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Whole genome sequencing

Tìm thấy 11+ kết quả cho từ khóa "Whole genome sequencing"

Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants

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Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral. High throughput characterization of full genome, within-host variants is still not possible despite advances in next generation sequencing. This limitation constrains viral genomic studies that depend on accurate identification of hemi-genome or whole genome, within-host variants, especially those occurring at low frequencies.

Universal human papillomavirus typing by whole genome sequencing following target enrichment: Evaluation of assay reproducibility and limit of detection

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The positive correlation of mapped reads and fraction of genome covered with target concentra- tion as we observed with bait-based eWGS for HPV agrees with a recently reported study on whole genome sequencing of hepatitis C viral genomes following simi- lar target enrichment [23]. However, PCR-based methods either targeting whole genome or amplicon se- quencing did not show a copy number dependence with the number of mapped reads [2, 23].

QuantTB – a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data

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In contrast, whole genome sequencing offers sensitive views of the genetic differences between strains of M.. Full list of author information is available at the end of the article. one of the oldest diseases in the world - continues to devastate the lives of millions per year. Finally, spoligo- typing analyzes a series of 43 spacer oligonucleotides in the directed repeat region [12].

Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective

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Identification of Salmonella for public health surveillance using whole genome sequencing. opportunities of whole genome sequencing (WGS) for foodborne pathogen surveillance, source tracking and risk assessment. Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. The utility of multiple molecular methods including whole genome sequencing as tools to differentiate Escherichia coli O157: H7 outbreaks.

Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources

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Characterization of foodborne outbreaks of Salmonella enterica serovar Enteritidis with whole-genome sequencing single nucleotide. Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica. Whole-genome sequencing for detecting antimicrobial resistance in nontyphoidal Salmonella. Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar Enteritidis.

Whole genome sequence based capsular typing and antimicrobial resistance prediction of Group B streptococcal isolates from colonized pregnant women in Nigeria

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The isolates were shipped on Columbia agar with chocolated horse blood (Oxoid, UK) to the Streptococcus Laboratory, Centers for Disease Control and Prevention (CDC), for whole genome sequencing.. Whole genome sequencing and strain feature prediction At CDC, GBS isolates were cultured on Trypticase soy agar supplemented with 5 % sheep blood prior to DNA extrac- tion from single colonies as previously described [13]..

Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks

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According to the cell morphology and 16S rDNA sequence, the differ- ent candidate isolates were ready for whole genome sequencing.. Whole-genome sequencing. Whole-genome sequencing was performed on both the Illumina HiSeq Xten platform (Illumina, California, USA) at GeneSeeq Co., Ltd. The ANI of each assembly against the genome of the reference strain was calculated using Fas- tANI. tygs.dsmz.de) [39] and Ribosomal Multilocus Sequence Typing (rMLST, https://pubmlst.org/bigsdb?

A clinically validated whole genome pipeline for structural variant detection and analysis

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Figure S2 Analytical validation statistics of small sequence changes by Variantyx Unity test basing on combination of 3 different Genome in a Bottle samples. Method S1 Variantyx diagnostic procedure for reporting pathogenic structural variants. 4 Structural variant filtration in Diagnostic Console. SV: Structural Variant. TP: True Positive. WGS: Whole Genome Sequencing.

Evaluation of whole exome sequencing as an alternative to BeadChip and whole genome sequencing in human population genetic analysis

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The largest publicly accessible set of human genomic sequence data available today originates from exome sequencing that comprises around 1.2% of the whole genome (approximately 30 million base pairs)..

Attack of the clones: Whole genome-based characterization of two closely related enterohemorrhagic Escherichia coli O26 epidemic lineages

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Attack of the clones: whole genome-based characterization of two closely related. enterohemorrhagic Escherichia coli O26 epidemic lineages. Background: Enterohemorrhagic Escherichia coli (EHEC) O26:H11/H. Here, we investigated the population structure of EHEC O26 isolated from patients in several European countries using whole genome sequencing, with emphasis on a detailed analysis of strains of the highly virulent new European clone (nEC) which has spread since 1990s..

Genome-wide segregation of single nucleotide and structural variants into single cancer cells

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The genome amplification consistently resulted in the generation of 120-150 ng of product that was harvested in 13 μl of. Microfluidic Single Cell Isolation and Whole Genome. Whole Genome Sequencing To Identify Putative SNVs and SVs. Confirmation and Single Cell Evaluations. Single Cell SV Calls. Single Cell SNV/Indel Calls.

Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture

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Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture.

Population analysis of the Korean native duck using whole-genome sequencing data

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Although some recent stud- ies have investigated the unique characteristics of the Korean native duck [17–20], whole genome-level studies for the Korean native duck still lag behind other domes- tic animals and duck breeds.. To address this, we apply a population-level genome ana- lysis based on whole-genome sequencing data from popula- tions of various duck breeds including KD.

Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania

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Whole genome sequencing of Mycobacterium tuberculosis for detection of drug resistance: a systematic review. Removing the bottleneck in whole genome sequencing of mycobacterium tuberculosis for rapid drug resistance analysis: a call to action. Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti- tuberculosis drug resistance. Whole genome sequencing to complement tuberculosis drug resistance surveys in Uganda.

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features

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However, the whole-genome sequencing of Siberian musk deer has not been performed, and their potential value has yet to be discovered.. In this study, we perform high-quality whole-genome sequencing of three wild Siberian musk deer (WSMD) from Mongolia, and transcriptome sequencing of one mixture of tissue from a naturally died female WSMD..

Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential

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Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its. tubingensis G131. tubingensis G131.. tubingensis, which is part of the A.. A complete review of the putative SM gene biosynthetic clusters is also reported.. tubingensis G131 produces asperazine and NGPs under laboratory condi- tions. tubingensis G131 genome is robust. tubingensis G131 (35,18 Mb) is equivalent to the genome size of A. Table 1 Genome characteristics and predicted features of the assembled A.

Whole genome sequencing of Nontuberculous Mycobacterium (NTM) isolates from sputum specimens of cohabiting patients with NTM pulmonary disease and NTM isolates from their environment

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Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP, Moreno P, et al. Harris KA, Underwood A, Kenna DT, Brooks A, Kavaliunaite E, Kapatai G, et al.. Whole-genome sequencing and epidemiological analysis do not provide evidence for cross-transmission of mycobacterium abscessus in a cohort of pediatric cystic fibrosis patients.

Gen2Epi: An automated whole-genome sequencing pipeline for linking full genomes to antimicrobial susceptibility and molecular epidemiological data in Neisseria gonorrhoeae

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The median genome coverage of full-length scaffolds and “ N ” statistics (N50, NG50, and NGA50) were higher than, or comparable to, previously published results and the scaffolding process improved the quality of the draft genome assemblies. Keywords: Bioinformatics, Whole-genome sequencing (WGS), De novo genome assembly, Scaffolding, Molecular epidemiology, Strain typing, Antimicrobial resistance, Molecular typing, Neisseria gonorrhoeae. [email protected].

Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre

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Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre. Background: Chronic lung infections caused by Pseudomonas aeruginosa are a significant cause of morbidity and mortality in people with cystic fibrosis (CF). The main aim of this study was to resolve the relationship of the emergent M3L7 sub-type within the AUST-02 group of strains using whole genome sequencing..

Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing

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Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) cultures. Ultra-long read sequencing protocol for RAD004, on protocols.Io.. Assembly of the mycobacterial Cell Wall. scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. visualizing and processing long-read sequencing data