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Clinical whole genome sequencing

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https://www.readbyqxmd.com/read/28230522/multinational-outbreak-of-travel-related-salmonella-chester-infections-in-europe-summers-2014-and-2015
#1
Laure Fonteneau, Nathalie Jourdan Da Silva, Laetitia Fabre, Philip Ashton, Mia Torpdahl, Luise Müller, Brahim Bouchrif, Abdellah El Boulani, Eleni Valkanou, Wesley Mattheus, Ingrid Friesema, Silvia Herrera Leon, Carmen Varela Martínez, Joël Mossong, Ettore Severi, Kathie Grant, François-Xavier Weill, Céline M Gossner, Sophie Bertrand, Tim Dallman, Simon Le Hello
Between 2014 and 2015, the European Centre for Disease Prevention and Control was informed of an increase in numbers of Salmonella enterica serotype Chester cases with travel to Morocco occurring in six European countries. Epidemiological and microbiological investigations were conducted. In addition to gathering information on the characteristics of cases from the different countries in 2014, the epidemiological investigation comprised a matched case-case study involving French patients with salmonellosis who travelled to Morocco that year...
February 16, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/28228490/short-read-whole-genome-sequencing-for-laboratory-based-surveillance-of-bordetella-pertussis
#2
Alex Marchand-Austin, Raymond S W Tsang, Jennifer L Guthrie, Jennifer H Ma, Gillian Lim, Natasha S Crowcroft, Shelley L Deeks, David J Farrell, Frances B Jamieson
Bordetella pertussis (BP) is a Gram-negative bacterium that causes respiratory infections in humans. Ongoing molecular surveillance of BP acellular vaccine (aP) antigens is critical for understanding the interaction between evolutionary pressures, disease pathogenesis, and vaccine effectiveness. Methods currently used to characterize aP components are relatively labour intensive and low throughput. To address this challenge, we sought to derive aP antigen genotypes from minimally processed short-read whole genome sequencing data generated from 40 clinical BP isolates and analyzed using the SRST2 bioinformatic package...
February 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28228131/whole-genome-sequencing-of-one-complex-pedigree-illustrates-challenges-with-genomic-medicine
#3
Han Fang, Yiyang Wu, Hui Yang, Margaret Yoon, Laura T Jiménez-Barrón, David Mittelman, Reid Robison, Kai Wang, Gholson J Lyon
BACKGROUND: Human Phenotype Ontology (HPO) has risen as a useful tool for precision medicine by providing a standardized vocabulary of phenotypic abnormalities to describe presentations of human pathologies; however, there have been relatively few reports combining whole genome sequencing (WGS) and HPO, especially in the context of structural variants. METHODS: We illustrate an integrative analysis of WGS and HPO using an extended pedigree, which involves Prader-Willi Syndrome (PWS), hereditary hemochromatosis (HH), and dysautonomia-like symptoms...
February 23, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28223977/staphylococcal-aureus-enterotoxin-c-and-enterotoxin-like-l-associated-with-post-partum-mastitis
#4
Kristina T Franck, Heidi Gumpert, Bente Olesen, Anders R Larsen, Andreas Petersen, Jette Bangsborg, Per Albertsen, Henrik Westh, Mette D Bartels
Denmark is a low prevalence country with regard to methicillin resistant Staphylococcus aureus (MRSA). In 2008 and 2014, two neonatal wards in the Copenhagen area experienced outbreaks with a typical community acquired MRSA belonging to the same spa type and sequence type (t015:ST45) and both were PVL and ACME negative. In outbreak 1, the isolates harbored SCCmec IVa and in outbreak 2 SCCmec V. The clinical presentation differed between the two outbreaks, as none of five MRSA positive mothers in outbreak 1 had mastitis vs...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28223389/analysis-of-serial-isolates-of-mcr-1-positive-escherichia-coli-reveals-a-highly-active-isapl1-transposon
#5
Erik Snesrud, Ana C Ong, Brendan Corey, Yoon I Kwak, Robert Clifford, Todd Gleeson, Shannon Wood, Timothy J Whitman, Emil P Lesho, Mary Hinkle, Patrick Mc Gann
The emergence of the transferable colistin resistance gene mcr-1 is of global concern. The insertion sequence (IS) Apl1 is a key component in the mobilization of this gene, but its role remains poorly understood.Six Escherichia coli were cultured from the same patient over one month in Germany and the USA after a brief hospitalization in Bahrain for an unconnected illness. Four carried mcr-1 by real-time PCR, but two were negative. Two additional mcr-1-negative E. coli were collected during follow-up surveillance nine months later...
February 21, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28222731/genomic-newborn-screening-public-health-policy-considerations-and-recommendations
#6
Jan M Friedman, Martina C Cornel, Aaron J Goldenberg, Karla J Lister, Karine Sénécal, Danya F Vears
BACKGROUND: The use of genome-wide (whole genome or exome) sequencing for population-based newborn screening presents an opportunity to detect and treat or prevent many more serious early-onset health conditions than is possible today. METHODS: The Paediatric Task Team of the Global Alliance for Genomics and Health's Regulatory and Ethics Working Group reviewed current understanding and concerns regarding the use of genomic technologies for population-based newborn screening and developed, by consensus, eight recommendations for clinicians, clinical laboratory scientists, and policy makers...
February 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28222677/molecular-characterization-of-invasive-capsule-null-neisseria-meningitidis-in-south-africa
#7
Karistha Ganesh, Mushal Allam, Nicole Wolter, Holly B Bratcher, Odile B Harrison, Jay Lucidarme, Ray Borrow, Linda de Gouveia, Susan Meiring, Monica Birkhead, Martin C J Maiden, Anne von Gottberg, Mignon du Plessis
BACKGROUND: The meningococcal capsule is an important virulence determinant. Unencapsulated meningococci lacking capsule biosynthesis genes and containing the capsule null locus (cnl) are predominantly non-pathogenic. Rare cases of invasive meningococcal disease caused by cnl isolates belonging to sequence types (ST) and clonal complexes (cc) ST-845 (cc845), ST-198 (cc198), ST-192 (cc192) and ST-53 (cc53) have been documented. The clinical significance of these isolates however remains unclear...
February 21, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28219825/first-report-on-whole-genome-shotgun-sequences-of-23-biochemically-indistinguishable-clinical-shigella-isolates
#8
Dhiviya Prabaa Muthuirulandi Sethuvel, Naveen Kumar Devanga Ragupathi, Shalini Anandan, Valsan Philip Verghese, Balaji Veeraraghavan
Shigella spp. are a major diarrhoeal disease pathogen worldwide and can cause considerable morbidity and mortality. Notably, limited genome data are available for serogroups/sub-serogroups of Shigella. Here we report the whole-genome shotgun sequences of 23 non-typeable Shigella from stool specimens that biochemically resembled Shigella spp. but were non-typeable with Shigella-specific antisera.
February 17, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28218305/interaction-of-cutibacterium-%C3%A2-formerly-propionibacterium-acnes-with-bone-cells-a-step-toward-understanding-bone-and-joint-infection-development
#9
Guillaume Ghislain Aubin, Marc Baud'huin, Jean-Philippe Lavigne, Régis Brion, François Gouin, Didier Lepelletier, Cédric Jacqueline, Dominique Heymann, Karim Asehnoune, Stéphane Corvec
Cutibacterium acnes (formerly Propionibacterium acnes) is recognized as a pathogen in foreign-body infections (arthroplasty or spinal instrumentation). To date, the direct impact of C. acnes on bone cells has never been explored. The clade of 11 C. acnes clinical isolates was determined by MLST. Human osteoblasts and osteoclasts were infected by live C. acnes. The whole genome sequence of six isolates of this collection was analyzed. CC36 C. acnes strains were significantly less internalized by osteoblasts and osteoclasts than CC18 and CC28 C...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28213104/isolation-and-characterization-of-a-virulent-bacteriophage-infecting-acinetobacter-johnsonii-from-activated-sludge
#10
Niansi Fan, Rong Qi, Min Yang
A double-stranded DNA phage named AJO1, infecting Acinetobacter johnsonii, which plays an important role in wastewater treatment, was isolated from activated sludge in a full-scale municipal wastewater treatment plant. Based on morphological taxonomy, AJO1, with an icosahedral head 55 ± 2 nm in diameter and a non-contractile tail 8 ± 2 nm in length, was classified as a member of the Podoviridae family. Bacterial infection characteristics were as follows: no polyvalent infectivity, optimal multiplicity of infection of 10(-2); eclipse and burst size of 30 min and 51...
February 14, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28212966/estimating-preferences-for-complex-health-technologies-lessons-learned-and-implications-for-personalized-medicine
#11
Deborah A Marshall, Juan Marcos Gonzalez, Karen V MacDonald, F Reed Johnson
We examine key study design challenges of using stated-preference methods to estimate the value of whole-genome sequencing (WGS) as a specific example of genomic testing. Assessing the value of WGS is complex because WGS provides multiple findings, some of which can be incidental in nature and unrelated to the specific health concerns that motivated the test. In addition, WGS results can include actionable findings (variants considered to be clinically useful and can be acted on), findings for which evidence for best clinical action is not available (variants considered clinically valid but do not meet as high of a standard for clinical usefulness), and findings of unknown significance...
January 2017: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
https://www.readbyqxmd.com/read/28212566/genetic-characterization-of-polish-ccrcc-patients-somatic-mutation-analysis-of-pbrm1-bap1-and-kdmc5-genomic-snp-array-analysis-in-tumor-biopsy-and-preliminary-results-of-chromosome-aberrations-analysis-in-plasma-cell-free-dna
#12
Katarzyna Kluzek, Malgorzata I Srebniak, Weronika Majer, Agnieszka Ida, Tomasz Milecki, Kinga Huminska, Robert M van der Helm, Adrian Silesian, Tomasz M Wrzesinski, Jacek Wojciechowicz, Berna H Beverloo, Zbigniew Kwias, Hans A R Bluyssen, Joanna Wesoly
BACKGROUND: Mutation analysis and cytogenetic testing in clear cell renal cell carcinoma (ccRCC) is not yet implemented in a routine diagnostics of ccRCC. MATERIAL AND METHODS: We characterized the chromosomal alterations in 83 ccRCC tumors from Polish patients using whole genome SNP genotyping assay. Moreover, the utility of next generation sequencing of cell free DNA (cfDNA) in patients plasma as a potential tool for non-invasive cytogenetic analysis was tested...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28211990/homozygous-mutation-in-prune1-in-an-oji-cree-male-with-a-complex-neurological-phenotype
#13
Gregory Costain, Andrea Shugar, Pradeep Krishnan, Saadet Mahmutoglu, Suzanne Laughlin, Peter Kannu
The PRUNE1 gene encodes a member of the phosphoesterases (DHH) protein superfamily that is highly expressed in the human fetal brain and involved in the regulation of cell migration. Homozygous or compound heterozygous PRUNE1 mutations were recently identified in five individuals with brain malformations from four families. We present a case of a 2-year-old male with a complex neurological phenotype and abnormalities on brain MRI. Re-annotation of clinical whole-exome sequencing data revealed a homozygous likely pathogenic variant in PRUNE1 (c...
March 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28210247/genome-insight-and-comparative-pathogenomic-analysis-of-nesterenkonia-jeotgali-strain-cd08_7-isolated-from-duodenal-mucosa-of-celiac-disease-patient
#14
Atul M Chander, Ramesan G Nair, Gurwinder Kaur, Rakesh Kochhar, Devinder K Dhawan, Sanjay K Bhadada, Shanmugam Mayilraj
Species of the genus Nesterenkonia have been isolated from different ecological niches, especially from saline habitats and reported as weak human pathogens causing asymptomatic bacteraemia. Here, for the first time we are reporting the genome sequence and pathogenomic analysis of a strain designated as CD08_7 isolated from the duodenal mucosa of a celiac disease patient, identified as Nesterenkonia jeotgali. To date, only five strains of the genus Nesterenkonia (N. massiliensis strain NP1(T), Nesterenkonia sp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28207789/carbapenem-resistance-and-pathogenicity-of-bovine-acinetobacter-indicus-like-isolates
#15
Peter Klotz, Stephan Göttig, Ursula Leidner, Torsten Semmler, Sandra Scheufen, Christa Ewers
The objective of this study was to characterize blaOXA-23 harbouring Acinetobacter indicus-like strains from cattle including genomic and phylogenetic analyses, antimicrobial susceptibility testing and evaluation of pathogenicity in vitro and in vivo. Nasal and rectal swabs (n = 45) from cattle in Germany were screened for carbapenem-non-susceptible Acinetobacter spp. Thereby, two carbapenem resistant Acinetobacter spp. from the nasal cavities of two calves could be isolated. MALDI-TOF mass spectrometry and 16S rDNA sequencing identified these isolates as A...
2017: PloS One
https://www.readbyqxmd.com/read/28205635/deciphering-the-distance-to-antibiotic-resistance-for-the-pneumococcus-using-genome-sequencing-data
#16
Fredrick M Mobegi, Amelieke J H Cremers, Marien I de Jonge, Stephen D Bentley, Sacha A F T van Hijum, Aldert Zomer
Advances in genome sequencing technologies and genome-wide association studies (GWAS) have provided unprecedented insights into the molecular basis of microbial phenotypes and enabled the identification of the underlying genetic variants in real populations. However, utilization of genome sequencing in clinical phenotyping of bacteria is challenging due to the lack of reliable and accurate approaches. Here, we report a method for predicting microbial resistance patterns using genome sequencing data. We analyzed whole genome sequences of 1,680 Streptococcus pneumoniae isolates from four independent populations using GWAS and identified probable hotspots of genetic variation which correlate with phenotypes of resistance to essential classes of antibiotics...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28205220/comprehensive-genome-profiling-of-single-sperm-cells-by-multiple-annealing-and-looping-based-amplification-cycles-and-next-generation-sequencing-from-carriers-of-robertsonian-translocation
#17
Yanwei Sha, Yankun Sha, Zhiyong Ji, Lu Ding, Qing Zhang, Honggen Ouyang, Shaobin Lin, Xu Wang, Lin Shao, Chong Shi, Ping Li, Yueqiang Song
Robertsonian translocation (RT) is a common cause for male infertility, recurrent pregnancy loss, and birth defects. Studying meiotic recombination in RT-carrier patients helps decipher the mechanism and improve the clinical management of infertility and birth defects caused by RT. Here we present a new method to study spermatogenesis on a single-gamete basis from two RT carriers. By using a combined single-cell whole-genome amplification and sequencing protocol, we comprehensively profiled the chromosomal copy number of 88 single sperms from two RT-carrier patients...
March 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/28202802/multi-laboratory-survey-to-evaluate-salmonella-prevalence-in-diarrheic-and-non-diarrheic-dogs-and-cats-in-the-usa-between-2012-and-2014
#18
Renate Reimschuessel, Michael Grabenstein, Jake Guag, Sarah M Nemser, Kyunghee Song, Junshan Qiu, Kristin A Clothier, Barbara A Byrne, Stanley L Marks, Kyran Cadmus, Kristy Pabilonia, Susan Sanchez, Sreekumari Rajeev, Steve Ensley, Timothy S Frana, Albert E Jergens, Kimberly H Chappell, Siddhartha Thakur, Beverly Byrum, Jing Cui, Yan Zhang, Matthew M Erdman, Shelley C Rankin, Russell Daly, Seema Das, Laura Ruesch, Sara D Lawhon, Shuping Zhang, Timothy Baszler, Dubraska Diaz-Campos, Faye Hartmann, Ogi Okwumabua
Eleven laboratories collaborated to determine the periodic prevalence of Salmonella in a population of dogs and cats in the USA visiting veterinary clinics. Fecal samples (2965) solicited from 11 geographically dispersed veterinary testing laboratories were collected in 36 states between January 2012 and April 2014 and tested using a harmonized method. The overall study prevalence of Salmonella in cats (3 of 542) was <1%. Prevalence in dogs (60 of 2422) was 2.5%. Diarrhea was present in only 55% of positive dogs; however 3...
February 15, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28199897/real-world-utility-of-whole-exome-sequencing-with-targeted-gene-analysis-for-focal-epilepsy
#19
Piero Perucca, Ingrid E Scheffer, A Simon Harvey, Paul A James, Sebastian Lunke, Natalie Thorne, Clara Gaff, Brigid M Regan, John A Damiano, Michael S Hildebrand, Samuel F Berkovic, Terence J O'Brien, Patrick Kwan
OBJECTIVE: Driven by advances in genomic technology and reduction in costs, next-generation sequencing (NGS) is venturing into routine clinical care. The 'real-world' clinical utility of NGS remains to be determined in focal epilepsies, which account for 60% of all epilepsies and for which the importance of genetic factors is just beginning to emerge. We investigated the diagnostic yield and management implications of whole exome sequencing (WES)-based screening of selected genes in the routine care of common focal epilepsies suspected to have a genetic basis...
February 7, 2017: Epilepsy Research
https://www.readbyqxmd.com/read/28199314/whole-genome-landscape-of-pancreatic-neuroendocrine-tumours
#20
Aldo Scarpa, David K Chang, Katia Nones, Vincenzo Corbo, Ann-Marie Patch, Peter Bailey, Rita T Lawlor, Amber L Johns, David K Miller, Andrea Mafficini, Borislav Rusev, Maria Scardoni, Davide Antonello, Stefano Barbi, Katarzyna O Sikora, Sara Cingarlini, Caterina Vicentini, Skye McKay, Michael C J Quinn, Timothy J C Bruxner, Angelika N Christ, Ivon Harliwong, Senel Idrisoglu, Suzanne McLean, Craig Nourse, Ehsan Nourbakhsh, Peter J Wilson, Matthew J Anderson, J Lynn Fink, Felicity Newell, Nick Waddell, Oliver Holmes, Stephen H Kazakoff, Conrad Leonard, Scott Wood, Qinying Xu, Shivashankar Hiriyur Nagaraj, Eliana Amato, Irene Dalai, Samantha Bersani, Ivana Cataldo, Angelo P Dei Tos, Paola Capelli, Maria Vittoria Davì, Luca Landoni, Anna Malpaga, Marco Miotto, Vicki L J Whitehall, Barbara A Leggett, Janelle L Harris, Jonathan Harris, Marc D Jones, Jeremy Humphris, Lorraine A Chantrill, Venessa Chin, Adnan M Nagrial, Marina Pajic, Christopher J Scarlett, Andreia Pinho, Ilse Rooman, Christopher Toon, Jianmin Wu, Mark Pinese, Mark Cowley, Andrew Barbour, Amanda Mawson, Emily S Humphrey, Emily K Colvin, Angela Chou, Jessica A Lovell, Nigel B Jamieson, Fraser Duthie, Marie-Claude Gingras, William E Fisher, Rebecca A Dagg, Loretta M S Lau, Michael Lee, Hilda A Pickett, Roger R Reddel, Jaswinder S Samra, James G Kench, Neil D Merrett, Krishna Epari, Nam Q Nguyen, Nikolajs Zeps, Massimo Falconi, Michele Simbolo, Giovanni Butturini, George Van Buren, Stefano Partelli, Matteo Fassan, Kum Kum Khanna, Anthony J Gill, David A Wheeler, Richard A Gibbs, Elizabeth A Musgrove, Claudio Bassi, Giampaolo Tortora, Paolo Pederzoli, John V Pearson, Nicola Waddell, Andrew V Biankin, Sean M Grimmond
The diagnosis of pancreatic neuroendocrine tumours (PanNETs) is increasing owing to more sensitive detection methods, and this increase is creating challenges for clinical management. We performed whole-genome sequencing of 102 primary PanNETs and defined the genomic events that characterize their pathogenesis. Here we describe the mutational signatures they harbour, including a deficiency in G:C > T:A base excision repair due to inactivation of MUTYH, which encodes a DNA glycosylase. Clinically sporadic PanNETs contain a larger-than-expected proportion of germline mutations, including previously unreported mutations in the DNA repair genes MUTYH, CHEK2 and BRCA2...
February 15, 2017: Nature
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