Analyzing Gene Pathways from Microarrays to Sequencing Platforms

2020 ◽  
pp. 289-296
Author(s):  
Jeffrey Miecznikowski ◽  
Dan Wang ◽  
Xing Ren ◽  
Jianmin Wang ◽  
Song Liu
Keyword(s):  
Sequencing Platforms

scholarly journals Detection of Tumor Recurrence via Circulating Tumor DNA Profiling in Patients with Localized Lung Cancer: Clinical Considerations and Challenges

Cancers ◽  
2021 ◽  
Vol 13 (15) ◽  
pp. 3759
Author(s):  
Bryan Ulrich ◽  
Anne Pradines ◽  
Julien Mazières ◽  
Nicolas Guibert
Keyword(s):  
Lung Cancer ◽  
Residual Disease ◽  
Lung Cancer Screening ◽  
Circulating Tumor Dna ◽  
Definitive Treatment ◽  
Curative Intent ◽  
Screening Programs ◽  
Adjuvant Therapies ◽  
Sequencing Platforms ◽  
Tumor Dna

Approximately 30% of patients with non-small-cell lung cancer (NSCLC) present with localized/non-metastatic disease and are eligible for surgical resection or other “treatment with curative intent”. Due to the high prevalence of recurrence after treatment, adjuvant therapy is standard care for most patients. The effect of adjuvant chemotherapy is, however, modest, and new tools are needed to identify candidates for adjuvant treatments (chemotherapy, immunotherapy, or targeted therapies), especially since expanded lung cancer screening programs will increase the rate of patients detected with localized NSCLC. Circulating tumor DNA (ctDNA) has shown strong potential to detect minimal residual disease (MRD) and to guide adjuvant therapies. In this manuscript, we review the technical aspects and performances of the main ctDNA sequencing platforms (TRACERx, CAPP-seq) investigated in this purpose, and discuss the potential of this approach to guide or spare adjuvant therapies after definitive treatment of NSCLC.

scholarly journals Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Aoife J. McHugh ◽  
Min Yap ◽  
Fiona Crispie ◽  
Conor Feehily ◽  
Colin Hill ◽  
...  
Keyword(s):  
Environmental Monitoring ◽  
Illumina Sequencing ◽  
Food Chain ◽  
Control Measures ◽  
Initial Assessment ◽  
Limiting Factor ◽  
Accurate Identification ◽  
Processing Facility ◽  
High Concentrations ◽  
Sequencing Platforms

AbstractEfficient and accurate identification of microorganisms throughout the food chain can potentially allow the identification of sources of contamination and the timely implementation of control measures. High throughput DNA sequencing represents a potential means through which microbial monitoring can be enhanced. While Illumina sequencing platforms are most typically used, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. Initial assessment of the ability of rapid MinION-based sequencing to identify microbes within a simple mock metagenomic mixture is performed. Subsequently, we compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility. Overall, ONT MinION sequencing provides accurate classification to species level, comparable to Illumina-derived outputs. However, while the MinION-based approach provides a means of easy library preparations and portability, the high concentrations of DNA needed is a limiting factor.

scholarly journals Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1304
Author(s):  
Nicolás Bejerman ◽  
Ralf G. Dietzgen ◽  
Humberto Debat
Keyword(s):  
Plant Species ◽  
High Throughput Sequencing ◽  
Plant Viruses ◽  
The Novel ◽  
Coding Regions ◽  
Public Data ◽  
Invaluable Tool ◽  
Sequencing Platforms ◽  
Viral Sequences ◽  
Plant Rhabdovirus

Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here, we report the discovery of 27 novel rhabdovirus genomes associated with 25 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3000 plant and insect transcriptomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using known plant rhabdovirus sequences as the query. The identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses and seven to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provided additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrated that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomy.

scholarly journals Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Calvin P. Sjaarda ◽  
Nazneen Rustom ◽  
Gerald A. Evans ◽  
David Huang ◽  
Santiago Perez-Patrigeon ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Surveillance ◽  
Early Stage ◽  
Emerging Diseases ◽  
Contact Tracing ◽  
Travel History ◽  
Infectious Disease Surveillance ◽  
Viral Genomes ◽  
Heterozygous Variant ◽  
Sequencing Platforms

AbstractThe emergence and rapid global spread of SARS-CoV-2 demonstrates the importance of infectious disease surveillance, particularly during the early stages. Viral genomes can provide key insights into transmission chains and pathogenicity. Nasopharyngeal swabs were obtained from thirty-two of the first SARS-CoV-2 positive cases (March 18–30) in Kingston Ontario, Canada. Viral genomes were sequenced using Ion Torrent (n = 24) and MinION (n = 27) sequencing platforms. SARS-CoV-2 genomes carried forty-six polymorphic sites including two missense and three synonymous variants in the spike protein gene. The D614G point mutation was the predominate viral strain in our cohort (92.6%). A heterozygous variant (C9994A) was detected by both sequencing platforms but filtered by the ARTIC network bioinformatic pipeline suggesting that heterozygous variants may be underreported in the SARS-CoV-2 literature. Phylogenetic analysis with 87,738 genomes in the GISAID database identified global origins and transmission events including multiple, international introductions as well as community spread. Reported travel history validated viral introduction and transmission inferred by phylogenetic analysis. Molecular epidemiology and evolutionary phylogenetics may complement contact tracing and help reconstruct transmission chains of emerging diseases. Earlier detection and screening in this way could improve the effectiveness of regional public health interventions to limit future pandemics.

scholarly journals Genome Insights into the Novel Species Jejubacter calystegiae, a Plant Growth-Promoting Bacterium in Saline Conditions

Diversity ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 24
Author(s):  
Ling Min Jiang ◽  
Yong Jae Lee ◽  
Ho Le Han ◽  
Myoung Hui Lee ◽  
Jae Cheol Jeong ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Plant Growth ◽  
Novel Species ◽  
Endophytic Bacterium ◽  
Morning Glory ◽  
Plant Growth Promoting Bacteria ◽  
Illumina Hiseq ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Sequencing Platforms

Jejubacter calystegiae KSNA2T, a moderately halophilic, endophytic bacterium isolated from beach morning glory (Calystegia soldanella), was determined to be a novel species in a new genus in the family Enterobacteriaceae. To gain insights into the genetic basis of the salinity stress response of strain KSNA2T, we sequenced its genome using two complementary sequencing platforms (Illumina HiSeq and PacBio RSII). The genome contains a repertoire of metabolic pathways, such as those for nitrogen, phosphorus, and some amino acid metabolism pathways. Functional annotation of the KSNA2T genome revealed several genes involved in salt tolerance pathways, such as those encoding sodium transporters, potassium transporters, and osmoprotectant enzymes. Plant growth-promoting bacteria-based experiments indicated that strain KSNA2T promotes the germination of vegetable seeds in saline conditions. Overall, the genetic and biological analyses of strain KSNA2T provide valuable insights into bacteria-mediated salt tolerance in agriculture.

scholarly journals The Accuracy, Feasibility and Challenges of Sequencing Short Tandem Repeats Using Next-Generation Sequencing Platforms

PLoS ONE ◽  
2014 ◽  
Vol 9 (12) ◽  
pp. e113862 ◽  
Author(s):  
Monika Zavodna ◽  
Andrew Bagshaw ◽  
Rudiger Brauning ◽  
Neil J. Gemmell
Keyword(s):  
Next Generation Sequencing ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Next Generation ◽  
Sequencing Platforms ◽  
Generation Sequencing ◽  
Short Tandem

scholarly journals Sequencing and Computational Approaches to Identification and Characterization of Microbial Organisms

2013 ◽  
Vol 5 ◽  
pp. BECB.S10886 ◽  
Author(s):  
Brijesh Singh Yadav ◽  
Venkateswarlu Ronda ◽  
Dinesh P. Vashista ◽  
Bhaskar Sharma
Keyword(s):  
Sequence Data ◽  
Microbial Interactions ◽  
Microbial Pathogens ◽  
Nucleotide Sequence Data ◽  
Computational Approaches ◽  
Microbial Detection ◽  
Sequencing Technologies ◽  
Sequencing Platforms ◽  
Identification And Characterization

The recent advances in sequencing technologies and computational approaches are propelling scientists ever closer towards complete understanding of human-microbial interactions. The powerful sequencing platforms are rapidly producing huge amounts of nucleotide sequence data which are compiled into huge databases. This sequence data can be retrieved, assembled, and analyzed for identification of microbial pathogens and diagnosis of diseases. In this article, we present a commentary on how the metagenomics incorporated with microarray and new sequencing techniques are helping microbial detection and characterization.

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