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https://www.readbyqxmd.com/read/29221171/proteogenomic-analysis-prioritises-functional-single-nucleotide-variants-in-cancer-samples
#1
Shiyong Ma, Ranjeeta Menon, Rebecca C Poulos, Jason W H Wong
Massively parallel DNA sequencing enables the detection of thousands of germline and somatic single nucleotide variants (SNVs) in cancer samples. The functional analysis of these mutations is often carried out through in silico predictions, with further downstream experimental validation rarely performed. Here, we examine the potential of using mass spectrometry-based proteomics data to further annotate the function of SNVs in cancer samples. RNA-seq and whole genome sequencing (WGS) data from Jurkat cells were used to construct a custom database of single amino acid variant (SAAV) containing peptides and identified over 1,000 such peptides in two Jurkat proteomics datasets...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29220507/assessing-the-heterogeneity-of-in-silico-plasmid-predictions-based-on-whole-genome-sequenced-clinical-isolates
#2
Cedric C Laczny, Valentina Galata, Achim Plum, Andreas E Posch, Andreas Keller
High-throughput next-generation shotgun sequencing of pathogenic bacteria is growing in clinical relevance, especially for chromosomal DNA-based taxonomic identification and for antibiotic resistance prediction. Genetic exchange is facilitated for extrachromosomal DNA, e.g. plasmid-borne antibiotic resistance genes. Consequently, accurate identification of plasmids from whole-genome sequencing (WGS) data remains one of the major challenges for sequencing-based precision medicine in infectious diseases. Here, we assess the heterogeneity of four state-of-the-art tools (cBar, PlasmidFinder, plasmidSPAdes and Recycler) for the in silico prediction of plasmid-derived sequences from WGS data...
December 5, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29216350/italian-nationwide-survey-on-pseudomonas-aeruginosa-from-invasive-infections-activity-of-ceftolozane-tazobactam-and-comparators-and-molecular-epidemiology-of-carbapenemase-producers
#3
Tommaso Giani, Fabio Arena, Simona Pollini, Vincenzo Di Pilato, Marco Maria D'Andrea, Lucia Henrici De Angelis, Matteo Bassetti, Gian Maria Rossolini
Objectives: Pseudomonas aeruginosa is a major cause of severe healthcare-associated infections and often shows MDR phenotypes. Ceftolozane/tazobactam is a new cephalosporin/β-lactamase inhibitor combination with potent activity against P. aeruginosa. This survey was carried out to evaluate the susceptibility of P. aeruginosa, circulating in Italy, to ceftolozane/tazobactam and comparators and to investigate the molecular epidemiology of carbapenemase-producing strains. Methods: Consecutive non-replicate P...
December 5, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29216342/comparison-of-phenotypic-and-wgs-derived-antimicrobial-resistance-profiles-of-salmonella-enterica-serovars-typhi-and-paratyphi
#4
Martin R Day, Michel Doumith, Vivienne Do Nascimento, Satheesh Nair, Philip M Ashton, Claire Jenkins, Timothy J Dallman, Flora J Stevens, Joanne Freedman, Katie L Hopkins, Neil Woodford, Elizabeth M De Pinna, Gauri Godbole
Objectives: Surveillance of antimicrobial resistance (AMR) in Salmonella enterica serovars Typhi and Paratyphi is essential to provide an evidence base for empirical treatment protocols and to monitor emerging AMR. We sought to compare phenotypic and WGS-based genotypic methods for the detection of AMR in Salmonella Typhi and Salmonella Paratyphi. Methods: WGS data from 603 isolates of Salmonella Typhi (n = 332) and Salmonella Paratyphi (n = 271) were mapped to genes or chromosomal mutations known to be associated with phenotypic AMR and compared with phenotypic susceptibility data interpreted using breakpoints recommended by EUCAST...
December 5, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29216251/molecular-characterization-of-hepatitis-b-virus-in-bangladesh-reveals-a-highly-recombinant-population
#5
Saif Ullah Munshi, Thanh Thi Thanh Tran, Truc Nhu Thanh Vo, Shahina Tabassum, Nahida Sultana, Trang Hoa Nguyen, Munira Jahan, Chau Ngoc Le, Stephen Baker, Motiur Rahman
The natural history and treatment outcome of hepatitis B viruses (HBV) infection is largely dependent on genotype, subgenotype, and the presence or absence of virulence associated mutations. We have studied the prevalence of genotype and subgenotype as well as virulence and drug resistance associated mutations and prevalence of recombinant among HBV from Bangladesh. A prospective cross-sectional study was conducted among treatment naïve chronic HBV patients attending at Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh for HBV viral load assessment between June and August 2015...
2017: PloS One
https://www.readbyqxmd.com/read/29215633/measuring-mutation-accumulation-in-single-human-adult-stem-cells-by-whole-genome-sequencing-of-organoid-cultures
#6
Myrthe Jager, Francis Blokzijl, Valentina Sasselli, Sander Boymans, Roel Janssen, Nicolle Besselink, Hans Clevers, Ruben van Boxtel, Edwin Cuppen
Characterization of mutational processes in adult stem cells (ASCs) will improve our understanding of aging-related diseases, such as cancer and organ failure, and may ultimately help prevent the development of these diseases. Here, we present a method for cataloging mutations in individual human ASCs without the necessity of using error-prone whole-genome amplification. Single ASCs are expanded in vitro into clonal organoid cultures to generate sufficient DNA for accurate whole-genome sequencing (WGS) analysis...
January 2018: Nature Protocols
https://www.readbyqxmd.com/read/29208648/optimizing-genomic-methods-for-mapping-and-identification-of-candidate-variants-in-enu-mutagenesis-screens-using-inbred-mice
#7
Krista A Geister, Andrew E Timms, David R Beier
Positional cloning of ENU-induced mutations has traditionally relied on analysis of polymorphic variation between two strains.  In contrast, the application of whole genome sequencing (WGS) has enabled gene discovery in mutant lines maintained on an inbred genetic background.  This approach utilizes genetic variation derived from ENU-induced variants for mapping, and reduces the likelihood of phenotypic variation, making it an ideal method for genetic modifier screening.  Here, we describe the results of such a screen, wherein we determined the minimal number of mutant genomic DNA samples to include in our analyses, and improved the sensitivity of our screen by individually barcoding each genomic DNA library...
December 5, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29207129/identification-of-susceptibility-loci-for-thoracic-ossification-of-the-posterior-longitudinal-ligament-by-whole-genome-sequencing
#8
Peng Wang, Xiao Liu, Bin Zhu, Yunlong Ma, Lei Yong, Ze Teng, Yongqiang Wang, Chen Liang, Guanping He, Xiaoguang Liu
Ossification of the posterior longitudinal ligament (OPLL) is a myelopathy commonly observed in the cervical spine. By contrast, thoracic OPLL (T‑OPLL) is rare but more severe. Previous studies have identified several polymorphisms in osteogenic genes that are associated with the occurrence and development of cervical OPLL. However, few genetic studies have evaluated T‑OPLL. The present study aimed to identify the genetic factors for OPLL by performing whole‑genome sequencing (WGS) in 30 unrelated northern Chinese Han patients with T‑OPLL...
November 28, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29203764/3d-genome-of-multiple-myeloma-reveals-spatial-genome-disorganization-associated-with-copy-number-variations
#9
Pengze Wu, Tingting Li, Ruifeng Li, Lumeng Jia, Ping Zhu, Yifang Liu, Qing Chen, Daiwei Tang, Yuezhou Yu, Cheng Li
The Hi-C method is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. Here, we integrate Hi-C, whole-genome sequencing (WGS) and RNA-seq to study the 3D genome architecture of multiple myeloma (MM) and how it associates with genomic variation and gene expression. Our results show that Hi-C interaction matrices are biased by copy number variations (CNVs) and can be used to detect CNVs. Also, combining Hi-C and WGS data can improve the detection of translocations...
December 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/29202180/emergence-and-spread-of-epidemic-multidrug-resistant-pseudomonas-aeruginosa
#10
Tohru Miyoshi-Akiyama, Tatsuya Tada, Norio Ohmagari, Nguyen Viet Hung, Prasit Tharavichitkul, Bharat Mani Pokhrel, Marek Gniadkowski, Masahiro Shimojima, Teruo Kirikae
Pseudomonas aeruginosa (P. aeruginosa) is one of the most common nosocomial pathogens worldwide. Although the emergence of multidrug-resistant (MDR) P. aeruginosa is a critical problem in medical practice, the key features involved in the emergence and spread of MDR P. aeruginosa remain unknown. This study utilized whole genome sequence (WGS) analyses to define the population structure of 185 P. aeruginosa clinical isolates from several countries. Of these 185 isolates, 136 were categorized into sequence type (ST) 235, one of the most common types worldwide...
November 29, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29198370/whole-genome-sequencing-analysis-of-salmonella-enterica-serovar-weltevreden-isolated-from-human-stool-and-contaminated-food-samples-collected-from-the-southern-coastal-area-of-china
#11
Baisheng Li, Xingfen Yang, Hailing Tan, Bixia Ke, Dongmei He, Haiyan Wang, Qiuxia Chen, Changwen Ke, Yonghui Zhang
Salmonella enterica serovar Weltevreden is the most common non-typhoid Salmonella found in South and Southeast Asia. It causes zoonoses worldwide through the consumption of contaminated foods and seafood, and is considered as an important food-borne pathogen in China, especially in the Southern coastal area. We compared the whole genomes of 44 S. Weltevreden strains isolated from human stool and contaminated food samples from Southern Coastal China, in order to investigate their phylogenetic relationships and establish their genetic relatedness to known international strains...
October 31, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29197946/first-large-genomic-inversion-in-familial-cerebral-cavernous-malformation-identified-by-whole-genome-sequencing
#12
Stefanie Spiegler, Matthias Rath, Sabine Hoffjan, Philipp Dammann, Ulrich Sure, Axel Pagenstecher, Tim Strom, Ute Felbor
Familial cerebral cavernous malformations (CCMs) predispose to seizures and hemorrhagic stroke. Molecular genetic analyses of CCM1, CCM2, and CCM3 result in a mutation detection rate of up to 98%. However, only whole genome sequencing (WGS) in combination with the Manta algorithm for analyses of structural variants revealed a heterozygous 24 kB inversion including exon 1 of CCM2 in a 12-year-old boy with familial CCMs. Its breakpoints were fine-mapped, and quantitative analysis on RNA confirmed reduced CCM2 expression...
December 2, 2017: Neurogenetics
https://www.readbyqxmd.com/read/29197647/genetic-basis-of-chromosomally-encoded-mcr-1-gene
#13
Ruichao Li, Hua Yu, Miaomiao Xie, Kaichao Chen, Ning Dong, Dachuan Lin, Edward Wai-Chi Chan, Sheng Chen
Compared to plasmid-bearing mcr-1, the occurrence of chromosomally-encoded mcr-1 was rare although it has been reported in several cases. This study aims to investigate the genetic features of chromosomally-encoded mcr-1 among E. coli strains and potential genetic basis governing the mobilization of mcr-1 in bacterial chromosomes. The genome sequences of 16 E. coli strains containing a chromosomal mcr-1 gene were obtained and analyzed. Phylogenetic and WGS (Whole Genome Sequencing) analysis demonstrated that mcr-1 was associated with four major types of genetic arrangements, namely ISApl1-mcr1-orf, Tn6330, complex Tn6330 and ΔTn6330 in chromosomes of genetically unrelated E...
November 29, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29191164/weighted-likelihood-inference-of-genomic-autozygosity-patterns-in-dense-genotype-data
#14
Alexandra Blant, Michelle Kwong, Zachary A Szpiech, Trevor J Pemberton
BACKGROUND: Genomic regions of autozygosity (ROA) arise when an individual is homozygous for haplotypes inherited identical-by-descent from ancestors shared by both parents. Over the past decade, they have gained importance for understanding evolutionary history and the genetic basis of complex diseases and traits. However, methods to infer ROA in dense genotype data have not evolved in step with advances in genome technology that now enable us to rapidly create large high-resolution genotype datasets, limiting our ability to investigate their constituent ROA patterns...
December 1, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29186015/establishing-genotype-to-phenotype-relationships-in-bacteria-causing-hospital-acquired-pneumonia-a-prelude-to-the-application-of-clinical-metagenomics
#15
REVIEW
Etienne Ruppé, Abdessalam Cherkaoui, Vladimir Lazarevic, Stéphane Emonet, Jacques Schrenzel
Clinical metagenomics (CMg), referred to as the application of next-generation sequencing (NGS) to clinical samples, is a promising tool for the diagnosis of hospital-acquired pneumonia (HAP). Indeed, CMg allows identifying pathogens and antibiotic resistance genes (ARGs), thereby providing the information required for the optimization of the antibiotic regimen. Hence, provided that CMg would be faster than conventional culture, the probabilistic regimen used in HAP could be tailored faster, which should lead to an expected decrease of mortality and morbidity...
November 29, 2017: Antibiotics
https://www.readbyqxmd.com/read/29183554/molecular-characterisation-of-human-shiga-toxin-producing-escherichia-coli-o26-strains-results-of-an-outbreak-investigation-romania-february-to-august-2016
#16
Codruţa-Romaniţa Usein, Adriana Simona Ciontea, Cornelia Mãdãlina Militaru, Maria Condei, Sorin Dinu, Mihaela Oprea, Daniela Cristea, Valeria Michelacci, Gaia Scavia, Lavinia Cipriana Zota, Alina Zaharia, Stefano Morabito
IntroductionAt the beginning of 2016, an increase in paediatric haemolytic uremic syndrome (HUS) cases was observed in Romania. The microbiological investigations allowed isolation of Shiga toxin-producing Escherichia coli (STEC) O26 as the causative agent from most cases. Methods: An enhanced national surveillance of HUS and severe diarrhoea was established across the country following the identification of the first cases and was carried out until August 2016. A total of 15 strains were isolated from 10 HUS and five diarrhoea cases...
November 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/29182725/genomic-epidemiology-and-antimicrobial-resistance-of-neisseria-gonorrhoeae-in-new-zealand
#17
Robyn S Lee, Torsten Seemann, Helen Heffernan, Jason C Kwong, Anders Gonçalves da Silva, Glen P Carter, Rosemary Woodhouse, Kristin H Dyet, Dieter M Bulach, Timothy P Stinear, Benjamin P Howden, Deborah A Williamson
Background: Antimicrobial-resistant Neisseria gonorrhoeae is a major threat to public health. No studies to date have examined the genomic epidemiology of gonorrhoea in the Western Pacific Region, where the incidence of gonorrhoea is particularly high. Methods: A population-level study of N. gonorrhoeae in New Zealand (October 2014 to May 2015). Comprehensive susceptibility testing and WGS data were obtained for 398 isolates. Relatedness was inferred using phylogenetic trees, and pairwise core SNPs...
November 22, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29181276/i-atac-interactive-pipeline-for-the-management-and-pre-processing-of-atac-seq-samples
#18
Zeeshan Ahmed, Duygu Ucar
Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology, we are now accumulating ATAC-seq samples from clinical samples at an unprecedented rate. These epigenomic profiles hold the key to uncovering how transcriptional programs are established in diverse human cells and are disrupted by genetic or environmental factors...
2017: PeerJ
https://www.readbyqxmd.com/read/29180984/risk-of-transmission-of-antimicrobial-resistant-escherichia-coli-from-commercial-broiler-and-free-range-retail-chicken-in-india
#19
Arif Hussain, Sabiha Shaik, Amit Ranjan, Nishant Nandanwar, Sumeet K Tiwari, Mohammad Majid, Ramani Baddam, Insaf A Qureshi, Torsten Semmler, Lothar H Wieler, Mohammad A Islam, Dipshikha Chakravortty, Niyaz Ahmed
Multidrug-resistant Escherichia coli infections are a growing public health concern. This study analyzed the possibility of contamination of commercial poultry meat (broiler and free-range) with pathogenic and or multi-resistant E. coli in retail chain poultry meat markets in India. We analyzed 168 E. coli isolates from broiler and free-range retail poultry (meat/ceca) sampled over a wide geographical area, for their antimicrobial sensitivity, phylogenetic groupings, virulence determinants, extended-spectrum-β-lactamase (ESBL) genotypes, fingerprinting by Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR and genetic relatedness to human pathogenic E...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29179772/recurrent-de-novo-mutations-in-neurodevelopmental-disorders-properties-and-clinical-implications
#20
REVIEW
Amy B Wilfert, Arvis Sulovari, Tychele N Turner, Bradley P Coe, Evan E Eichler
Next-generation sequencing (NGS) is now more accessible to clinicians and researchers. As a result, our understanding of the genetics of neurodevelopmental disorders (NDDs) has rapidly advanced over the past few years. NGS has led to the discovery of new NDD genes with an excess of recurrent de novo mutations (DNMs) when compared to controls. Development of large-scale databases of normal and disease variation has given rise to metrics exploring the relative tolerance of individual genes to human mutation. Genetic etiology and diagnosis rates have improved, which have led to the discovery of new pathways and tissue types relevant to NDDs...
November 27, 2017: Genome Medicine
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