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Clinical whole genome sequencing

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https://www.readbyqxmd.com/read/28820946/proteogenomic-investigation-of-strain-variation-in-clinical-mycobacterium-tuberculosis-isolates
#1
Tiaan Heunis, Anzaan Dippenaar, Robin M Warren, Paul D van Helden, Ruben G van der Merwe, Nicolaas C Gey van Pittius, Arnab Pain, Samantha L Sampson, David L Tabb
Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M...
August 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28819111/community-outbreaks-of-group-a-streptococcus-revealed-by-genome-sequencing
#2
Claire E Turner, Luke Bedford, Nicholas M Brown, Kim Judge, M Estée Török, Julian Parkhill, Sharon J Peacock
The frequent occurrence of disease outbreaks in humans caused by group A Streptococcus (GAS) is an on-going public health threat. Conventional bacterial typing methods lack the discriminatory power to confidently confirm or refute outbreaks in hospital and community settings. Microbial whole genome sequencing (WGS) provides a potential solution to this, but, there has been limited population-based surveillance with accompanying sequence data. We performed retrospective genomic surveillance of 93 clinical GAS isolates from individuals in a defined geographic region...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818272/on-human-parthenogenesis
#3
Gabriel Jose de Carli, Tiago Campos Pereira
Spontaneous parthenogenetic and androgenetic events occur in humans, but they result in tumours: the ovarian teratoma and the hydatidiform mole, respectively. However, the observation of fetiform (ovarian) teratomas, the serependious identification of several chimeric human parthenotes and androgenotes in the last two decades, along with the creation of viable bi-maternal mice in the laboratory based on minor genetic interferences, raises the question of whether natural cases of clinically healthy human parthenotes have gone unnoticed to science...
September 2017: Medical Hypotheses
https://www.readbyqxmd.com/read/28817238/stakeholders-in-psychiatry-and-their-attitudes-toward-receiving-pertinent-and-incident-findings-in-genomic-research
#4
Anna Sundby, Merete W Boolsen, Kristoffer S Burgdorf, Henrik Ullum, Thomas F Hansen, Anna Middleton, Ole Mors
Increasingly more psychiatric research studies use whole genome sequencing or whole exome sequencing. Consequently, researchers face difficult questions, such as which genomic findings to return to research participants and how. This study aims to gain more knowledge on the attitudes among potential research participants and health professionals toward receiving pertinent and incidental findings. A cross-sectional online survey was developed to investigate the attitudes among research participants toward receiving genomic findings...
August 17, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28813472/an-intronic-line-1-insertion-in-mertk-is-strongly-associated-with-retinopathy-in-swedish-vallhund-dogs
#5
Richard Everson, Louise Pettitt, Oliver P Forman, Olivia Dower-Tylee, Bryan McLaughlin, Saija Ahonen, Maria Kaukonen, András M Komáromy, Hannes Lohi, Cathryn S Mellersh, Jane Sansom, Sally L Ricketts
The domestic dog segregates a significant number of inherited progressive retinal diseases, several of which mirror human retinal diseases and which are collectively termed progressive retinal atrophy (PRA). In 2014, a novel form of PRA was reported in the Swedish Vallhund breed, and the disease was mapped to canine chromosome 17. The causal mutation was not identified, but expression analyses of the retinas of affected Vallhunds demonstrated a 6-fold increased expression of the MERTK gene compared to unaffected dogs...
2017: PloS One
https://www.readbyqxmd.com/read/28812650/autosomal-recessive-cone-rod-dystrophy-can-be-caused-by-mutations-in-the-atf6-gene
#6
Anna Skorczyk-Werner, Wei-Chieh Chiang, Anna Wawrocka, Katarzyna Wicher, Małgorzata Jarmuż-Szymczak, Magdalena Kostrzewska-Poczekaj, Aleksander Jamsheer, Rafał Płoski, Małgorzata Rydzanicz, Dorota Pojda-Wilczek, Nicole Weisschuh, Bernd Wissinger, Susanne Kohl, Jonathan H Lin, Maciej R Krawczyński
Inherited retinal dystrophies (IRDs) are clinically and genetically highly heterogeneous, making clinical diagnosis difficult. The advances in high-throughput sequencing (ie, panel, exome and genome sequencing) have proven highly effective on defining the molecular basis of these disorders by identifying the underlying variants in the respective gene. Here we report two siblings affected by an IRD phenotype and a novel homozygous c.1691A>G (p.(Asp564Gly)) ATF6 (activating transcription factor 6A) missense substitution identified by whole exome sequencing analysis...
August 16, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28812537/leveraging-network-analytics-to-infer-patient-syndrome-and-identify-causal-genes-in-rare-disease-cases
#7
Andreas Krämer, Sohela Shah, Robert Anthony Rebres, Susan Tang, Daniel Rene Richards
BACKGROUND: Next-generation sequencing is widely used to identify disease-causing variants in patients with rare genetic disorders. Identifying those variants from whole-genome or exome data can be both scientifically challenging and time consuming. A significant amount of time is spent on variant annotation, and interpretation. Fully or partly automated solutions are therefore needed to streamline and scale this process. RESULTS: We describe Phenotype Driven Ranking (PDR), an algorithm integrated into Ingenuity Variant Analysis, that uses observed patient phenotypes to prioritize diseases and genes in order to expedite causal-variant discovery...
August 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28810711/whole-rna-sequencing-and-transcriptome-assembly-of-candida-albicans-and-candida-africana-under-chlamydospore-inducing-conditions
#8
Domenico Giosa, Maria Rosa Felice, Travis J Lawrence, Megha Gulati, Fabio Scordino, Letterio Giuffrè, Carla Lo Passo, Enrico D'Alessandro, Giuseppe Criseo, David H Ardell, Aaron D Hernday, Clarissa J Nobile, Orazio Romeo
Candida albicans is the most common cause of life-threatening fungal infections in humans, especially in immunocompromised individuals. Crucial to its success as an opportunistic pathogen is the considerable dynamism of its genome, which readily undergoes genetic changes generating new phenotypes and shaping the evolution of new strains. Candida africana is an intriguing C. albicans biovariant strain that exhibits remarkable genetic and phenotypic differences when compared with standard C. albicans isolates...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28810143/genomic-evolution-of-breast-cancer-metastasis-and-relapse
#9
Lucy R Yates, Stian Knappskog, David Wedge, James H R Farmery, Santiago Gonzalez, Inigo Martincorena, Ludmil B Alexandrov, Peter Van Loo, Hans Kristian Haugland, Peer Kaare Lilleng, Gunes Gundem, Moritz Gerstung, Elli Pappaemmanuil, Patrycja Gazinska, Shriram G Bhosle, David Jones, Keiran Raine, Laura Mudie, Calli Latimer, Elinor Sawyer, Christine Desmedt, Christos Sotiriou, Michael R Stratton, Anieta M Sieuwerts, Andy G Lynch, John W Martens, Andrea L Richardson, Andrew Tutt, Per Eystein Lønning, Peter J Campbell
Patterns of genomic evolution between primary and metastatic breast cancer have not been studied in large numbers, despite patients with metastatic breast cancer having dismal survival. We sequenced whole genomes or a panel of 365 genes on 299 samples from 170 patients with locally relapsed or metastatic breast cancer. Several lines of analysis indicate that clones seeding metastasis or relapse disseminate late from primary tumors, but continue to acquire mutations, mostly accessing the same mutational processes active in the primary tumor...
August 14, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28809007/method-to-identify-silent-codon-mutations-that-may-alter-peptide-elongation-kinetics-and-co-translational-protein-folding
#10
Ronald Worthington, Elijah Ball, Brentsen Wolf, Gregory Takacs
Due to the redundancy of the protein genetic code, mutational changes in the second or third nucleotide of an existing codon may not change the amino acid specification of the resulting modified codon. When peptide primary sequence is unchanged by mutation, that mutation is assumed to have no functional consequences. However, for one key gene involved in drug transport, MDR-1, several silent, synonymous mutations have been shown to alter protein structure and substrate affinity (Kimchi-Sarfaty et al., Science 315:525-528, 2007)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808687/whole-exome-sequencing-associates-novel-csmd1-gene-mutations-with-familial-parkinson-disease
#11
Javier Ruiz-Martínez, Luis J Azcona, Alberto Bergareche, Jose F Martí-Massó, Coro Paisán-Ruiz
OBJECTIVE: Despite the enormous advancements made in deciphering the genetic architecture of Parkinson disease (PD), the majority of PD is idiopathic, with single gene mutations explaining only a small proportion of the cases. METHODS: In this study, we clinically evaluated 2 unrelated Spanish families diagnosed with PD, in which known PD genes were previously excluded, and performed whole-exome sequencing analyses in affected individuals for disease gene identification...
October 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28807864/reducing-diagnostic-turnaround-times-of-exome-sequencing-for-families-requiring-timely-diagnoses
#12
Aurélie Bourchany, Christel Thauvin-Robinet, Daphné Lehalle, Ange-Line Bruel, Alice Masurel-Paulet, Nolwenn Jean, Sophie Nambot, Marjorie Willems, Laetitia Lambert, Salima El Chehadeh-Djebbar, Elise Schaefer, Aurélia Jaquette, Judith St-Onge, Charlotte Poe, Thibaud Jouan, Martin Chevarin, Patrick Callier, Anne-Laure Mosca-Boidron, Nicole Laurent, Mathilde Lefebvre, Frédéric Huet, Nada Houcinat, Sébastien Moutton, Christophe Philippe, Frédéric Tran-Mau-Them, Antonio Vitobello, Paul Kuentz, Yannis Duffourd, Jean-Baptiste Rivière, Julien Thevenon, Laurence Faivre
BACKGROUND AND OBJECTIVE: Whole-exome sequencing (WES) has now entered medical practice with powerful applications in the diagnosis of rare Mendelian disorders. Although the usefulness and cost-effectiveness of WES have been widely demonstrated, it is essential to reduce the diagnostic turnaround time to make WES a first-line procedure. Since 2011, the automation of laboratory procedures and advances in sequencing chemistry have made it possible to carry out diagnostic whole genome sequencing from the blood sample to molecular diagnosis of suspected genetic disorders within 50 h...
August 11, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28807100/two-cases-of-multi-antibiotic-resistant-cronobacter-spp-infections-of-infants-in-china
#13
Jing Hua Cui, Bo Yu, Yun Xiang, Zhen Zhang, Ting Zhang, Ying Chun Zeng, Zhi Gang Cui, Xi Xiang Huo
Infections by Cronobacter spp. are hazardous to infants since they can lead to neonatal meningitis, bacteremia, and necrotizing enterocolitis. Cronobacter spp. are frequently resistant to β-lactam derivatives, macrolides, and aminoglycosides. In addition, multi-resistant strains have also been detected. In China, the isolation rate of Cronobacter spp. from commercial powdered infant formula (PIF) or follow-up formula (FUF) is relatively high. Nevertheless, clinical cases of Cronobacter infection have been ignored to date...
August 2017: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/28803969/molecular-detection-and-characterization-of-influenza-c-viruses-from-western-india
#14
V A Potdar, D D Hinge, M R Dakhave, A Manchanda, N Jadhav, P B Kulkarni, M S Chadha
Since 2003, India has had a well-established influenza surveillance network, though Influenza C virus was not the focus of study. We therefore retrospectively analyzed clinical samples from Pune, western India collected during January 2009 to August 2015, by real-time RT-PCR. Three of 2530 samples of patients with influenza-like illness (ILI) or severe acute respiratory illness (SARI) showed positivity for Influenza C virus infection, while 105 and 31 samples were positive for Influenza A and B viruses respectively...
August 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28800764/lrp-a-global-regulator-regulates-the-virulence-of-vibrio-vulnificus
#15
Yu-Chi Ho, Feng-Ru Hung, Chao-Hui Weng, Wei-Ting Li, Tzu-Hung Chuang, Tsung-Lin Liu, Ching-Yuan Lin, Chien-Jung Lo, Chun-Liang Chen, Jen-Wei Chen, Masayuki Hashimoto, Lien-I Hor
BACKGROUND: An attenuated mutant (designated NY303) of Vibrio vulnificus, which causes serious wound infection and septicemia in humans, was isolated fortuitously from a clinical strain YJ016. This mutant was defective in cytotoxicity, migration on soft agar and virulence in the mouse. The purpose of this study was to map the mutation in this attenuated mutant and further explore how the gene thus identified is involved in virulence. METHODS: The whole genome sequence of mutant NY303 determined by next-generation sequencing was compared with that of strain YJ016 to map the mutations...
August 11, 2017: Journal of Biomedical Science
https://www.readbyqxmd.com/read/28799681/genomic-and-clinical-evidence-uncovers-the-enterohepatic-species-helicobacter-valdiviensis-as-a-potential-human-intestinal-pathogen
#16
Pablo Fresia, Ronald Jara, Rafael Sierra, Ignacio Ferrés, Gonzalo Greif, Gregorio Iraola, Luis Collado
BACKGROUND: Helicobacter valdiviensis is a recently described enterohepatic species isolated from wild bird's fecal samples. Currently, its pathogenic potential and clinical significance are unknown mainly due to the lack of whole-genome sequences to compare with other helicobacters and the absence of specific screenings to determine its prevalence in humans. MATERIALS AND METHODS: The species type strain (WBE14(T) ) was whole-genome-sequenced, and comparative analyses were carried out including the genomes from other Helicobacter species to determine the exact phylogenetic position of H...
August 11, 2017: Helicobacter
https://www.readbyqxmd.com/read/28799012/mtdna-genomes-reveal-a-relaxation-of-selective-constraints-in-low-bmi-individuals-in-a-uyghur-population
#17
Hong-Xiang Zheng, Lei Li, Xiao-Yan Jiang, Shi Yan, Zhendong Qin, Xiaofeng Wang, Li Jin
Considerable attention has been focused on the effect of deleterious mutations caused by the recent relaxation of selective constraints on human health, including the prevalence of obesity, which might represent an adaptive response of energy-conserving metabolism under the conditions of modern society. Mitochondrial DNA (mtDNA) encoding 13 core subunits of oxidative phosphorylation plays an important role in metabolism. Therefore, we hypothesized that a relaxation of selection constraints on mtDNA and an increase in the proportion of deleterious mutations have played a role in obesity prevalence...
August 10, 2017: Human Genetics
https://www.readbyqxmd.com/read/28798179/whole-genome-sequences-of-two-carbapenem-resistant-klebsiella-quasipneumoniae-strains-isolated-from-a-tertiary-hospital-in-johor-malaysia
#18
Han Ming Gan, Ganeswrie Rajasekaram, Wilhelm Wei Han Eng, Priyatharisni Kaniappan, Amreeta Dhanoa
We report the whole-genome sequences of two carbapenem-resistant clinical isolates of Klebsiella quasipneumoniae subsp. similipneumoniae obtained from two different patients. Both strains contained three different extended-spectrum β-lactamase genes and showed strikingly high pairwise average nucleotide identity of 99.99% despite being isolated 3 years apart from the same hospital.
August 10, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28797094/whole-gene-sequencing-identifies-deep-intronic-variants-with-potential-functional-impact-in-patients-with-hypertrophic-cardiomyopathy
#19
Rita Mendes de Almeida, Joana Tavares, Sandra Martins, Teresa Carvalho, Francisco J Enguita, Dulce Brito, Maria Carmo-Fonseca, Luís Rocha Lopes
BACKGROUND: High throughput sequencing technologies have revolutionized the identification of mutations responsible for genetic diseases such as hypertrophic cardiomyopathy (HCM). However, approximately 50% of individuals with a clinical diagnosis of HCM have no causal mutation identified. This may be due to the presence of pathogenic mutations located deep within the introns, which are not detected by conventional sequencing analysis restricted to exons and exon-intron boundaries. OBJECTIVE: The aim of this study was to develop a whole-gene sequencing strategy to prioritize deep intronic variants that may play a role in HCM pathogenesis...
2017: PloS One
https://www.readbyqxmd.com/read/28797043/next-generation-sequencing-reveals-the-antibiotic-resistant-variants-in-the-genome-of-pseudomonas-aeruginosa
#20
Babu Ramanathan, Hassan Mahmood Jindal, Cheng Foh Le, Ranganath Gudimella, Arif Anwar, Rozaimi Razali, Johan Poole-Johnson, Rishya Manikam, Shamala Devi Sekaran
Rapid progress in next generation sequencing and allied computational tools have aided in identification of single nucleotide variants in genomes of several organisms. In the present study, we have investigated single nucleotide polymorphism (SNP) in ten multi-antibiotic resistant Pseudomonas aeruginosa clinical isolates. All the draft genomes were submitted to Rapid Annotations using Subsystems Technology (RAST) web server and the predicted protein sequences were used for comparison. Non-synonymous single nucleotide polymorphism (nsSNP) found in the clinical isolates compared to the reference genome (PAO1), and the comparison of nsSNPs between antibiotic resistant and susceptible clinical isolates revealed insights into the genome variation...
2017: PloS One
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