keyword
MENU ▼
Read by QxMD icon Read
search

WGS

keyword
https://www.readbyqxmd.com/read/29036710/a-disulfide-bond-a-like-oxidoreductase-is-a-strong-candidate-gene-for-self-incompatibility-in-apricot-prunus-armeniaca-pollen
#1
Juan Vicente Muñoz-Sanz, Elena Zuriaga, María L Badenes, Carlos Romero
S-RNase based gametophytic self-incompatibility (SI) is a widespread prezygotic reproductive barrier in flowering plants. In the Solanaceae, Plantaginaceae and Rosaceae gametophytic SI is controlled by the pistil-specific S-RNases and the pollen S-locus F-box proteins but non-S-specific factors, namely modifiers, are also required. In apricot, Prunus armeniaca (Rosaceae), we previously mapped two pollen-part mutations that confer self-compatibility in cultivars Canino and Katy at the distal end of chromosome 3 (M-locus) unlinked to the S-locus...
September 25, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29036291/phylotyper-in-silico-predictor-of-gene-subtypes
#2
Matthew D Whiteside, Victor P J Gannon, Chad R Laing
Summary: Whole genome sequencing (WGS) is being adopted in public health for improved surveillance and outbreak analysis. In public health, subtyping has been used to infer phenotypes and distinguish bacterial strain groups. In silico tools that predict subtypes from sequences data are needed to transition historical data to WGS-based protocols. Phylotyper is a novel solution for in silico subtype prediction from gene sequences. Designed for incorporation into WGS pipelines, it is a general prediction tool that can be applied to different subtype schemes...
July 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29031637/molecular-epidemiology-of-multi-and-extensively-drug-resistant-mycobacterium-tuberculosis-in-ireland-2001-2014
#3
E Roycroft, R F O'Toole, M M Fitzgibbon, L Montgomery, M O'Meara, P Downes, S Jackson, J O'Donnell, I F Laurenson, A M McLaughlin, J Keane, T R Rogers
OBJECTIVES: The primary objective of this work was to examine the acquisition and spread of multi-drug resistant (MDR) tuberculosis (TB) in Ireland. METHODS: All available Mycobacterium tuberculosis complex (MTBC) isolates (n=42), from MDR-TB cases diagnosed in Ireland between 2001 and 2014, were analysed using phenotypic drug-susceptibility testing, Mycobacterial-Interspersed-Repetitive-Units Variable-Number Tandem-Repeat (MIRU-VNTR) genotyping, and whole-genome sequencing (WGS)...
October 11, 2017: Journal of Infection
https://www.readbyqxmd.com/read/29030401/a-comparison-of-whole-genome-sequencing-to-multigene-panel-testing-in-hypertrophic-cardiomyopathy-patients
#4
Allison L Cirino, Neal K Lakdawala, Barbara McDonough, Lauren Conner, Dale Adler, Mark Weinfeld, Patrick O'Gara, Heidi L Rehm, Kalotina Machini, Matthew Lebo, Carrie Blout, Robert C Green, Calum A MacRae, Christine E Seidman, Carolyn Y Ho
BACKGROUND: As DNA sequencing costs decline, genetic testing options have expanded. Whole exome sequencing and whole genome sequencing (WGS) are entering clinical use, posing questions about their incremental value compared with disease-specific multigene panels that have been the cornerstone of genetic testing. METHODS AND RESULTS: Forty-one patients with hypertrophic cardiomyopathy who had undergone targeted hypertrophic cardiomyopathy genetic testing (either multigene panel or familial variant test) were recruited into the MedSeq Project, a clinical trial of WGS...
October 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/29030167/turnaround-time-of-whole-genome-sequencing-for-mycobacterial-identification-and-drug-susceptibility-testing-in-routine-practice
#5
Ioana D Olaru, Hemu Patel, Katharina Kranzer, Nelun Perera
OBJECTIVES: Until recently whole genome sequencing (WGS) for mycobacteria has been restricted mostly to the research setting. However, in 2017 Public Health England has implemented WGS for routine mycobacterial identification and susceptibility testing for Mycobacterium tuberculosis. Our objective was to evaluate the impact of this change on the laboratory turnaround times and availability of results. METHODS: Over the years 2016 and 2017, the period January 1(st) to April 30(th) was selected to represent before and after implementation of WGS...
October 10, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29029083/unravelling-the-genome-of-a-pseudomonas-aeruginosa-isolate-belonging-to-the-high-risk-clone-st235-reveals-an-integrative-conjugative-element-housing-a-blages-6-carbapenemase
#6
João Botelho, Filipa Grosso, Luísa Peixe
Objectives: In Pseudomonas aeruginosa, the blaGES-6 carbapenemase gene was previously associated with an In1076 class I integron. Here, we conducted a genome-based analysis and explored the genetic platform associated with the mobility of this gene. Methods: WGS of a blaGES-6-harbouring P. aeruginosa isolate (FFUP_PS_690) was performed with Illumina HiSeq, de novo assembly was performed using SPAdes and subsequent bioinformatic analysis was performed concerning antibiotic resistance genes, virulence features and mobile genetic elements...
October 4, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29029072/detection-of-optra-in-the-african-continent-tunisia-within-a-mosaic-enterococcus-faecalis-plasmid-from-urban-wastewaters
#7
Ana R Freitas, Houyem Elghaieb, Ricardo León-Sampedro, Mohamed Salah Abbassi, Carla Novais, Teresa M Coque, Abdennaceur Hassen, Luisa Peixe
Objectives: Oxazolidinone resistance is a serious limitation in the treatment of MDR Enterococcus infections. Plasmid-mediated oxazolidinone resistance has been strongly linked to animals where the use of phenicols might co-select resistance to both antibiotic families. Our goal was to assess the diversity of genes conferring phenicol/oxazolidinone resistance among diverse enterococci and to characterize the optrA genetic environment. Methods: Chloramphenicol-resistant isolates (>16 mg/L, n = 245) from different sources (hospitals/healthy humans/wastewaters/animals) in Portugal, Angola and Tunisia (1996-2016) were selected...
September 26, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29027470/next-generation-sequencing-applications-for-cardiovascular-disease
#8
Samira Kalayinia, Hamidreza Goodarzynejad, Majid Maleki, Nejat Mahdieh
The Human Genome Project (HGP), as the primary sequencing of the human genome, lasted more than one decade to be completed using the traditional Sanger's method. At present, next-generation sequencing (NGS) technology could provide the genome sequence data in hours. NGS has also decreased the expense of sequencing; therefore, nowadays it is possible to carry out both whole-genome (WGS) and whole-exome sequencing (WES) for the variations detection in patients with rare genetic diseases as well as complex disorders such as common cardiovascular diseases (CVDs)...
October 13, 2017: Annals of Medicine
https://www.readbyqxmd.com/read/29026651/snvphyl-a-single-nucleotide-variant-phylogenomics-pipeline-for-microbial-genomic-epidemiology
#9
Aaron Petkau, Philip Mabon, Cameron Sieffert, Natalie C Knox, Jennifer Cabral, Mariam Iskander, Mark Iskander, Kelly Weedmark, Rahat Zaheer, Lee S Katz, Celine Nadon, Aleisha Reimer, Eduardo Taboada, Robert G Beiko, William Hsiao, Fiona Brinkman, Morag Graham, Gary Van Domselaar
The recent widespread application of whole-genome sequencing (WGS) for microbial disease investigations has spurred the development of new bioinformatics tools, including a notable proliferation of phylogenomics pipelines designed for infectious disease surveillance and outbreak investigation. Transitioning the use of WGS data out of the research laboratory and into the front lines of surveillance and outbreak response requires user-friendly, reproducible and scalable pipelines that have been well validated...
June 30, 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29026631/salmonella-typhimurium-gastroenteritis-leading-to-chronic-prosthetic-vascular-graft-infection
#10
Milo Cullinan, Michael Clarke, Tim Dallman, Steven Peart, Deborah Wilson, Daniel Weiand
Introduction. It is estimated up to 6 % of prosthetic vascular grafts become infected. Staphylococcus aureus is predominant in early infection and coagulase-negative staphylococci are predominant in late infections. Enterobacteriaceae cause 14-40 % of prosthetic vascular graft infections. This is, to our knowledge the first reported case of Salmonella gastroenteritis causing chronic prosthetic vascular graft infection (PVGI). Case presentation. A 57 years old lady presented with signs and symptoms of prosthetic vascular graft infection...
August 2017: JMM Case Reports
https://www.readbyqxmd.com/read/29021406/whole-genome-sequencing-of-neisseria-gonorrhoeae-reveals-transmission-clusters-involving-patients-of-mixed-hiv-serostatus
#11
Joanna Peters, Fiona Cresswell, Lauren Amor, Kevin Cole, Gillian Dean, Xavier Didelot, Dilrini De Silva, David W Eyre, John Paul
OBJECTIVES: Prevention and control of gonorrhoea depends on understanding the nature of sexual networks and risk factors for infection. We aimed to use high-resolution typing (whole genome sequencing (WGS)) of Neisseria gonorrhoeae isolates plus patient questionnaire data to gain insights into transmission patterns in a high prevalence setting. METHODS: During a 9-month period (July 2014-March 2015), patients diagnosed with gonorrhoea attending sexual health service in Brighton, UK, were invited to provide anonymised detailed information by questionnaire about risk factors for infection...
October 11, 2017: Sexually Transmitted Infections
https://www.readbyqxmd.com/read/29021291/a-genome-wide-interactome-of-dna-associated-proteins-in-the-human-liver
#12
Ryne C Ramaker, Daniel Savic, Andrew A Hardigan, Kimberly Newberry, Gregory M Cooper, Richard M Myers, Sara J Cooper
Large-scale efforts like the ENCODE Project have made tremendous progress in cataloging the genomic binding patterns of DNA-associated proteins (DAPs), such as transcription factors (TFs). However, most chromatin immunoprecipitation-sequencing (ChIP-seq) analyses have focused on a few immortalized cell lines whose activities and physiology differ in important ways from endogenous cells and tissues. Consequently, binding data from primary human tissue are essential to improving our understanding of in vivo gene regulation...
October 11, 2017: Genome Research
https://www.readbyqxmd.com/read/29017575/evidence-for-viable-and-stable-triploid-trypanosoma-congolense-parasites
#13
Eliane Tihon, Hideo Imamura, Jean-Claude Dujardin, Jan Van Den Abbeele
BACKGROUND: Recent whole genome sequencing (WGS) analysis identified a viable triploid strain of Trypanosoma congolense. This triploid strain BANANCL2 was a clone of the field isolate BANAN/83/CRTRA/64 that was collected from cattle in Burkina Faso in 1983. RESULTS: We demonstrated the viability and stability of triploidy throughout the complete life-cycle of the parasite by infecting tsetse flies with the triploid clone BANANCL2. Proboscis-positive tsetse flies efficiently transmitted the parasites to mice resulting in systemic infections...
October 10, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28993792/the-price-of-whole-genome-sequencing-may-be-decreasing-but-who-will-be-sequenced
#14
Deborah A Marshall, Karen V MacDonald, Jill Oliver Robinson, Lisa F Barcellos, Milena Gianfrancesco, Monica Helm, Amy McGuire, Robert C Green, Michael P Douglas, Michael A Goldman, Kathryn A Phillips
AIM: Since whole-genome sequencing (WGS) information can have positive and negative personal utility for individuals, we examined predictors of willingness to pay (WTP) for WGS. PATIENTS & METHODS: We surveyed two independent populations: adult patients (n = 203) and college seniors (n = 980). Ordinal logistic regression models were used to characterize the relationship between predictors and WTP. RESULTS: Sex, age, education, income, genomic knowledge and knowing someone who had genetic testing or having had genetic testing done personally were associated with significantly higher WTP for WGS...
May 2017: Personalized Medicine
https://www.readbyqxmd.com/read/28992259/wgssat-a-high-throughput-computational-pipeline-for-mining-and-annotation-of-ssr-markers-from-whole-genomes
#15
Manmohan Pandey, Ravindra Kumar, Prachi Srivastava, Suyash Agarwal, Shreya Srivastava, N S Nagpure, J K Jena, Basdeo Kushwaha
Mining and characterization of SSR markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. WGS-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, ncRNA, core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic and core gene region) along with primer identification and mining of cross-species markers...
September 16, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28983307/qtl-mapping-by-whole-genome-re-sequencing-and-analysis-of-candidate-genes-for-nitrogen-use-efficiency-in-rice
#16
Xinghai Yang, Xiuzhong Xia, Zongqiong Zhang, Baoxuan Nong, Yu Zeng, Faqian Xiong, Yanyan Wu, Ju Gao, Guofu Deng, Danting Li
Nitrogen is a major nutritional element in rice production. However, excessive application of nitrogen fertilizer has caused severe environmental pollution. Therefore, development of rice varieties with improved nitrogen use efficiency (NUE) is urgent for sustainable agriculture. In this study, bulked segregant analysis (BSA) combined with whole genome re-sequencing (WGS) technology was applied to finely map quantitative trait loci (QTL) for NUE. A key QTL, designated as qNUE6 was identified on chromosome 6 and further validated by Insertion/Deletion (InDel) marker-based substitutional mapping in recombinants from F2 population (NIL-13B4 × GH998)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28983088/emergence-and-clonal-spread-of-colistin-resistance-due-to-multiple-mutational-mechanisms-in-carbapenemase-producing-klebsiella-pneumoniae-in-london
#17
Jonathan A Otter, Michel Doumith, Frances Davies, Siddharth Mookerjee, Eleonora Dyakova, Mark Gilchrist, Eimear T Brannigan, Kathleen Bamford, Tracey Galletly, Hugo Donaldson, David M Aanensen, Matthew J Ellington, Robert Hill, Jane F Turton, Katie L Hopkins, Neil Woodford, Alison Holmes
Carbapenemase-producing Enterobacteriaceae (CPE) are emerging worldwide, limiting therapeutic options. Mutational and plasmid-mediated mechanisms of colistin resistance have both been reported. The emergence and clonal spread of colistin resistance was analysed in 40 epidemiologically-related NDM-1 carbapenemase producing Klebsiella pneumoniae isolates identified during an outbreak in a group of London hospitals. Isolates from July 2014 to October 2015 were tested for colistin susceptibility using agar dilution, and characterised by whole genome sequencing (WGS)...
October 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28983068/the-glyphosate-based-herbicide-roundup-does-not-elevate-genome-wide-mutagenesis-of-escherichia-coli
#18
Clayton Tincher, Hongan Long, Megan Behringer, Noah Walker, Michael Lynch
Mutations induced by pollutants may promote pathogen evolution, for example by accelerating mutations conferring antibiotic resistance. Generally, evaluating the genome-wide mutagenic effects of long-term sublethal pollutant exposure at single-nucleotide resolution is extremely difficult. To overcome this technical barrier, we use the mutation accumulation/whole-genome sequencing (MA/WGS) method as a mutagenicity test, to quantitatively evaluate genome-wide mutagenesis of Escherichia coli after long-term exposure to a wide gradient of the glyphosate-based herbicide (GBH) Roundup Concentrate Plus...
October 5, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28982116/application-of-whole-genome-sequence-analysis-to-the-study-of-mycobacterium-tuberculosis-in-nunavut-canada
#19
Andrea D Tyler, Elaine Randell, Maureen Baikie, Kym Antonation, Debra Janella, Sara Christianson, Gregory J Tyrrell, Morag Graham, Gary Van Domselaar, Meenu K Sharma
Canada has one of the lowest rates of tuberculosis (TB) in the world, however, among certain sub-populations, disease incidence rates approach those observed in sub-Saharan Africa, and other high incidence regions. In this study, we applied mycobacterial interspersed repetitive unit (MIRU) variable number of tandem repeat (VNTR) and whole genome sequencing (WGS) to the analysis of Mycobacterium tuberculosis isolates obtained from Northern communities in the territory of Nunavut. WGS was carried out using the Illumina MiSeq, with identified variants used to infer phylogenetic relationships and annotated to infer functional implications...
2017: PloS One
https://www.readbyqxmd.com/read/28974944/whole-genome-sequencing-for-national-surveillance-of-shigella-flexneri
#20
Marie A Chattaway, David R Greig, Amy Gentle, Hassan B Hartman, Timothy J Dallman, Claire Jenkins
National surveillance of Shigella flexneri ensures the rapid detection of outbreaks to facilitate public health investigation and intervention strategies. In this study, we used whole-genome sequencing (WGS) to type S. flexneri in order to detect linked cases and support epidemiological investigations. We prospectively analyzed 330 isolates of S. flexneri received at the Gastrointestinal Bacteria Reference Unit at Public Health England between August 2015 and January 2016. Traditional phenotypic and WGS sub-typing methods were compared...
2017: Frontiers in Microbiology
keyword
keyword
9643
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"