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Human whole genome sequencing

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https://www.readbyqxmd.com/read/28938720/deep-whole-genome-sequencing-of-90-han-chinese-genomes
#1
Tianming Lan, Haoxiang Lin, Wenjuan Zhu, Tellier Christian Asker Melchior Laurent, Mengcheng Yang, Xin Liu, Jun Wang, Jian Wang, Huanming Yang, Xun Xu, Xiaosen Guo
Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938719/population-wide-sampling-of-retrotransposon-insertion-polymorphisms-using-deep-sequencing-and-efficient-detection
#2
Qichao Yu, Wei Zhang, Xiaolong Zhang, Yongli Zeng, Yeming Wang, Yanhui Wang, Liqin Xu, Xiaoyun Huang, Nannan Li, Xinlan Zhou, Jie Lu, Xiaosen Guo, Guibo Li, Yong Hou, Shiping Liu, Bo Li
Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population. Herein, we present a novel and efficient computational tool called Specific Insertions Detector (SID) for the detection of non-reference RIPs...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938470/genetic-disruption-of-21-hydroxylase-in-zebrafish-causes-interrenal-hyperplasia
#3
Helen Eachus, Andreas Zaucker, James A Oakes, Aliesha Griffin, Meltem Weger, Tülay Güran, Angela Taylor, Abigail Harris, Andy Greenfield, Jonathan L Quanson, Karl-Heinz Storbeck, Vincent T Cunliffe, Ferenc Müller, Nils Krone
Congenital adrenal hyperplasia is a group of common inherited disorders leading to glucocorticoid deficiency. Most cases are caused by 21-hydroxylase deficiency (21OHD). The systemic consequences of imbalanced steroid hormone biosynthesis due to severe 21OHD remains poorly understood. Therefore, we have developed a zebrafish model for 21OHD, which focuses on the impairment of glucocorticoid biosynthesis. A single 21-hydroxylase gene (cyp21a2) is annotated in the zebrafish genome based on sequence homology. Our in silico analysis of the Cyp21a2 protein sequence suggests a sufficient degree of similarity for the usage of zebrafish cyp21a2 to model aspects of human 21OHD in vivo...
September 13, 2017: Endocrinology
https://www.readbyqxmd.com/read/28938154/massively-parallel-sequencing-of-forensic-strs-and-snps-using-the-illumina-%C3%A2-forenseq%C3%A2-dna-signature-prep-kit-on-the-miseq-fgx%C3%A2-forensic-genomics-system
#4
Fei Guo, Jiao Yu, Lu Zhang, Jun Li
The ForenSeq™ DNA Signature Prep Kit (ForenSeq Kit) is designed to detect more than 200 forensically relevant markers in a single reaction on the MiSeq FGx™ Forensic Genomics System (MiSeq FGx System), including Amelogenin, 27 autosomal short tandem repeats (A-STRs), 7 X chromosomal STRs (X-STRs), 24 Y chromosomal STRs (Y-STRs) and 94 identity-informative single nucleotide polymorphisms (iSNPs) with the option to contain 22 phenotypic-informative SNPs (pSNPs) and 56 ancestry-informative SNPs (aSNPs). In this study, we evaluated the MiSeq FGx System on three major parts: methodological optimization (DNA extraction, sample quantification, library normalization, diluted libraries concentration, and sample-to-cell arrangement), massively parallel sequencing (MPS) performance (depth of coverage, sequence coverage ratio, and allele coverage ratio), and ForenSeq Kit characteristics (repeatability and concordance, sensitivity, mixture, stability and case-type samples)...
September 8, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28936424/acid-stress-response-mechanisms-of-group-b-streptococci
#5
REVIEW
Sarah Shabayek, Barbara Spellerberg
Group B streptococcus (GBS) is a leading cause of neonatal mortality and morbidity in the United States and Europe. It is part of the vaginal microbiota in up to 30% of pregnant women and can be passed on to the newborn through perinatal transmission. GBS has the ability to survive in multiple different host niches. The pathophysiology of this bacterium reveals an outstanding ability to withstand varying pH fluctuations of the surrounding environments inside the human host. GBS host pathogen interations include colonization of the acidic vaginal mucosa, invasion of the neutral human blood or amniotic fluid, breaching of the blood brain barrier as well as survival within the acidic phagolysosomal compartment of macrophages...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28934422/low-frequency-of-acquired-isoniazid-and-rifampicin-resistance-in-rifampicin-susceptible-pulmonary-tuberculosis-in-a-setting-of-high-hiv-1-infection-and-tuberculosis-coprevalence
#6
Neesha Rockwood, Frederick Sirgel, Elizabeth Streicher, Robin Warren, Graeme Meintjes, Robert J Wilkinson
Background: We estimated the incidence of acquired isoniazid and rifampicin resistance in rifampicin-susceptible tuberculosis in a setting of high human immunodeficiency virus type 1 (HIV-1) infection and tuberculosis coprevalence. Methods: GeneXpert MTB/RIF-confirmed patients with rifampicin-susceptible tuberculosis were recruited at antituberculosis treatment initiation in Khayelitsha, South Africa. Liquid culture and adherence assessment were performed at 2 and 5-6 months...
September 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28934377/the-environmental-acinetobacter-baumannii-isolate-dsm30011-reveals-clues-into-the-preantibiotic-era-genome-diversity-virulence-potential-and-niche-range-of-a-predominant-nosocomial-pathogen
#7
Guillermo D Repizo, Alejandro M Viale, Vítor Borges, María M Cameranesi, Najwa Taib, Martín Espariz, Céline Brochier-Armanet, João Paulo Gomes, Suzana P Salcedo
Acinetobacter baumannii represents nowadays an important nosocomial opportunistic pathogen whose reservoirs outside the clinical setting are obscure. Here, we traced the origins of the collection strain A. baumannii DSM30011 to an isolate first reported in 1944, obtained from the enriched microbiota responsible of the aerobic decomposition of the resinous desert shrub guayule. Whole-genome sequencing and phylogenetic analysis based on core genes confirmed DSM30011 affiliation to A. baumannii. Comparative studies with 32 complete A...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28933320/neisseria-dumasiana-sp-nov-from-human-sputum-and-a-dog-s-mouth
#8
Danielle Wroblewski, Jocelyn Cole, Jana McGinnis, Maria Perez, Harriet Wilson, Lisa A Mingle, Kimberlee A Musser, William J Wolfgang
Three independent isolates of Gram-reaction-negative cocci collected from two New York State patients and a dog's mouth in California were subjected to a polyphasic analysis. The 16S rRNA gene sequence similarity among these isolates is 99.66 to 99.86 %. The closest species with a validly published name is Neisseria zoodegmatis (98.7 % 16S rRNA gene sequence similarity) with six additional species of the genus Neisseria with greater than 97 % similarity. Average nucleotide identity (ANI) and genome-to-genome distance calculator (GGDC 2...
September 21, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28932815/a-multicenter-study-to-evaluate-the-performance-of-high-throughput-sequencing-for-virus-detection
#9
Arifa S Khan, Siemon H S Ng, Olivier Vandeputte, Aisha Aljanahi, Avisek Deyati, Jean-Pol Cassart, Robert L Charlebois, Lanyn P Taliaferro
The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses makes it a powerful tool for broad microbial investigations, such as evaluation of novel cell substrates that may be used for the development of new biological products. However, like any new assay, regulatory applications of HTS need method standardization. Therefore, our three laboratories initiated a study to evaluate performance of HTS for potential detection of viral adventitious agents by spiking model viruses in different cellular matrices to mimic putative materials for manufacturing of biologics...
September 2017: MSphere
https://www.readbyqxmd.com/read/28932221/diversity-of-vibrio-navarrensis-revealed-by-genomic-comparison-veterinary-isolates-are-related-to-strains-associated-with-human-illness-and-sewage-isolates-while-seawater-strains-are-more-distant
#10
Keike Schwartz, Cindy Kukuc, Nadja Bier, Karin Taureck, Jens A Hammerl, Eckhard Strauch
Strains of Vibrio navarrensis are present in aquatic environments like seawater, rivers, and sewage. Recently, strains of this species were identified in human clinical specimens. In this study, V. navarrensis strains isolated from livestock in Germany were characterized that were found in aborted fetuses and/or placentas after miscarriages. The veterinary strains were analyzed using phenotypical and genotypical methods and compared to isolates from marine environments of the Baltic Sea and North Sea. The investigated phenotypical traits were similar in all German strains...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28932212/comparative-genomics-of-burkholderia-singularis-sp-nov-a-low-g-c-content-free-living-bacterium-that-defies-taxonomic-dissection-of-the-genus-burkholderia
#11
Peter Vandamme, Charlotte Peeters, Birgit De Smet, Erin P Price, Derek S Sarovich, Deborah A Henry, Trevor J Hird, James E A Zlosnik, Mark Mayo, Jeffrey Warner, Anthony Baker, Bart J Currie, Aurélien Carlier
Four Burkholderia pseudomallei-like isolates of human clinical origin were examined by a polyphasic taxonomic approach that included comparative whole genome analyses. The results demonstrated that these isolates represent a rare and unusual, novel Burkholderia species for which we propose the name B. singularis. The type strain is LMG 28154(T) (=CCUG 65685(T)). Its genome sequence has an average mol% G+C content of 64.34%, which is considerably lower than that of other Burkholderia species. The reduced G+C content of strain LMG 28154(T) was characterized by a genome wide AT bias that was not due to reduced GC-biased gene conversion or reductive genome evolution, but might have been caused by an altered DNA base excision repair pathway...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28931649/sequencing-of-the-variable-region-of-rpsb-to-discriminate-between-streptococcus-pneumoniae-and-other-streptococcal-species
#12
Anne L Wyllie, Yvonne Pannekoek, Sandra Bovenkerk, Jody van Engelsdorp Gastelaars, Bart Ferwerda, Diederik van de Beek, Elisabeth A M Sanders, Krzysztof Trzciński, Arie van der Ende
The vast majority of streptococci colonizing the human upper respiratory tract are commensals, only sporadically implicated in disease. Of these, the most pathogenic is Mitis group member, Streptococcus pneumoniae Phenotypic and genetic similarities between streptococci can cause difficulties in species identification. Using ribosomal S2-gene sequences extracted from whole-genome sequences published from 501 streptococci, we developed a method to identify streptococcal species. We validated this method on non-pneumococcal isolates cultured from cases of severe streptococcal disease (n = 101) and from carriage (n = 103), and on non-typeable pneumococci from asymptomatic individuals (n = 17) and on whole-genome sequences of 1157 pneumococcal isolates from meningitis in the Netherlands...
September 2017: Open Biology
https://www.readbyqxmd.com/read/28930002/investigation-of-outbreaks-of-salmonella-enterica-serovar-typhimurium-and-its-monophasic-variants-using-whole-genome-sequencing-denmark
#13
Pernille Gymoese, Gitte Sørensen, Eva Litrup, John Elmerdal Olsen, Eva Møller Nielsen, Mia Torpdahl
Whole-genome sequencing is rapidly replacing current molecular typing methods for surveillance purposes. Our study evaluates core-genome single-nucleotide polymorphism analysis for outbreak detection and linking of sources of Salmonella enterica serovar Typhimurium and its monophasic variants during a 7-month surveillance period in Denmark. We reanalyzed and defined 8 previously characterized outbreaks from the phylogenetic relatedness of the isolates, epidemiologic data, and food traceback investigations. All outbreaks were identified, and we were able to exclude unrelated and include additional related human cases...
October 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28925528/relatedness-of-wildlife-and-livestock-avian-isolates-of-the-nosocomial-pathogen-acinetobacter-baumannii-to-lineages-spread-in-hospitals-worldwide
#14
Gottfried Wilharm, Evelyn Skiebe, Paul G Higgins, Marie T Poppel, Ulrike Blaschke, Sarah Leser, Christine Heider, Magdalena Heindorf, Paul Brauner, Udo Jäckel, Karin Böhland, Christiane Cuny, Andżelina Łopińska, Piotr Kaminski, Mariusz Kasprzak, Marcin Bochenski, Olaf Ciebiera, Marcin Tobółka, Katarzyna M Żołnierowicz, Joachim Siekiera, Harald Seifert, Stéphanie Gagné, Suzana P Salcedo, Michael Kaatz, Franziska Layer, Jennifer K Bender, Stephan Fuchs, Torsten Semmler, Yvonne Pfeifer, Leszek Jerzak
The natural habitats and potential reservoirs of the nosocomial pathogen Acinetobacter baumannii are poorly defined. Here, we put forth and tested the hypothesis of avian reservoirs of A. baumannii. We screened tracheal and rectal swab samples from livestock (chicken, geese) and wild birds (white stork nestlings) and isolated A. baumannii from 3% of sampled chicken (n=220), 8% of geese (n=40) and 25% of white stork nestlings (n=661). Virulence of selected avian A. baumannii isolates was comparable to that of clinical isolates in the Galleria mellonella infection model...
September 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28924718/comprehensive-annotation-and-evolutionary-insights-into-the-canine-canis-lupus-familiaris-antigen-receptor-loci
#15
Jolyon Martin, Hannes Ponstingl, Marie-Paule Lefranc, Joy Archer, David Sargan, Allan Bradley
Dogs are an excellent model for human disease. For example, the treatment of canine lymphoma has been predictive of the human response to that treatment. However, an incomplete picture of canine (Canis lupus familiaris) immunoglobulin (IG) and T cell receptor (TR)-or antigen receptor (AR)-gene loci has restricted their utility. This work advances the annotation of the canine AR loci and looks into breed-specific features of the loci. Bioinformatic analysis of unbiased RNA sequence data was used to complete the annotation of the canine AR genes...
September 19, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28924032/staphylococcus-aureus-strain-newman-d2c-contains-mutations-in-major-regulatory-pathways-that-cripple-its-pathogenesis
#16
William E Sause, Richard Copin, Aidan O'malley, Rita Chan, Brian J Morrow, Peter T Buckley, Jeffrey Fernandez, A Simon Lynch, Bo Shopsin, Victor J Torres
Staphylococcus aureus is a major human pathogen that imposes a great burden on the healthcare system. In the development of anti-staphylococcal modalities intended to reduce the burden of staphylococcal disease, it is imperative to select appropriate models of S. aureus strains when assessing the efficacy of novel agents. Here, using whole genome sequencing, we reveal that the commonly used strain Newman D2C from the American Type Culture Collection (ATCC) contains mutations that render the strain essentially avirulent...
September 18, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28923495/crispr-cas9-engineering-of-adult-mouse-liver-demonstrates-that-the-dnajb1-prkaca-gene-fusion-is-sufficient-to-induce-tumors-resembling-fibrolamellar-hepatocellular-carcinoma
#17
Lars H Engelholm, Anjum Riaz, Denise Serra, Frederik Dagnæs-Hansen, Jens V Johansen, Eric Santoni-Rugiu, Steen H Hansen, Francesco Niola, Morten Frödin
BACKGROUND & AIMS: Fibrolamellar hepatocellular carcinoma (FL-HCC) is a primary liver cancer that predominantly affects young adults with no underlying liver disease. A somatic, 400 Kb deletion on chromosome 19 that fuses part of the DnaJ heat shock protein family (Hsp40) member B1 gene (DNAJB1) to the protein kinase cAMP-activated catalytic subunit alpha gene (PRKACA) has been repeatedly identified in patients with FL-HCC. However, the DNAJB1-PRKACA gene fusion has not been shown to induce liver tumorigenesis...
September 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28923009/apophysomyces-variabilis-draft-genome-sequence-and-comparison-of-predictive-virulence-determinants-with-other-medically-important-mucorales
#18
Hariprasath Prakash, Shivaprakash Mandya Rudramurthy, Prasad S Gandham, Anup Kumar Ghosh, Milner M Kumar, Chandan Badapanda, Arunaloke Chakrabarti
BACKGROUND: Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A. trapeziformis and A. variabilis are commonly incriminated in human infections. The genome sequences of A. elegans and A. trapeziformis are available in public database, but not A. variabilis. We, therefore, performed the whole genome sequence of A. variabilis to explore its genomic structure and possible genes determining the virulence of the organism...
September 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28922838/comparative-genomics-of-a-drug-resistant-pseudomonas-aeruginosa-panel-and-the-challenges-of-antimicrobial-resistance-prediction-from-genomes
#19
J Jeukens, I Kukavica-Ibrulj, J G Emond-Rheault, L Freschi, R C Levesque
Antimicrobial resistance (AMR) is now recognized as a global threat to human health. The accessibility of microbial whole-genome sequencing offers an invaluable opportunity for resistance surveillance via the resistome, i.e. the genes and mutations underlying AMR. Unfortunately, AMR prediction from genomic data remains extremely challenging, especially for species with a large pan-genome. One such organism, for which multidrug-resistant (MDR) isolates are frequently encountered in the clinic, is Pseudomonas aeruginosa...
October 2, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28920571/recurrent-seasonal-outbreak-of-an-emerging-serotype-of-shiga-toxin-producing-escherichia-coli-stec-o55-h7-stx2a-in-the-south-west-of-england-july-2014-to-september-2015
#20
Noëleen McFarland, Nick Bundle, Claire Jenkins, Gauri Godbole, Amy Mikhail, Tim Dallman, Catherine O'Connor, Noel McCarthy, Emer O'Connell, Juli Treacy, Girija Dabke, James Mapstone, Yvette Landy, Janet Moore, Rachel Partridge, Frieda Jorgensen, Caroline Willis, Piers Mook, Chas Rawlings, Richard Acornley, Charlotte Featherstone, Sharleen Gayle, Joanne Edge, Eleanor McNamara, Jeremy Hawker, Sooria Balasegaram
The first documented British outbreak of Shiga toxin-producing Escherichia coli (STEC) O55:H7 began in the county of Dorset, England, in July 2014. Since then, there have been a total of 31 cases of which 13 presented with haemolytic uraemic syndrome (HUS). The outbreak strain had Shiga toxin (Stx) subtype 2a associated with an elevated risk of HUS. This strain had not previously been isolated from humans or animals in England. The only epidemiological link was living in or having close links to two areas in Dorset...
September 7, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
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