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Clinical whole genome sequencing

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https://www.readbyqxmd.com/read/28922838/comparative-genomics-of-a-drug-resistant-pseudomonas-aeruginosa-panel-and-the-challenges-of-antimicrobial-resistance-prediction-from-genomes
#1
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/28919550/improving-the-genotyping-resolution-of-cryptosporidium-hominis-subtype-iba10g2-using-one-step-pcr-based-amplicon-sequencing
#2
Jessica Beser, Björn M Hallström, Abdolreza Advani, Sofia Andersson, Gabriel Östlund, Jadwiga Winiecka-Krusnell, Marianne Lebbad, Erik Alm, Karin Troell, Romanico B G Arrighi
Cryptosporidium hominis gp60 subtype IbA10G2 is a common cause of cryptosporidiosis. This subtype is responsible for many waterborne outbreaks as well as sporadic cases and is considered virulent and highly important in the epidemiology of cryptosporidiosis. Due to low heterogeneity within the genome of C. hominis it has been difficult to identify epidemiological markers with higher resolution than gp60. However, new markers are required in order to improve outbreak investigations and studies of the transmission dynamics of this clinically important subtype...
September 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28916928/newborn-screening-in-the-era-of-precision-medicine
#3
Lan Yang, Jiajia Chen, Bairong Shen
As newborn screening success stories gained general confirmation during the past 50 years, scientists quickly discovered diagnostic tests for a host of genetic disorders that could be treated at birth. Outstanding progress in sequencing technologies over the last two decades has made it possible to comprehensively profile newborn screening (NBS) and identify clinically relevant genomic alterations. With the rapid developments in whole-genome sequencing (WGS) and whole-exome sequencing (WES) recently, we can detect newborns at the genomic level and be able to direct the appropriate diagnosis to the different individuals at the appropriate time, which is also encompassed in the concept of precision medicine...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28916646/serac1-deficiency-causes-complicated-hsp-evidence-from-a-novel-splice-mutation-in-a-large-family
#4
Benjamin Roeben, Rebecca Schüle, Susanne Ruf, Benjamin Bender, Bader Alhaddad, Tanja Benkert, Thomas Meitinger, Selina Reich, Judith Böhringer, Claus-Dieter Langhans, Frédéric M Vaz, Saskia B Wortmann-Hagemann, Thorsten Marquardt, Tobias B Haack, Ingeborg Krägeloh-Mann, Ludger Schöls, Matthis Synofzik
OBJECTIVE: To demonstrate that mutations in the phosphatidylglycerol remodelling enzyme SERAC1 can cause juvenile-onset complicated hereditary spastic paraplegia (cHSP) clusters, thus adding SERAC1 to the increasing number of complex lipid cHSP genes. METHODS: Combined genomic and functional validation studies (whole-exome sequencing, mRNA, cDNA and protein), biomarker investigations (3-methyl-glutaconic acid, filipin staining and phosphatidylglycerols PG34:1/PG36:1), and clinical and imaging phenotyping were performed in six affected subjects from two different branches of a large consanguineous family...
September 15, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28916491/controversy-and-debate-on-clinical-genomics-sequencing-paper-2-clinical-genome-wide-sequencing-don-t-throw-out-the-baby-with-the-bathwater
#5
Shelin Adam, Jan M Friedman
Genome-wide (exome or whole genome) sequencing with appropriate genetic counselling should be considered for any patient with a suspected mendelian disease that has not been identified by conventional testing.Clinical genome-wide sequencing provides a powerful and effective meansof identifying specific genetic causes of serious disease and improving clinical care.
September 12, 2017: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/28916321/analysis-of-resistance-genes-in-pan-resistant-myroides-odoratimimus-clinical-strain-pr63039-using-whole-genome-sequencing
#6
Desong Ming, Qing-Qing Chen, Xiao-Tin Chen
To clarify the antibiotic resistance mechanisms of Myroides odoratimimus, pan-resistant M. odoratimimus strain PR63039 was isolated and its genome sequenced and analyzed. Antimicrobial susceptibility testing was conducted using the Kirby-Bauer disk diffusion method, and the Phoenix-100 Automated Microbiology System with a NMIC/ID-4 panel including aminoglycosides, β-lactams, polypeptides, quinolones, sulfonamides, chloramphenicols, and tetracyclines. Single-molecule real-time whole genome sequencing was conducted using the PacBio RSII system, and genome annotation was performed using RAST and IMG ER...
September 12, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28914635/clinical-genetics-of-craniosynostosis
#7
Andrew O M Wilkie, David Johnson, Steven A Wall
PURPOSE OF REVIEW: When providing accurate clinical diagnosis and genetic counseling in craniosynostosis, the challenge is heightened by knowledge that etiology in any individual case may be entirely genetic, entirely environmental, or anything in between. This review will scope out how recent genetic discoveries from next-generation sequencing have impacted on the clinical genetic evaluation of craniosynostosis. RECENT FINDINGS: Survey of a 13-year birth cohort of patients treated at a single craniofacial unit demonstrates that a genetic cause of craniosynostosis can be identified in one quarter of cases...
September 14, 2017: Current Opinion in Pediatrics
https://www.readbyqxmd.com/read/28905882/identification-of-causative-variants-in-txnl4a-in-burn-mckeown-syndrome-and-isolated-choanal-atresia
#8
Jacqueline A C Goos, Sigrid M A Swagemakers, Stephen R F Twigg, Marieke F van Dooren, A Jeannette M Hoogeboom, Christian Beetz, Sven Günther, Frank J Magielsen, Charlotte W Ockeloen, Maria A Ramos-Arroyo, Rolph Pfundt, Helger G Yntema, Peter J van der Spek, Philip Stanier, Dagmar Wieczorek, Andrew O M Wilkie, Ans M W van den Ouweland, Irene M J Mathijssen, Jane A Hurst
Burn-McKeown syndrome (BMKS) is a rare syndrome characterized by choanal atresia, prominent ears, abnormalities of the outer third of the lower eyelid, structural cardiac abnormalities, conductive and sensorineural hearing loss, and cleft lip. Recently, causative compound heterozygous variants were identified in TXNL4A. We analyzed an individual with clinical features of BMKS and her parents by whole-genome sequencing and identified compound heterozygous variants in TXNL4A (a novel splice site variant (c.258-2A>G, (p...
October 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28904649/harnessing-whole-genome-sequencing-in-medical-mycology
#9
REVIEW
Christina A Cuomo
PURPOSE OF REVIEW: Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically important fungal pathogens. RECENT FINDINGS: Genomes for some important fungal pathogens were only recently assembled, revealing gene family expansions in many species and extreme gene loss in one obligate species...
2017: Current Fungal Infection Reports
https://www.readbyqxmd.com/read/28904385/rapid-discovery-of-de-novo-deleterious-mutations-in-cattle-enhances-the-value-of-livestock-as-model-species
#10
E Bourneuf, P Otz, H Pausch, V Jagannathan, P Michot, C Grohs, G Piton, S Ammermüller, M-C Deloche, S Fritz, H Leclerc, C Péchoux, A Boukadiri, C Hozé, R Saintilan, F Créchet, M Mosca, D Segelke, F Guillaume, S Bouet, A Baur, A Vasilescu, L Genestout, A Thomas, A Allais-Bonnet, D Rocha, M-A Colle, C Klopp, D Esquerré, C Wurmser, K Flisikowski, H Schwarzenbacher, J Burgstaller, M Brügmann, E Dietschi, N Rudolph, M Freick, S Barbey, G Fayolle, C Danchin-Burge, L Schibler, B Bed'Hom, B J Hayes, H D Daetwyler, R Fries, D Boichard, D Pin, C Drögemüller, A Capitan
In humans, the clinical and molecular characterization of sporadic syndromes is often hindered by the small number of patients and the difficulty in developing animal models for severe dominant conditions. Here we show that the availability of large data sets of whole-genome sequences, high-density SNP chip genotypes and extensive recording of phenotype offers an unprecedented opportunity to quickly dissect the genetic architecture of severe dominant conditions in livestock. We report on the identification of seven dominant de novo mutations in CHD7, COL1A1, COL2A1, COPA, and MITF and exploit the structure of cattle populations to describe their clinical consequences and map modifier loci...
September 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28904182/finegoldia-magna-isolated-from-orthopedic-joint-implant-associated-infections
#11
Bo Söderquist, Sanna Björklund, Bengt Hellmark, Anders Jensen, Holger Brüggemann
Background: The anaerobic Gram-positive coccus Finegoldia magna is a rare cause of infections of bone and joints. The aim of this study was to describe the microbiological and clinical characteristics of orthopedic implant-associated infections caused by F. magnaMethods: We retrospectively analyzed samples consisting of anaerobic Gram-positive cocci and samples already identified as F. magna from patients with orthopedic infections. The isolates found were determined to species level by MALDI-TOF MS. The antibiotic susceptibility pattern was determined by Etest...
September 13, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28903905/the-pathogenicity-of-genomic-genetic-variant-of-x-chromosomal-genes-in-males-with-intellectual-disability
#12
Ji-Ping Peng, Fang Liu, Hua Xie, Xiao-Li Chen
Intellectual Disability (ID, previously named mental retardation) is a group of common pediatric neurology disorders characterized by extensive genetic and phenotypic heterogeneity. About 25%-50% of ID was caused by genomic/genetic variants, in which genomic/genetic variants of X-chromosome are one of key pathogenic causation (25%-30%), resulting in X-linked ID (XLID). The epidemiological data showed that the male to female ratio is 1.3: 1 in ID patients. The prevalence of XLID in the whole ID population is 10%-15%, and this prevalence reaches 20%-25% in the male ID population...
June 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28903777/modest-heterologous-protection-after-plasmodium-falciparum-sporozoite-immunization-a-double-blind-randomized-controlled-clinical-trial
#13
Jona Walk, Isaie J Reuling, Marije C Behet, Lisette Meerstein-Kessel, Wouter Graumans, Geert-Jan van Gemert, Rianne Siebelink-Stoter, Marga van de Vegte-Bolmer, Thorsten Janssen, Karina Teelen, Johannes H W de Wilt, Quirijn de Mast, André J van der Ven, Ernest Diez Benavente, Susana Campino, Taane G Clark, Martijn A Huynen, Cornelus C Hermsen, Else M Bijker, Anja Scholzen, Robert W Sauerwein
BACKGROUND: A highly efficacious vaccine is needed for malaria control and eradication. Immunization with Plasmodium falciparum NF54 parasites under chemoprophylaxis (chemoprophylaxis and sporozoite (CPS)-immunization) induces the most efficient long-lasting protection against a homologous parasite. However, parasite genetic diversity is a major hurdle for protection against heterologous strains. METHODS: We conducted a double-blind, randomized controlled trial in 39 healthy participants of NF54-CPS immunization by bites of 45 NF54-infected (n = 24 volunteers) or uninfected mosquitoes (placebo; n = 15 volunteers) against a controlled human malaria infection with the homologous NF54 or the genetically distinct NF135...
September 13, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28901403/whole-wiskott%C3%A2-aldrich-syndrome-protein-gene-deletion-identified-by-high-throughput-sequencing
#14
Xiangling He, Runying Zou, Bing Zhang, Yalan You, Yang Yang, Xin Tian
Wiskott‑Aldrich syndrome (WAS) is a rare X‑linked recessive immunodeficiency disorder, characterized by thrombocytopenia, small platelets, eczema and recurrent infections associated with increased risk of autoimmunity and malignancy disorders. Mutations in the WAS protein (WASP) gene are responsible for WAS. To date, WASP mutations, including missense/nonsense, splicing, small deletions, small insertions, gross deletions, and gross insertions have been identified in patients with WAS. In addition, WASP‑interacting proteins are suspected in patients with clinical features of WAS, in whom the WASP gene sequence and mRNA levels are normal...
August 31, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28899476/-advances-in-genetic-research-of-cerebral-palsy
#15
Fang-Fang Wang, Rong Luo, Yi Qu, De-Zhi Mu
Cerebral palsy is a group of syndromes caused by non-progressive brain injury in the fetus or infant and can cause disabilities in childhood. Etiology of cerebral palsy has always been a hot topic for clinical scientists. More and more studies have shown that genetic factors are closely associated with the development of cerebral palsy. With the development and application of various molecular and biological techniques such as chromosome microarray analysis, genome-wide association study, and whole exome sequencing, new achievements have been made in the genetic research of cerebral palsy...
September 2017: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/28895585/habitual-sleep-duration-and-sleep-duration-variation-are-independently-associated-with-body-mass-index
#16
X Xu, M P Conomos, O Manor, J E Rohwer, A T Magis, J C Lovejoy
BACKGROUND: Sleep plays a vital role in maintaining homeostasis and promoting health. Previous studies show that shorter sleep duration is associated with elevated body mass index (BMI) and other cardiovascular risk factors. The goal of this study was to investigate the effects of habitual sleep duration and nightly sleep duration variation based on daily device-recorded data on BMI and obesity-related biomarkers. METHOD: 748 individuals (50.6% females, 85.4% European-Americans, average age: 49...
September 12, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/28893788/genomic-and-molecular-characterization-of-clinical-isolates-of-enterobacteriaceae-harboring-mcr-1-in-colombia-2002-2016
#17
Sandra Yamile Saavedra, Lorena Diaz, Magdalena Wiesner, Adriana Correa, Stefany Alejandra Arévalo, Jinnethe Reyes, Andrea Melissa Hidalgo, Elsa de la Cadena, Marcela Perenguez, Lucy Angeline Montaño, Javier Ardila, Rafael Ríos, María Victoria Ovalle, Paula Díaz, Paola Porras, Maria V Villegas, Cesar A Arias, Mauricio Beltrán, Carolina Duarte
Polymyxins are last resort antimicrobial agents used to treat infections caused by carbapenem-resistant Enterobacteriaceae Due to the worldwide dissemination of polymyxin resistance in animal and human isolates, we aimed to characterize polymyxin resistance associated with the presence of mcr-1 in Enterobacteriaceae and nonfermenter Gram-negative bacilli, in isolates collected retrospectively in Colombia from 2002 to 2016. A total of 5,887 Gram-negative clinical isolates were studied and 513 were found to be resistant to the polymyxins...
September 11, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28891274/breast-cancer-risk-and-germline-genomic-profiling-of-women-with-neurofibromatosis-type-1-who-developed-breast-cancer
#18
Xia Wang, Jamie K Teer, Renee N Tousignant, Albert M Levin, David Boulware, Dhananjay A Chitale, Brandon M Shaw, Zhihua Chen, Yonghong Zhang, Jaishri O Blakeley, Maria T Acosta, Ludwine M Messiaen, Bruce R Korf, Michael A Tainsky
NF1 mutations predispose to neurofibromatosis type1 (NF1) and women with NF1 have a moderately elevated risk for breast cancer, especially under age 50. Germline genomic analysis may better define the risk so screening and prevention can be applied to the individuals who benefit the most. Survey conducted in several neurofibromatosis clinics in the United States has demonstrated a 17.2% lifetime risk of breast cancer in women affected with NF1. Cumulated risk to age 50 is estimated to be 9.27%. For genomic profiling, fourteen women with NF1 and a history of breast cancer were recruited and underwent whole exon sequencing (WES), targeted genomic DNA based and RNA based analysis of the NF1 gene...
September 10, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28891138/epidemiology-of-helicobacter-pylori-infection
#19
REVIEW
Christophe Burucoa, Anthony Axon
The study of Helicobacter pylori genetic variability brought us interesting data on the history of mankind. Based on multilocus sequence typing and more recently on whole-genome sequencing, paleomicrobiology still attracts the attention of global researchers in relation to its ancestor roots and coexistence with humans. Three studies determining the prevalence of virulence factors illustrates the controversial results obtained since 30 years by studies trying to associate prevalence of different virulence markers and clinical outcomes of H...
September 2017: Helicobacter
https://www.readbyqxmd.com/read/28886384/hpv16-e7-genetic-conservation-is-critical-to-carcinogenesis
#20
Lisa Mirabello, Meredith Yeager, Kai Yu, Gary M Clifford, Yanzi Xiao, Bin Zhu, Michael Cullen, Joseph F Boland, Nicolas Wentzensen, Chase W Nelson, Tina Raine-Bennett, Zigui Chen, Sara Bass, Lei Song, Qi Yang, Mia Steinberg, Laurie Burdett, Michael Dean, David Roberson, Jason Mitchell, Thomas Lorey, Silvia Franceschi, Philip E Castle, Joan Walker, Rosemary Zuna, Aimée R Kreimer, Daniel C Beachler, Allan Hildesheim, Paula Gonzalez, Carolina Porras, Robert D Burk, Mark Schiffman
Although most cervical human papillomavirus type 16 (HPV16) infections become undetectable within 1-2 years, persistent HPV16 causes half of all cervical cancers. We used a novel HPV whole-genome sequencing technique to evaluate an exceptionally large collection of 5,570 HPV16-infected case-control samples to determine whether viral genetic variation influences risk of cervical precancer and cancer. We observed thousands of unique HPV16 genomes; very few women shared the identical HPV16 sequence, which should stimulate a careful re-evaluation of the clinical implications of HPV mutation rates, transmission, clearance, and persistence...
September 7, 2017: Cell
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