probability of sequencing errors (i.e. the quality value) is important to distinguish an FP-SNP but also the conditional probability of "correcting" this error (the "second best call" probability, conditional on that of the first call). Surprisingly, around 80% of mismatches can be "corrected" with this second call. Another way to reduce the rate of FP-SNPs is to retrieve DNA motifs that seem to be prone to sequencing errors, and to attach a corresponding conditional quality value to these motifs. We have developed several measures to distinguish between sequence errors and candidate SNPs, based on a base call's nucleotide context and its mismatch type. In addition, we suggested a simple method to correct the majority of mismatches, based on conditional probability of their "second" best intensity call. We attach a corresponding second call confidence (quality value) of being corrected to each mismatch.

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