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https://www.readbyqxmd.com/read/28548082/whole-genome-sequencing-and-imputation-in-isolated-populations-identify-genetic-associations-with-medically-relevant-complex-traits
#1
Lorraine Southam, Arthur Gilly, Dániel Süveges, Aliki-Eleni Farmaki, Jeremy Schwartzentruber, Ioanna Tachmazidou, Angela Matchan, Nigel W Rayner, Emmanouil Tsafantakis, Maria Karaleftheri, Yali Xue, George Dedoussis, Eleftheria Zeggini
Next-generation association studies can be empowered by sequence-based imputation and by studying founder populations. Here we report ∼9.5 million variants from whole-genome sequencing (WGS) of a Cretan-isolated population, and show enrichment of rare and low-frequency variants with predicted functional consequences. We use a WGS-based imputation approach utilizing 10,422 reference haplotypes to perform genome-wide association analyses and observe 17 genome-wide significant, independent signals, including replicating evidence for association at eight novel low-frequency variant signals...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28545446/whole-genome-sequencing-reveals-within-host-genetic-changes-in-paired-meningococcal-carriage-isolates-from-ethiopia
#2
Guro K Bårnes, Ola Brønstad Brynildsrud, Bente Børud, Bereket Workalemahu, Paul A Kristiansen, Demissew Beyene, Abraham Aseffa, Dominique A Caugant
BACKGROUND: Meningococcal colonization is a prerequisite for transmission and disease, but the bacterium only very infrequently causes disease while asymptomatic carriage is common. Carriage is highly dynamic, showing a great variety across time and space within and across populations, but also within individuals. The understanding of genetic changes in the meningococcus during carriage, when the bacteria resides in its natural niche, is important for understanding not only the carriage state, but the dynamics of the entire meningococcal population...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28541565/emergence-of-vana-enterococcus-faecium-in-denmark-2005-15
#3
Anette M Hammerum, Sharmin Baig, Yasmin Kamel, Louise Roer, Mette Pinholt, Heidi Gumpert, Barbara Holzknecht, Bent Røder, Ulrik S Justesen, Jurgita Samulioniené, Mona Kjærsgaard, Claus Østergaard, Anette Holm, Esad Dzajic, Turid Snekloth Søndergaard, Shahin Gaini, Petra Edquist, Erik Alm, Berit Lilje, Henrik Westh, Marc Stegger, Henrik Hasman
Objectives: To describe the changing epidemiology of vancomycin-resistant Enterococcus faecium and Enterococcus faecalis in clinical samples in Denmark 2005-15 according to species and van type, and, furthermore, to investigate the genetic relatedness of the clinical E. faecium isolates from 2015. Methods: During 2005-14, all clinical VRE isolates were tested for the presence of vanA/B/C genes by PCR. In 2015, all clinical VRE isolates were whole-genome sequenced...
May 25, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28539126/knowledge-driven-binning-approach-for-rare-variant-association-analysis-application-to-neuroimaging-biomarkers-in-alzheimer-s-disease
#4
Dokyoon Kim, Anna O Basile, Lisa Bang, Emrin Horgusluoglu, Seunggeun Lee, Marylyn D Ritchie, Andrew J Saykin, Kwangsik Nho
BACKGROUND: Rapid advancement of next generation sequencing technologies such as whole genome sequencing (WGS) has facilitated the search for genetic factors that influence disease risk in the field of human genetics. To identify rare variants associated with human diseases or traits, an efficient genome-wide binning approach is needed. In this study we developed a novel biological knowledge-based binning approach for rare-variant association analysis and then applied the approach to structural neuroimaging endophenotypes related to late-onset Alzheimer's disease (LOAD)...
May 18, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28539120/comprehensive-whole-genome-sequence-analyses-yields-novel-genetic-and-structural-insights-for-intellectual-disability
#5
Farah R Zahir, Jill C Mwenifumbo, Hye-Jung E Chun, Emilia L Lim, Clara D M Van Karnebeek, Madeline Couse, Karen L Mungall, Leora Lee, Nancy Makela, Linlea Armstrong, Cornelius F Boerkoel, Sylvie L Langlois, Barbara M McGillivray, Steven J M Jones, Jan M Friedman, Marco A Marra
BACKGROUND: Intellectual Disability (ID) is among the most common global disorders, yet etiology is unknown in ~30% of patients despite clinical assessment. Whole genome sequencing (WGS) is able to interrogate the entire genome, providing potential to diagnose idiopathic patients. METHODS: We conducted WGS on eight children with idiopathic ID and brain structural defects, and their normal parents; carrying out an extensive data analyses, using standard and discovery approaches...
May 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28532386/extremely-low-coverage-whole-genome-sequencing-in-south-asians-captures-population-genomics-information
#6
Navin Rustagi, Anbo Zhou, W Scott Watkins, Erika Gedvilaite, Shuoguo Wang, Naveen Ramesh, Donna Muzny, Richard A Gibbs, Lynn B Jorde, Fuli Yu, Jinchuan Xing
BACKGROUND: The cost of Whole Genome Sequencing (WGS) has decreased tremendously in recent years due to advances in next-generation sequencing technologies. Nevertheless, the cost of carrying out large-scale cohort studies using WGS is still daunting. Past simulation studies with coverage at ~2x have shown promise for using low coverage WGS in studies focused on variant discovery, association study replications, and population genomics characterization. However, the performance of low coverage WGS in populations with a complex history and no reference panel remains to be determined...
May 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28530888/genomic-relatedness-of-staphylococcus-pettenkoferi-isolates-of-different-origins
#7
Emeli Månsson, Bengt Hellmark, Marc Stegger, Paal Skytt Andersen, Martin Sundqvist, Bo Söderquist
PURPOSE: The aim of the study was to characterize clinical and environmental Staphylococcus pettenkoferi isolates with regard to genomic diversity and antibiotic susceptibility pattern. Repetitive-sequence-based PCR and core genome phylogenetic analysis of whole-genome sequencing (WGS) data verified the presence of distinct clades comprising closely related S. pettenkoferi isolates from different geographical locations and origins. METHODOLOGY: Phylogenetic relationships between 25 S...
May 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28526698/improving-response-in-genomic-selection-with-a-population-based-selection-strategy-optimal-population-value-selection
#8
Matthew Goiffon, Aaron Kusmec, Lizhi Wang, Guiping Hu, Patrick Schnable
Genomic selection (GS) identifies individuals for inclusion in breeding programs based on the sum of their estimated marker effects or genomic estimated breeding values (GEBVs). Due to significant correlation between GEBVs and true breeding values, this has resulted in enhanced rates of genetic gain as compared to traditional methods of selection. Three extensions to GS, weighted genomic selection (WGS), optimal haploid value (OHV) selection, and genotype building (GB) selection have been proposed to improve long-term response and to facilitate the efficient development of doubled haploids...
May 19, 2017: Genetics
https://www.readbyqxmd.com/read/28521784/functional-regression-method-for-whole-genome-eqtl-epistasis-analysis-with-sequencing-data
#9
Kelin Xu, Li Jin, Momiao Xiong
BACKGROUND: Epistasis plays an essential rule in understanding the regulation mechanisms and is an essential component of the genetic architecture of the gene expressions. However, interaction analysis of gene expressions remains fundamentally unexplored due to great computational challenges and data availability. Due to variation in splicing, transcription start sites, polyadenylation sites, post-transcriptional RNA editing across the entire gene, and transcription rates of the cells, RNA-seq measurements generate large expression variability and collectively create the observed position level read count curves...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28520983/genomic-epidemiology-of-global-vim-producing-enterobacteriaceae
#10
Yasufumi Matsumura, Gisele Peirano, Rebekah Devinney, Patricia A Bradford, Mary R Motyl, Mark D Adams, Liang Chen, Barry Kreiswirth, Johann D D Pitout
Background: : International data on the molecular epidemiology of Enterobacteriaceae with VIM carbapenemases are limited. Methods: We performed short read (Illumina) WGS on a global collection of 89 VIM-producing clinical Enterobacteriaceae (2008-14). Results: VIM-producing (11 varieties within 21 different integrons) isolates were mostly obtained from Europe. Certain integrons with bla VIM were specific to a country in different species and clonal complexes (CCs) (In 87 , In 624 , In 916 and In 1323 ), while others had spread globally among various Enterobacteriaceae species (In 110 and In 1209 )...
May 16, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28520856/control-of-multidrug-resistant-pseudomonas-aeruginosa-in-allogeneic-hematopoietic-stem-cell-transplant-recipients-by-a-novel-bundle-including-remodeling-of-sanitary-and-water-supply-systems
#11
A Kossow, S Kampmeier, S Willems, W E Berdel, A H Groll, B Burckhardt, Rossig C, C Groth, E A Idelevich, F Kipp, A Mellmann, M Stelljes
Background.: Infections by multidrug-resistant Pseudomonas aeruginosa (MDRPa) are an important cause of morbidity and mortality in patients after allogeneic hematopoietic stem cell transplantation (HSCT). Humid environments can serve as a reservoir and source of infection by this pathogen. To minimize the risk of infection from these reservoirs, we performed extensive remodeling of sanitation and water installations as the focus of our hygiene bundle. Methods.: During the reconstruction of our transplantation unit (April 2011- April 2014) we implemented several technical modifications to reduce environmental contamination by and subsequent spreading of MDRPa, including a newly designed shower drain, disinfecting siphons underneath the sinks, and rimless toilets...
May 18, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28515904/weekly-screening-supports-terminating-nosocomial-transmissions-of-vancomycin-resistant-enterococci-on-an-oncologic-ward-a-retrospective-analysis
#12
Stefanie Kampmeier, Dennis Knaack, Annelene Kossow, Stefanie Willems, Christoph Schliemann, Wolfgang E Berdel, Frank Kipp, Alexander Mellmann
BACKGROUND: To investigate the impact of weekly screening within the bundle of infection control measures to terminate vancomycin-resistant enterococci (VRE) transmissions on an oncologic ward. METHODS: A cluster of 12 VRE colonisation and five infections was detected on an oncologic ward between January and April 2015. Subsequently, the VRE point prevalence was detected and, as part of a the bundle of infection control strategies to terminate the VRE cluster, we isolated affected patients, performed hand hygiene training among staff on ward, increased observations by infection control specialists, intensified surface disinfection, used personal protective equipment and initiated an admission screening in May 2015...
2017: Antimicrobial Resistance and Infection Control
https://www.readbyqxmd.com/read/28511677/a-strategy-to-improve-phasing-of-whole-genome-sequenced-individuals-through-integration-of-familial-information-from-dense-genotype-panels
#13
Pierre Faux, Tom Druet
BACKGROUND: Haplotype reconstruction (phasing) is an essential step in many applications, including imputation and genomic selection. The best phasing methods rely on both familial and linkage disequilibrium (LD) information. With whole-genome sequence (WGS) data, relatively small samples of reference individuals are generally sequenced due to prohibitive sequencing costs, thus only a limited amount of familial information is available. However, reference individuals have many relatives that have been genotyped (at lower density)...
May 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28511110/determination-of-regional-relationships-among-salmonella-spp-isolated-from-retail-pork-circulating-in-the-chiang-mai-municipality-area-using-a-wgs-data-approach
#14
Prapas Patchanee, Thanaporn Eiamsam-Ang, Juntakarn Vanaseang, Phacharaporn Boonkhot, Pakpoom Tadee
Salmonella is recognized as a significant zoonotic foodborne pathogen, and pork products are involved in one-fifth of infections. Whole genome sequencing data of Salmonella isolated from retail's pork circulating in the Chiang Mai Municipality area between April 2013 and September 2014, were used to focus on genetic diversity and proven in pig-human transmission based on Multilocus Sequence Typing (MLST). Additionally, WGS data were used to investigate virulence genes, to assess the hazard or pathogenic potential transferred into the food production chain...
May 10, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28510723/decreased-azithromycin-susceptibility-of-neisseria-gonorrhoeae-isolates-in-patients-recently-treated-with-azithromycin
#15
Carolien M Wind, Esther de Vries, Maarten F Schim van der Loeff, Martijn S van Rooijen, Alje P van Dam, Walter H B Demczuk, Irene Martin, Henry J C de Vries
Background.: Increasing azithromycin usage and resistance in Neisseria gonorrhoeae threatens current dual treatment. Because antimicrobial exposure influences resistance, we analyzed the association between azithromycin exposure and decreased susceptibility of N. gonorrhoeae. Methods.: We included N. gonorrhoeae isolates of patients who visited the Amsterdam STI Clinic between 1999 and 2013 (t0), with another clinic visit in the previous 60 days (t-1). Exposure was defined as the prescription of azithromycin at t-1...
March 24, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28508085/intragenic-dok7-deletion-detected-by-whole-genome-sequencing-in-congenital-myasthenic-syndromes
#16
Yoshiteru Azuma, Ana Töpf, Teresinha Evangelista, Paulo José Lorenzoni, Andreas Roos, Pedro Viana, Hidehito Inagaki, Hiroki Kurahashi, Hanns Lochmüller
OBJECTIVE: To identify the genetic cause in a patient affected by ptosis and exercise-induced muscle weakness and diagnosed with congenital myasthenic syndromes (CMS) using whole-genome sequencing (WGS). METHODS: Candidate gene screening and WGS analysis were performed in the case. Allele-specific PCR was subsequently performed to confirm the copy number variation (CNV) that was suspected from the WGS results. RESULTS: In addition to the previously reported frameshift mutation c...
June 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28506277/quantifying-the-mapping-precision-of-genome-wide-association-studies-using-whole-genome-sequencing-data
#17
Yang Wu, Zhili Zheng, Peter M Visscher, Jian Yang
BACKGROUND: Understanding the mapping precision of genome-wide association studies (GWAS), that is the physical distances between the top associated single-nucleotide polymorphisms (SNPs) and the causal variants, is essential to design fine-mapping experiments for complex traits and diseases. RESULTS: Using simulations based on whole-genome sequencing (WGS) data from 3642 unrelated individuals of European descent, we show that the association signals at rare causal variants (minor allele frequency ≤ 0...
May 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28505284/pathogenic-anti-m%C3%A3-llerian-hormone-variants-in-polycystic-ovary-syndrome
#18
Lidija K Gorsic, Gulum Kosova, Brian Werstein, Ryan Sisk, Richard S Legro, M Geoffrey Hayes, Jose M Teixeira, Andrea Dunaif, Margrit Urbanek
CONTEXT: Polycystic ovary syndrome (PCOS), a common endocrine condition, is the leading cause of anovulatory infertility. OBJECTIVE: Given that common disease-susceptibility variants account for only a small percentage of the estimated PCOS heritability, we tested the hypothesis that rare variants contribute to this deficit in heritability. DESIGN, SETTING, AND PARTICIPANTS: Unbiased whole genome sequencing (WGS) of 80 PCOS cases and 24 reproductively normal control women identified potentially deleterious variants in AMH, the gene encoding anti-Müllerian hormone (AMH)...
May 12, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28497996/characterization-of-the-salmonella-enterica-serotype-isangi-isolated-from-patients-for-the-first-time-in-china
#19
Xin-Peng Li, Ri-Hong Gao, Pei-Bin Hou, Yan-Yan Ren, Hua-Ning Zhang, Kui-Ying Jiang, Yu-Zhen Chen, Zi-Gang Qi, Min Xu, Zhen-Wang Bi
No studies have reported the isolation of serotype Salmonella Isangi from cases of salmonellosis in mainland China. We investigated an outbreak of foodborne disease with salmonella and collected the samples from the patients and surplus foods. Salmonella strains were isolated and the serotype was identified according to the Kauffmann-White scheme. The relatedness of the isolates was determined using pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). Antimicrobial susceptibility was conducted by the broth microdilution method...
May 12, 2017: Foodborne Pathogens and Disease
https://www.readbyqxmd.com/read/28496993/successful-application-of-whole-genome-sequencing-in-a-medical-genetics-clinic
#20
David Bick, Pamela C Fraser, Michael F Gutzeit, Jeremy M Harris, Tina M Hambuch, Daniel C Helbling, Howard J Jacob, Juliet N Kersten, Steven R Leuthner, Thomas May, Paula E North, Sasha Z Prisco, Bryce A Schuler, Mary Shimoyama, Kimberly A Strong, Scott K Van Why, Regan Veith, James Verbsky, Arthur M Weborg, Brandon M Wilk, Rodney E Willoughby, Elizabeth A Worthey, David P Dimmock
A pilot program was initiated using whole genome sequencing (WGS) to diagnose suspected genetic disorders in the Genetics Clinic at Children's Hospital of Wisconsin. Twenty-two patients underwent WGS between 2010 and 2013. Initially, we obtained a 14% (3/22) diagnosis rate over 2 years; with subsequent reanalysis, this increased to 36% (8/22). Disease causing variants were identified in SKIV2L, CECR1, DGKE, PYCR2, RYR1, PDGFRB, EFTUD2, and BCS1L. In 75% (6/8) of diagnosed cases, the diagnosis affected treatment and/or medical surveillance...
June 2017: Journal of Pediatric Genetics
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