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https://www.readbyqxmd.com/read/29691385/deep-whole-genome-sequencing-reveals-recent-selection-signatures-linked-to-evolution-and-disease-risk-of-japanese
#1
Yukinori Okada, Yukihide Momozawa, Saori Sakaue, Masahiro Kanai, Kazuyoshi Ishigaki, Masato Akiyama, Toshihiro Kishikawa, Yasumichi Arai, Takashi Sasaki, Kenjiro Kosaki, Makoto Suematsu, Koichi Matsuda, Kazuhiko Yamamoto, Michiaki Kubo, Nobuyoshi Hirose, Yoichiro Kamatani
Understanding natural selection is crucial to unveiling evolution of modern humans. Here, we report natural selection signatures in the Japanese population using 2234 high-depth whole-genome sequence (WGS) data (25.9×). Using rare singletons, we identify signals of very recent selection for the past 2000-3000 years in multiple loci (ADH cluster, MHC region, BRAP-ALDH2, SERHL2). In large-scale genome-wide association study (GWAS) dataset (n = 171,176), variants with selection signatures show enrichment in heterogeneity of derived allele frequency spectra among the geographic regions of Japan, highlighted by two major regional clusters (Hondo and Ryukyu)...
April 24, 2018: Nature Communications
https://www.readbyqxmd.com/read/29691340/extensive-gene-amplification-as-a-mechanism-for-piperacillin-tazobactam-resistance-in-escherichia-coli
#2
Lisa M Schechter, David P Creely, Cherilyn D Garner, Dee Shortridge, Hoan Nguyen, Lei Chen, Blake M Hanson, Erica Sodergren, George M Weinstock, W Michael Dunne, Alex van Belkum, Shana R Leopold
Although the TEM-1 β-lactamase (BlaTEM-1 ) hydrolyzes penicillins and narrow-spectrum cephalosporins, organisms expressing this enzyme are typically susceptible to β-lactam/β-lactamase inhibitor combinations such as piperacillin-tazobactam (TZP). However, our previous work led to the discovery of 28 clinical isolates of Escherichia coli resistant to TZP that contained only bla TEM-1 One of these isolates, E. coli 907355, was investigated further in this study. E. coli 907355 exhibited significantly higher β-lactamase activity and BlaTEM-1 protein levels when grown in the presence of subinhibitory concentrations of TZP...
April 24, 2018: MBio
https://www.readbyqxmd.com/read/29691339/outbreak-of-invasive-wound-mucormycosis-in-a-burn-unit-due-to-multiple-strains-of-mucor-circinelloides-f-circinelloides-resolved-by-whole-genome-sequencing
#3
Dea Garcia-Hermoso, Alexis Criscuolo, Soo Chan Lee, Matthieu Legrand, Marc Chaouat, Blandine Denis, Matthieu Lafaurie, Martine Rouveau, Charles Soler, Jean-Vivien Schaal, Maurice Mimoun, Alexandre Mebazaa, Joseph Heitman, Françoise Dromer, Sylvain Brisse, Stéphane Bretagne, Alexandre Alanio
Mucorales are ubiquitous environmental molds responsible for mucormycosis in diabetic, immunocompromised, and severely burned patients. Small outbreaks of invasive wound mucormycosis (IWM) have already been reported in burn units without extensive microbiological investigations. We faced an outbreak of IWM in our center and investigated the clinical isolates with whole-genome sequencing (WGS) analysis. We analyzed M. circinelloides isolates from patients in our burn unit (BU1, Hôpital Saint-Louis, Paris, France) together with nonoutbreak isolates from Burn Unit 2 (BU2, Paris area) and from France over a 2-year period (2013 to 2015)...
April 24, 2018: MBio
https://www.readbyqxmd.com/read/29688850/first-case-of-aml-with-rare-chromosome-translocations-a-case-report-of-twins
#4
Lin Wang, Yanhua Sun, Yanli Sun, Lingbin Meng, Xin Xu
BACKGROUND: Leukemia is different from solid tumor by harboring genetic rearrangements that predict prognosis and guide treatment strategy. PML-RARA, RUNX1-RUNX1T1, and KMT2A-rearrangement are common genetic rearrangements that drive the development of acute myeloid leukemia (AML). By contrast, rare genetic rearrangements may also contribute to leukemogenesis but are less summarized. CASE PRESENTATION: Here we reported rare fusion genes ZNF717-ZNF37A, ZNF273-DGKA, and ZDHHC2-TTTY15 in a 47-year-old AML-M4 patient with FLT3 internal tandem duplication (ITD) discovered by whole genome sequencing (WGS) using the patient's healthy sibling as a sequencing control...
April 23, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29688339/4-5-years-within-patient-evolution-of-a-colistin-resistant-kpc-producing-klebsiella-pneumoniae-st258
#5
Agnès B Jousset, Rémy A Bonnin, Isabelle Rosinski-Chupin, Delphine Girlich, Gaëlle Cuzon, Nicolas Cabanel, Hélène Frech, Eric Farfour, Laurent Dortet, Philippe Glaser, Thierry Naas
Background: KPC-producing Klebsiella pneumoniae (KPC-Kp) have emerged globally over the last decade as a major nosocomial pathogen that threatens patient's care. These highly resistant bacteria are mostly associated with a single Kp clonal group (CG) CG258, but the reasons for its host and hospital adaptation remain largely unknown. Methods: We analyzed the in vivo evolution of a colistin-resistant KPC-Kp-CG258 strain that contaminated a patient following an endoscopy, and was responsible for a fatal bacteraemia 4...
April 21, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29688227/whole-genome-sequencing-of-caribbean-hispanic-families-with-late-onset-alzheimer-s-disease
#6
Badri N Vardarajan, Sandra Barral, James Jaworski, Gary W Beecham, Elizabeth Blue, Giuseppe Tosto, Dolly Reyes-Dumeyer, Martin Medrano, Rafael Lantigua, Adam Naj, Timothy Thornton, Anita DeStefano, Eden Martin, Li-San Wang, Lisa Brown, William Bush, Cornelia van Duijn, Allison Goate, Lindsay Farrer, Jonathan L Haines, Eric Boerwinkle, Gerard Schellenberg, Ellen Wijsman, Margaret A Pericak-Vance, Richard Mayeux, Li-San Wang
Objective: To identify rare causal variants underlying known loci that segregate with late-onset Alzheimer's disease (LOAD) in multiplex families. Methods: We analyzed whole genome sequences (WGS) from 351 members of 67 Caribbean Hispanic (CH) families from Dominican Republic and New York multiply affected by LOAD. Members of 67 CH and additional 47 Caucasian families underwent WGS as a part of the Alzheimer's Disease Sequencing Project (ADSP). All members of 67 CH families, an additional 48 CH families and an independent CH case-control cohort were subsequently genotyped for validation...
April 2018: Annals of Clinical and Translational Neurology
https://www.readbyqxmd.com/read/29681898/the-versatile-mutational-resistome-of-pseudomonas-aeruginosa
#7
REVIEW
Carla López-Causapé, Gabriel Cabot, Ester Del Barrio-Tofiño, Antonio Oliver
One of the most striking features of Pseudomonas aeruginosa is its outstanding capacity for developing antimicrobial resistance to nearly all available antipseudomonal agents through the selection of chromosomal mutations, leading to the failure of the treatment of severe hospital-acquired or chronic infections. Recent whole-genome sequencing (WGS) data obtained from in vitro assays on the evolution of antibiotic resistance, in vivo monitoring of antimicrobial resistance development, analysis of sequential cystic fibrosis isolates, and characterization of widespread epidemic high-risk clones have provided new insights into the evolutionary dynamics and mechanisms of P...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29673316/a-study-on-fast-calling-variants-from-next-generation-sequencing-data-using-decision-tree
#8
Zhentang Li, Yi Wang, Fei Wang
BACKGROUND: The rapid development of next-generation sequencing (NGS) technology has continuously been refreshing the throughput of sequencing data. However, due to the lack of a smart tool that is both fast and accurate, the analysis task for NGS data, especially those with low-coverage, remains challenging. RESULTS: We proposed a decision-tree based variant calling algorithm. Experiments on a set of real data indicate that our algorithm achieves high accuracy and sensitivity for SNVs and indels and shows good adaptability on low-coverage data...
April 19, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29672479/protracted-outbreak-of-salmonella-newport-infections-linked-to-ground-beef-possible-role-of-dairy-cows-21-states-2016-2017
#9
Katherine E Heiman Marshall, Mackenzie Tewell, Selam Tecle, Molly Leeper, Jennifer Sinatra, Bonnie Kissler, Adrienne Fung, Kerri Brown, Darlene Wagner, Eija Trees, Kelley B Hise, Vishnu Chaturvedi, Linda K Schlater, Brenda R Morningstar-Shaw, Laura Whitlock, Kristin Holt, Karen Becker, Megin Nichols, Ian T Williams, Michael Jhung, Matthew E Wise, Laura Gieraltowski
In January 2017, CDC identified a cluster of Salmonella enterica serotype Newport infections with isolates sharing an indistinguishable pulsed-field gel electrophoresis (PFGE) pattern, JJPX01.0010 (pattern 10), through PulseNet, the national molecular subtyping network for foodborne disease surveillance. This report summarizes the investigation by CDC, state and local health and agriculture departments, and the U.S. Department of Agriculture's Food Safety and Inspection Service (USDA-FSIS) and discusses the possible role of dairy cows as a reservoir for strains of Salmonella that persistently cause human illness...
April 20, 2018: MMWR. Morbidity and Mortality Weekly Report
https://www.readbyqxmd.com/read/29671389/modeling-and-correct-the-gc-bias-of-tumor-and-normal-wgs-data-for-scna-based-tumor-subclonal-population-inferring
#10
Yanshuo Chu, Mingxiang Teng, Yadong Wang
BACKGROUND: Somatic copy number alternations (SCNAs) can be utilized to infer tumor subclonal populations in whole genome seuqncing studies, where usually their read count ratios between tumor-normal paired samples serve as the inferring proxy. Existing SCNA based subclonal population inferring tools consider the GC bias of tumor and normal sample is of the same fature, and could be fully offset by read count ratio. However, we found that, the read count ratio on SCNA segments presents a Log linear biased pattern, which influence existing read count ratios based subclonal inferring tools performance...
April 11, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29669108/genomic-context-of-resistance-genes-within-a-french-clinical-mdr-proteus-mirabilis-identification-of-the-novel-genomic-resistance-island-gipmi1
#11
Eliane Siebor, Claire de Curraize, Catherine Neuwirth
Objectives: To determine the location of the antibiotic resistance genes in the MDR Proteus mirabilis PmPHI clinical isolate. Methods: WGS and de novo assembly were performed. BLAST searches were used to identify relevant contigs. PCR and Sanger sequencing were used to link the fragments of interest and fill the gaps. Results: P. mirabilis PmPHI was resistant to six classes of antibiotics: penicillins, aminoglycosides, phenicols, tetracyclines, folate inhibitors and fluoroquinolones...
April 12, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29668933/the-human-clone-st22-sccmec-iv-methicillin-resistant-staphylococcus-aureus-isolated-from-swine-herds-and-wild-primates-in-nepal-is-man-the-common-source
#12
Marilyn C Roberts, Prabhu Raj Joshi, Alexander L Greninger, Daira Melendez, Saroj Paudel, Mahesh Acharya, Nabin Kishor Bimali, Narayan P Koju, David No, Mukesh Chalise, Randall C Kyes
Swine nasal samples [n = 282] were collected from 12 randomly selected farms around Kathmandu, Nepal, from healthy animals. In addition, wild monkey (Macaca mulatta) saliva samples [n = 59] were collected near temples areas in Kathmandu using a non-invasive sampling technique. All samples were processed for MRSA using standardized selective media and conventional biochemical tests. MRSA verification was done and isolates characterized by SCCmec, multilocus sequence typing, whole genome sequencing [WGS] and antibiotic susceptibilities...
May 1, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29667179/characteristics-of-genomic-alterations-of-lung-adenocarcinoma-in-young-never-smokers
#13
Wenxin Luo, Panwen Tian, Yue Wang, Heng Xu, Lu Chen, Chao Tang, Yang Shu, Shouyue Zhang, Zhoufeng Wang, Jun Zhang, Li Zhang, Lili Jiang, Lunxu Liu, Guowei Che, Chenglin Guo, Hong Zhang, Jiali Wang, Weimin Li
Non-small cell lung cancer (NSCLC) has been recognized as a highly heterogeneous disease with phenotypic and genotypic diversity in each subgroup. While never-smoker patients with NSCLC have been well studied through next generation sequencing, we have yet to recognize the potentially unique molecular features of young never-smoker patients with NSCLC. In this study, we conducted whole genome sequencing (WGS) to characterize the genomic alterations of 36 never-smoker Chinese patients, who were diagnosed with lung adenocarcinoma (LUAD) at 45 years or younger...
April 18, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29664901/genetic-profiling-of-mycobacterium-bovis-strains-from-slaughtered-cattle-in-eritrea
#14
Michael Kahsay Ghebremariam, Tiny Hlokwe, Victor P M G Rutten, Alberto Allepuz, Simeon Cadmus, Adrian Muwonge, Suelee Robbe-Austerman, Anita L Michel
Mycobacterium bovis (M.bovis) is the main causative agent for bovine tuberculosis (BTB) and can also be the cause of zoonotic tuberculosis in humans. In view of its zoonotic nature, slaughterhouse surveillance, potentially resulting in total or partial condemnation of the carcasses and organs, is conducted routinely.Spoligotyping, VNTR profiling, and whole genome sequencing (WGS)ofM. bovis isolated from tissues with tuberculosis-like lesions collected from 14 cattle at Eritrea's largest slaughterhouse in the capital Asmara, were conducted...
April 17, 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29660021/mapping-of-genomic-egfrviii-deletions-in-glioblastoma-insight-into-rearrangement-mechanisms-and-biomarker-development
#15
Tomoyuki Koga, Bin Li, Javier M Figueroa, Bing Ren, Clark C Chen, Bob S Carter, Frank B Furnari
Background: Epidermal growth factor receptor (EGFR) variant III (vIII) is the most common oncogenic rearrangement in glioblastoma (GBM) generated by deletion of exons two to seven of EGFR. The proximal breakpoints occur in variable positions within the 123-kb intron one, presenting significant challenges in terms of PCR-based mapping. Molecular mechanisms underlying these deletions remain unclear. Methods: We determined the presence of EGFRvIII and its breakpoints for 29 GBM samples using quantitative polymerase chain reaction (qPCR), arrayed PCR mapping, Sanger sequencing, and whole genome sequencing (WGS)...
April 12, 2018: Neuro-oncology
https://www.readbyqxmd.com/read/29659873/two-new-salmonella-genomic-islands-1-from-proteus-mirabilis-and-description-of-blactx-m-15-on-a-variant-sgi1-k7
#16
Claire de Curraize, Catherine Neuwirth, Julien Bador, Angélique Chapuis, Lucie Amoureux, Eliane Siebor
Objectives: To characterize the structure of Salmonella genomic islands 1 (SGI1s) from two clinical Proteus mirabilis isolates: one producing an ESBL and the other a penicillinase. Methods: WGS completed by PCR and Sanger sequencing was performed to determine sequences of SGI1s from Pm2CHAMA and Pm37THOMI strains. Results: Two new variants of SGI1 named SGI1-Pm2CHAMA (53.6 kb) and SGI1-K7 (55.1 kb) were identified. The backbone of SGI1-Pm2CHAMA shared 99...
April 11, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29659855/mobile-colistin-resistance-gene-mcr-5-in-porcine-aeromonas-hydrophila
#17
Shizhen Ma, Chengtao Sun, Anette Hulth, Jiyun Li, Lennart E Nilsson, Yuqing Zhou, Stefan Börjesson, Zhenwang Bi, Zhenqiang Bi, Qiang Sun, Yang Wang
Objectives: To characterize the mobile colistin resistance gene mcr-5 in Aeromonas hydrophila from backyard pigs in rural areas of China. Methods: Pig faecal samples from 194 households were directly tested for the presence of mcr-5 by PCR assay and the phenotypic antimicrobial susceptibility profiles of the mcr-5-positive isolates were determined using the broth dilution method. The genomic location and transferability of mcr-5 were analysed by S1-PFGE with Southern blotting and DNA hybridization, and natural transformation, respectively...
April 11, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29659753/patient-and-strain-characteristics-associated-with-clostridium-difficile-transmission-and-adverse-outcomes
#18
Jessica S H Martin, David W Eyre, Warren N Fawley, David Griffiths, Kerrie Davies, Damian P C Mawer, Timothy E A Peto, Derrick W Crook, A Sarah Walker, Mark H Wilcox
Background: No previous study has used whole-genome sequencing (WGS) to investigate risk factors for C. difficile(CD) transmission between symptomatic cases, or assessed the impact of recent acquisition on patient outcome. Methods: This retrospective cohort study included consecutive diarrhoeal samples positive by cytotoxin assay in Leeds, UK(Aug10-Apr12). All samples underwent culture, ribotyping and WGS(Illumina). Sequenced isolates were compared using single nucleotide variants(SNVs)...
April 12, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29656860/truncating-variants-in-naa15-are-associated-with-variable-levels-of-intellectual-disability-autism-spectrum-disorder-and-congenital-anomalies
#19
Hanyin Cheng, Avinash V Dharmadhikari, Sylvia Varland, Ning Ma, Deepti Domingo, Robert Kleyner, Alan F Rope, Margaret Yoon, Asbjørg Stray-Pedersen, Jennifer E Posey, Sarah R Crews, Mohammad K Eldomery, Zeynep Coban Akdemir, Andrea M Lewis, Vernon R Sutton, Jill A Rosenfeld, Erin Conboy, Katherine Agre, Fan Xia, Magdalena Walkiewicz, Mauro Longoni, Frances A High, Marjon A van Slegtenhorst, Grazia M S Mancini, Candice R Finnila, Arie van Haeringen, Nicolette den Hollander, Claudia Ruivenkamp, Sakkubai Naidu, Sonal Mahida, Elizabeth E Palmer, Lucinda Murray, Derek Lim, Parul Jayakar, Michael J Parker, Stefania Giusto, Emanuela Stracuzzi, Corrado Romano, Jennifer S Beighley, Raphael A Bernier, Sébastien Küry, Mathilde Nizon, Mark A Corbett, Marie Shaw, Alison Gardner, Christopher Barnett, Ruth Armstrong, Karin S Kassahn, Anke Van Dijck, Geert Vandeweyer, Tjitske Kleefstra, Jolanda Schieving, Marjolijn J Jongmans, Bert B A de Vries, Rolph Pfundt, Bronwyn Kerr, Samantha K Rojas, Kym M Boycott, Richard Person, Rebecca Willaert, Evan E Eichler, R Frank Kooy, Yaping Yang, Joseph C Wu, James R Lupski, Thomas Arnesen, Gregory M Cooper, Wendy K Chung, Jozef Gecz, Holly A F Stessman, Linyan Meng, Gholson J Lyon
N-alpha-acetylation is a common co-translational protein modification that is essential for normal cell function in humans. We previously identified the genetic basis of an X-linked infantile lethal Mendelian disorder involving a c.109T>C (p.Ser37Pro) missense variant in NAA10, which encodes the catalytic subunit of the N-terminal acetyltransferase A (NatA) complex. The auxiliary subunit of the NatA complex, NAA15, is the dimeric binding partner for NAA10. Through a genotype-first approach with whole-exome or genome sequencing (WES/WGS) and targeted sequencing analysis, we identified and phenotypically characterized 38 individuals from 33 unrelated families with 25 different de novo or inherited, dominantly acting likely gene disrupting (LGD) variants in NAA15...
April 9, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29653190/evaluation-of-whole-genome-sequencing-and-software-tools-for-drug-susceptibility-testing-of-mycobacterium-tuberculosis
#20
Janko van Beek, Marjo Haanperä, Pieter W Smit, Silja Mentula, Hanna Soini
OBJECTIVES: Culture-based assays are currently the gold standard for drug susceptibility testing (DST) for Mycobacterium tuberculosis. They provide good sensitivity and specificity, but are time-consuming. The objective of this study was to evaluate whether whole genome sequencing (WGS), combined with software tools for data analysis, can replace routine culture based assays for drug susceptibility testing of M. tuberculosis. METHODS: M. tuberculosis cultures sent to the Finnish mycobacterial reference laboratory in 2014 (n=211) were phenotypically tested by Mycobacteria Growth Indicator Tube (MGIT) for first line drug susceptibilities...
April 10, 2018: Clinical Microbiology and Infection
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