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Clinical whole genome sequencing

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https://www.readbyqxmd.com/read/29776392/molecular-identification-of-tick-borne-pathogens-in-asymptomatic-individuals-with-human-immunodeficiency-virus-type-1-hiv-1-infection-a-retrospective-study
#1
Renata Welc-Falęciak, Justyna D Kowalska, Małgorzata Bednarska, Magdalena Szatan, Agnieszka Pawełczyk
BACKGROUND: The studies on the occurrence and diversity of tick-borne infections in HIV-infected individuals have been few, and the subject has been relatively neglected when compared with other common infections associated with HIV. In HIV-positive patients in whom a serological diagnostics is complicated due to reduced positive predictive value, a method where the microorganism is detected directly is of great value. Therefore, we performed a molecular study to ascertain the prevalence and incidence of tick-borne infections in HIV-infected persons in Poland, an endemic area for Ixodes ricinus ticks...
May 18, 2018: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29776391/the-clinical-implications-of-g1-g6-transcriptomic-signature-and-5-gene-score-in-korean-patients-with-hepatocellular-carcinoma
#2
Sung-Min Ahn, Farhan Haq, Inkeun Park, Jean-Charles Nault, Jessica Zucman-Rossi, Eunsil Yu
BACKGROUND: Efforts have been made to classify Hepatocellular Carcinoma (HCC) at surgically curable stages because molecular classification, which is prognostically informative, can accurately identify patients in need of additional early therapeutic interventions. Recently, HCC classification based French studies on the expression of 16 genes and 5 genes were proposed. In 16-gene classification, transcriptomic signatures (G1-G6) were used to classify HCC patients into clinical, genomic and pathway-specific subgroups...
May 18, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29774858/genomic-epidemiology-of-global-carbapenemase-producing-enterobacter-spp-2008-2014
#3
Gisele Peirano, Yasufumi Matsumura, Mark D Adams, Patricia Bradford, Mary Motyl, Liang Chen, Barry N Kreiswirth, Johann D D Pitout
We performed whole-genome sequencing on 170 clinical carbapenemase-producing Enterobacter spp. isolates collected globally during 2008-2014. The most common carbapenemase was VIM, followed by New Delhi metallo-β-lactamase (NDM), Klebsiella pneumoniae carbapenemase, oxacillin 48, and IMP. The isolates were of predominantly 2 species (E. xiangfangensis and E. hormaechei subsp. steigerwaltii) and 4 global clones (sequence type [ST] 114, ST93, ST90, and ST78) with different clades within ST114 and ST90. Particular genetic structures surrounding carbapenemase genes were circulating locally in various institutions within the same or between different STs in Greece, Guatemala, Italy, Spain, Serbia, and Vietnam...
June 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29774847/genomic-sequencing-of-bordetella-pertussis-for-epidemiology-and-global-surveillance-of-whooping-cough
#4
Valérie Bouchez, Julien Guglielmini, Mélody Dazas, Annie Landier, Julie Toubiana, Sophie Guillot, Alexis Criscuolo, Sylvain Brisse
Bordetella pertussis causes whooping cough, a highly contagious respiratory disease that is reemerging in many world regions. The spread of antigen-deficient strains may threaten acellular vaccine efficacy. Dynamics of strain transmission are poorly defined because of shortcomings in current strain genotyping methods. Our objective was to develop a whole-genome genotyping strategy with sufficient resolution for local epidemiologic questions and sufficient reproducibility to enable international comparisons of clinical isolates...
June 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29773658/detecting-quantifying-and-discriminating-the-mechanism-of-mosaic-chromosomal-aneuploidies-using-mad-seq
#5
Yu Kong, Esther R Berko, Anthony Marckette, Shahina B Maqbool, Claudia A Simões-Pires, David F Kronn, Qian K Ye, Masako Suzuki, Adam Auton, John Greally
Current approaches to detect and characterize mosaic chromosomal aneuploidy are limited by sensitivity, efficiency, cost or the need to culture cells. We describe the mosaic aneuploidy detection by massively-parallel sequencing (MAD-seq) capture assay and the MADSEQ analytical approach that allow low (<10%) levels of mosaicism for chromosomal aneuploidy or regional loss of heterozygosity to be detected, assigned to a meiotic or mitotic origin, and quantified as a proportion of the cells in the sample. We show results from a multi-ethnic MAD-seq (meMAD-seq) capture design that works equally well in populations of diverse racial and ethnic origins, and how the MADSEQ analytical approach can be applied to exome or whole genome sequencing data, revealing previously unrecognized aneuploidy or copy number neutral loss of heterozygosity in samples studied by the 1000 Genomes project, cell lines from public repositories, and one of the Illumina Platinum Genomes samples...
May 17, 2018: Genome Research
https://www.readbyqxmd.com/read/29771235/bordetella-pertussis-population-dynamics-and-phylogeny-in-japan-after-adoption-of-acellular-pertussis-vaccines
#6
Aldert Zomer, Nao Otsuka, Yukihiro Hiramatsu, Kazunari Kamachi, Naoko Nishimura, Takao Ozaki, Jan Poolman, Jeroen Geurtsen
Bordetella pertussis, the causative agent of whooping cough, has experienced a resurgence in the past 15 years, despite the existence of both whole-cell and acellular vaccines. Here, we performed whole genome sequencing analysis of 149 clinical strains, provided by the National Institute of Infectious Diseases (NIID), Japan, isolated in 1982-2014, after Japan became the first country to adopt acellular vaccines against B. pertussis. Additionally, we sequenced 39 strains provided by the Konan Kosei Hospital in Aichi prefecture, Japan, isolated in 2008-2013...
May 17, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29765361/biodiversity-of-environmental-leptospira-improving-identification-and-revisiting-the-diagnosis
#7
Roman Thibeaux, Dominique Girault, Emilie Bierque, Marie-Estelle Soupé-Gilbert, Anna Rettinger, Anthony Douyère, Michael Meyer, Gregorio Iraola, Mathieu Picardeau, Cyrille Goarant
Leptospirosis is an important environmental disease and a major threat to human health causing at least 1 million clinical infections annually. There has recently been a growing interest in understanding the environmental lifestyle of Leptospira . However, Leptospira isolation from complex environmental samples is difficult and time-consuming and few tools are available to identify Leptospira isolates at the species level. Here, we propose a polyphasic isolation and identification scheme, which might prove useful to recover and identify environmental isolates and select those to be submitted to whole-genome sequencing...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29765138/does-genomic-sequencing-early-in-the-diagnostic-trajectory-make-a-difference-a-follow-up-study-of-clinical-outcomes-and-cost-effectiveness
#8
Zornitza Stark, Deborah Schofield, Melissa Martyn, Luke Rynehart, Rupendra Shrestha, Khurshid Alam, Sebastian Lunke, Tiong Y Tan, Clara L Gaff, Susan M White
PURPOSE: To systematically investigate the longer-term clinical and health economic impacts of genomic sequencing for rare-disease diagnoses. METHODS: We collected information on continuing diagnostic investigation, changes in management, cascade testing, and parental reproductive outcomes in 80 infants who underwent singleton whole-exome sequencing (WES). RESULTS: The median duration of follow-up following result disclosure was 473 days. Changes in clinical management due to diagnostic WES results led to a cost saving of AU$1,578 per quality-adjusted life year gained, without increased hospital service use...
May 15, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29764212/the-clinical-application-of-single-sperm-based-snp-haplotyping-for-pgd-of-osteogenesis-imperfecta
#9
Linjun Chen, Zhenyu Diao, Zhipeng Xu, Jianjun Zhou, Guijun Yan, Haixiang Sun
Osteogenesis imperfecta (OI) is a genetically heterogeneous disorder, presenting either autosomal dominant, autosomal recessive or X-linked inheritance patterns. The majority of OI cases are autosomal dominant and are caused by heterozygous mutations in either the COL1A1 or COL1A2 gene. In these dominant disorders, allele dropout (ADO) can lead to misdiagnosis in preimplantation genetic diagnosis (PGD). Polymorphic markers linked to the mutated genes have been used to establish haplotypes for identifying ADO and ensuring the accuracy of PGD...
May 15, 2018: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/29763627/evaluation-of-minion-nanopore-sequencing-for-rapid-enterovirus-genotyping
#10
Emily Rames, Joanne Macdonald
Enteroviruses (EV) are associated with a range of serious infections, including aseptic meningitis, hand foot and mouth disease, myocarditis, acute flaccid paralysis and encephalitis. Improved methods for assessing EV genotypic diversity could assist molecular epidemiology studies, clinical diagnosis and environmental surveillance. We report new methods for EV genome amplification, and subsequent genotyping using the miniaturised MinION sequencing device. Importantly, this next-generation sequencer enabled correct strain-level assignment of identity for the EV-A71 isolate assessed, where strains with up to 99...
May 12, 2018: Virus Research
https://www.readbyqxmd.com/read/29762926/genetic-complexity-of-mitral-valve-prolapse-revealed-by-clinical-and-genetic-evaluation-of-a-large-family
#11
Gloria T Haskell, Brian C Jensen, Cecile Skrzynia, Thelsa Pulikkotil, Christian R Tilley, Yurong Lu, Daniel S Marchuk, Leigh Ann Samsa, Kirk C Wilhelmsen, Ethan Lange, Cam Patterson, James P Evans, Jonathan S Berg
BACKGROUND: A genetic component to familial mitral valve prolapse (MVP) has been proposed for decades. Despite this, very few genes have been linked to MVP. Herein is described a four-generation pedigree with numerous individuals affected with severe MVP, some at strikingly young ages. METHODS: A detailed clinical evaluation performed on all affected family members demonstrated a spectrum of MVP morphologies and associated phenotypes. RESULTS: Linkage analysis failed to identify strong candidate loci, but revealed significant regions, which were investigated further using whole-exome sequencing of one of the severely affected family members...
September 2017: Journal of Heart Valve Disease
https://www.readbyqxmd.com/read/29761480/whole-exome-sequencing-identifies-plec-exo5-and-dnah7-as-novel-susceptibility-genes-in-testicular-cancer
#12
Beatriz Paumard-Hernández, Oriol Calvete, Lucia Inglada Pérez, Héctor Tejero, Fátima Al-Shahrour, Guillermo Pita, Alicia Barroso, Juan Carlos Triviño, Miguel Urioste, Claudia Valverde, Enrique González Billalabeitia, Vanesa Quiroga, Juan Francisco Rodríguez Moreno, Antonio Fernández Aramburo, Cristina López, Pablo Maroto, Javier Sastre, María José Juan Fita, Ignacio Duran, Isabel Lorenzo-Lorenzo, Patricia Iranzo, Xavier García Del Muro, Silverio Ros, Francisco Zambrana, Ana María Autran, Javier Benítez
Testicular germ cell tumors (TGCTs) are a clinically and pathologically heterogeneous disease, and little is known of its genetic basis. Only low susceptibility risk loci have been identified for both sporadic and familial cases. Therefore, we tried to identify new susceptibility genes responsible for familial testicular cancer that may contribute to increasing our knowledge about the genetic basis of the disease. Nineteen Spanish families with at least two affected individuals with TGCT were selected. WES was performed on those individuals using an Illumina Hiseq2000 sequencing platform...
May 15, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29761214/analysis-of-resistance-genes-of-clinical-pannonibacter-phragmitetus-strain-31801-by-complete-genome-sequencing
#13
De-Song Ming, Qing-Qing Chen, Xiao-Tin Chen
To clarify the resistance mechanisms of Pannonibacter phragmitetus 31801, isolated from the blood of a liver abscess patient, at the genomic level, we performed whole genomic sequencing using a PacBio RS II single-molecule real-time long-read sequencer. Bioinformatic analysis of the resulting sequence was then carried out to identify any possible resistance genes. Analyses included Basic Local Alignment Search Tool searches against the Antibiotic Resistance Genes Database, ResFinder analysis of the genome sequence, and Resistance Gene Identifier analysis within the Comprehensive Antibiotic Resistance Database...
May 14, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29760690/two-new-lytic-bacteriophages-of-the-myoviridae-family-against-carbapenem-resistant-acinetobacter-baumannii
#14
Weilong Zhou, Yu Feng, Zhiyong Zong
Two lytic bacteriophages, WCHABP1 and WCHABP12, were recovered from hospital sewage and were able to infect 9 and 12 out of 18 carbapenem-resistant Acinetobacter baumannii clinical strains, which belonged to different clones. Electron microscopy scan showed that both bacteriophages had the similar morphology as those of the Myoviridae family. Whole genomic sequencing revealed 45.4- or 45.8-kb genome with a 37.6% GC content for WCHABP1 and WCHABP12, both of which showed significant DNA sequence similarity with bacteriophages of the Ap22virus genus within the Myoviridae family...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29760432/microcephaly-short-stature-and-limb-abnormality-disorder-due-to-novel-autosomal-biallelic-donson-mutations-in-two-german-siblings
#15
Solveig Schulz, Martin A Mensah, Heike de Vries, Rosemarie Fröber, Bernd Romeike, Uwe Schneider, Stephan Borte, Detlev Schindler, Karim Kentouche
Recently, variants in DONSON have been reported to cause different disorders of the microcephalic primordial dwarfism spectrum. Using whole-exome sequencing, we identified two novel, compound heterozygous DONSON variants in a pair of siblings, one of whom was previously diagnosed with Fanconi anemia. This occurred because the present cases exhibited clinical findings in addition to those of the microcephalic primordial dwarfism disorder, including severe limb malformations. These findings suggest that the DONSON and Fanconi anemia proteins could have supplementary roles in developmental processes as they have in the maintenance of genomic integrity, resulting in related disease phenotypes...
May 14, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29758565/clinical-and-genetic-analysis-of-a-rare-syndrome-associated-with-neoteny
#16
Richard F Walker, Serban Ciotlos, Qing Mao, Robert Chin, Snezana Drmanac, Nina Barua, Misha R Agarwal, Rebecca Yu Zhang, Zhenyu Li, Michelle Ka Yan Wu, Kevin Sun, Katharine Lee, Staci Nguyen, Jia Sophie Liu, Paolo Carnevali, Radoje Drmanac, Brock A Peters
PurposeWe describe a novel syndrome in seven female patients with extreme developmental delay and neoteny.MethodsAll patients in this study were female, aged 4 to 23 years, were well below the fifth percentile in height and weight, had failed to develop sexually, and lacked the use of language. Karyotype and array chromosome genomic hybridization analysis failed to identify large-scale structural variations. To further understand the underlying cause of disease in these patients, whole-genome sequencing was performed...
April 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29757395/genotyping-and-whole-genome-sequencing-to-identify-tuberculosis-transmission-to-pediatric-patients-in-british-columbia-canada-2005-2014
#17
Jennifer L Guthrie, Andy Delli Pizzi, David Roth, Clare Kong, Danielle Jorgensen, Mabel Rodrigues, Patrick Tang, Victoria J Cook, James Johnston, Jennifer L Gardy
Background: Tuberculosis (TB) in children is often an indicator of recent transmission. Genotyping and whole genome sequencing (WGS) can enhance pediatric TB investigations by confirming or refuting transmission events. Methods: Mycobacterium tuberculosis isolates from all pediatric patients <18 years with culture-confirmed TB in British Columbia (BC) from 2005-2014 (n=49) were genotyped by MIRU-VNTR and compared to adult isolates. Genotypically clustered cases underwent WGS...
May 11, 2018: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29755435/analysis-of-phylogenetic-variation-of-stenotrophomonas-maltophilia-reveals-human-specific-branches
#18
Joerg Steinmann, Uwe Mamat, Ebrahim M Abda, Lisa Kirchhoff, Wolfgang R Streit, Ulrich E Schaible, Stefan Niemann, Thomas A Kohl
Stenotrophomonas maltophilia is a non-fermenting Gram-negative bacterium that is ubiquitous in the environment. In humans, this opportunistic multi-drug-resistant pathogen is responsible for a plethora of healthcare-associated infections. Here, we utilized a whole genome sequencing (WGS)-based phylogenomic core single nucleotide polymorphism (SNP) approach to characterize S. maltophilia subgroups, their potential association with human infection, and to detect any possible transmission events. In total, 89 isolates (67 clinical and 22 environmental) from Germany were sequenced...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29755420/characterization-of-two-novel-bacteriophages-infecting-multidrug-resistant-mdr-acinetobacter-baumannii-and-evaluation-of-their-therapeutic-efficacy-in-vivo
#19
Kyoungeun Cha, Hynu K Oh, Jae Y Jang, Yunyeol Jo, Won K Kim, Geon U Ha, Kwan S Ko, Heejoon Myung
Acinetobacter baumannii is emerging as a challenging nosocomial pathogen due to its rapid evolution of antibiotic resistance. We report characterization of two novel bacteriophages, PBAB08 and PBAB25, infecting clinically isolated, multidrug-resistant (MDR) A. baumannii strains. Both phages belonged to Myoviridae of Caudovirales as their morphology observed under an electron microscope. Their genomes were double stranded linear DNAs of 42,312 base pairs and 40,260 base pairs, respectively. The two phages were distinct from known Acinetobacter phages when whole genome sequences were compared...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29755193/h9n2-avian-influenza-virus-retained-low-pathogenicity-after-serial-passage-in-chickens
#20
Akinlolu Jegede, Qigao Fu, Yohannes Berhane, Min Lin, Ashok Kumar, Jiewen Guan
The H9N2 strains of avian influenza viruses (AIVs) circulate worldwide in poultry and cause sporadic infection in humans. To better understand the evolution of these viruses while circulating in poultry, an H9N2 chicken isolate was passaged 19 times in chickens via aerosol inoculation. Whole-genome sequencing showed that the viruses from the initial stock and those after the 8th and 19th passages (P0, P8, and P19) all had the same monobasic cleavage site in the hemagglutinin (HA), typical for viruses of low pathogenicity...
April 2018: Canadian Journal of Veterinary Research, Revue Canadienne de Recherche Vétérinaire
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