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https://www.readbyqxmd.com/read/29342270/whole-genome-analysis-reveals-the-evolution-and-transmission-of-an-mdr-dh-nap11-106-clostridium-difficile-clone-in-a-paediatric-hospital
#1
Larry K Kociolek, Egon A Ozer, Dale N Gerding, David W Hecht, Sameer J Patel, Alan R Hauser
Background: Clostridium difficile strain DH/NAP11/106, a relatively antibiotic-susceptible strain, is now the most common cause of C. difficile infection (CDI) among adults in the USA. Objectives: To identify mechanisms underlying the evolution and transmission of an MDR DH/NAP11/106 clone. Methods: WGS (Illumina MiSeq), restriction endonuclease analysis (REA) and antibiotic susceptibility testing were performed on 134 C. difficile isolates collected from paediatric patients with CDI over a 2 year period...
January 12, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29290336/genome-wide-study-of-atrial-fibrillation-identifies-seven-risk-loci-and-highlights-biological-pathways-and-regulatory-elements-involved-in-cardiac-development
#2
Jonas B Nielsen, Lars G Fritsche, Wei Zhou, Tanya M Teslovich, Oddgeir L Holmen, Stefan Gustafsson, Maiken E Gabrielsen, Ellen M Schmidt, Robin Beaumont, Brooke N Wolford, Maoxuan Lin, Chad M Brummett, Michael H Preuss, Lena Refsgaard, Erwin P Bottinger, Sarah E Graham, Ida Surakka, Yunhan Chu, Anne Heidi Skogholt, Håvard Dalen, Alan P Boyle, Hakan Oral, Todd J Herron, Jacob Kitzman, José Jalife, Jesper H Svendsen, Morten S Olesen, Inger Njølstad, Maja-Lisa Løchen, Aris Baras, Omri Gottesman, Anthony Marcketta, Colm O'Dushlaine, Marylyn D Ritchie, Tom Wilsgaard, Ruth J F Loos, Timothy M Frayling, Michael Boehnke, Erik Ingelsson, David J Carey, Frederick E Dewey, Hyun M Kang, Gonçalo R Abecasis, Kristian Hveem, Cristen J Willer
Atrial fibrillation (AF) is a common cardiac arrhythmia and a major risk factor for stroke, heart failure, and premature death. The pathogenesis of AF remains poorly understood, which contributes to the current lack of highly effective treatments. To understand the genetic variation and biology underlying AF, we undertook a genome-wide association study (GWAS) of 6,337 AF individuals and 61,607 AF-free individuals from Norway, including replication in an additional 30,679 AF individuals and 278,895 AF-free individuals...
December 27, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29286146/immune-response-associated-gene-profiling-in-japanese-melanoma-patients-using-multi-omics-analysis
#3
Yasuto Akiyama, Yoshio Kiyohara, Shusuke Yoshikawa, Masaki Otsuka, Ryota Kondou, Chizu Nonomura, Haruo Miyata, Akira Iizuka, Tadashi Ashizawa, Keiichi Ohshima, Kenichi Urakami, Takeshi Nagashima, Masatoshi Kusuhara, Takashi Sugino, Ken Yamaguchi
Project High-tech Omics-based Patient Evaluation (HOPE), including comprehensive whole-exome sequencing (WES) and gene expression profiling (GEP) using freshly resected tumor specimens, has been in progress since its implementation in 2014. Among a total of 1,685 cancer patients, 13 melanoma patients were registered in the HOPE Project and were characterized using multi-omics analyses. Among the 13 melanoma patients, 4 were deceased, and 9 were alive. The mean overall survival (OS) and relapse‑free survival (RFS) times of the melanoma patients were 16...
December 21, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29250452/optical-coherence-tomography-angiography-of-macular-telangiectasia-type-2-with-associated-subretinal-neovascular-membrane
#4
Victor M Villegas, Jaclyn L Kovach
Optical coherence tomography angiography (OCTA) is a recently established noninvasive technology for evaluation of the retinal and choroidal vasculature. The literature regarding the findings in macular telangiectasia type 2 (MacTel2) is scarce. We report the OCTA findings associated with a subject with MacTel2 and secondary subretinal neovascularization (SNV). The commercially available Cirrus 5000 with AngioPlex (Zeiss, Jena, Germany) was used, without any subsequent image modification or processing. Subretinal neovascularization was detectable with OCTA at the level of the outer retina and choriocapillaris...
2017: Case Reports in Ophthalmological Medicine
https://www.readbyqxmd.com/read/29241584/a-schizophrenia-linked-kalrn-coding-variant-alters-neuron-morphology-protein-function-and-transcript-stability
#5
Theron A Russell, Melanie J Grubisha, Christine L Remmers, Seok Kyu Kang, Marc P Forrest, Katharine R Smith, Katherine J Kopeikina, Ruoqi Gao, Robert A Sweet, Peter Penzes
BACKGROUND: Large-scale genetic studies have revealed that rare sequence variants, including single nucleotide variants (SNVs), in glutamatergic synaptic genes are enriched in schizophrenia patients. However, the majority are too rare to show any association with disease and have not been examined functionally. One such SNV, KALRN-P2255T, displays a penetrance that greatly exceeds that of previously identified schizophrenia-associated SNVs. Therefore, we sought to characterize its effects on the function of kalirin (Kal)-9, a dual Ras-related C3 botulinum toxin substrate 1 and Ras homologue gene family, member A (RhoA) guanine nucleotide exchange factor, upregulated in human schizophrenia brain tissue...
November 7, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/29234056/identification-and-characterization-of-two-functional-variants-in-the-human-longevity-gene-foxo3
#6
Friederike Flachsbart, Janina Dose, Liljana Gentschew, Claudia Geismann, Amke Caliebe, Carolin Knecht, Marianne Nygaard, Nandini Badarinarayan, Abdou ElSharawy, Sandra May, Anne Luzius, Guillermo G Torres, Marlene Jentzsch, Michael Forster, Robert Häesler, Kathrin Pallauf, Wolfgang Lieb, Céline Derbois, Pilar Galan, Dmitriy Drichel, Alexander Arlt, Andreas Till, Ben Krause-Kyora, Gerald Rimbach, Hélène Blanché, Jean-François Deleuze, Lene Christiansen, Kaare Christensen, Michael Nothnagel, Philip Rosenstiel, Stefan Schreiber, Andre Franke, Susanne Sebens, Almut Nebel
FOXO3 is consistently annotated as a human longevity gene. However, functional variants and underlying mechanisms for the association remain unknown. Here, we perform resequencing of the FOXO3 locus and single-nucleotide variant (SNV) genotyping in three European populations. We find two FOXO3 SNVs, rs12206094 and rs4946935, to be most significantly associated with longevity and further characterize them functionally. We experimentally validate the in silico predicted allele-dependent binding of transcription factors (CTCF, SRF) to the SNVs...
December 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29233924/dna-mismatch-repair-preferentially-protects-genes-from-mutation
#7
Eric J Belfield, Zhong Jie Ding, Fiona J C Jamieson, Anne M Visscher, Shao Jian Zheng, Aziz Mithani, Nicholas P Harberd
Mutation is the source of genetic variation and fuels biological evolution. Many mutations first arise as DNA replication errors. These errors subsequently evade correction by cellular DNA repair, for example, by the well-known DNA mismatch repair (MMR) mechanism. Here, we determine the genome-wide effects of MMR on mutation. We first identify almost 9000 mutations accumulated over five generations in eight MMR-deficient mutation accumulation (MA) lines of the model plant species, Arabidopsis thaliana We then show that MMR deficiency greatly increases the frequency of both smaller-scale insertions and deletions (indels) and of single-nucleotide variant (SNV) mutations...
December 12, 2017: Genome Research
https://www.readbyqxmd.com/read/29229917/whole-genome-sequencing-and-snv-genotyping-of-nebbiolo-vitis-vinifera-l-clones
#8
Giorgio Gambino, Alessandra Dal Molin, Paolo Boccacci, Andrea Minio, Walter Chitarra, Carla Giuseppina Avanzato, Paola Tononi, Irene Perrone, Stefano Raimondi, Anna Schneider, Mario Pezzotti, Franco Mannini, Ivana Gribaudo, Massimo Delledonne
'Nebbiolo' (Vitis vinifera) is among the most ancient and prestigious wine grape varieties characterised by a wide genetic variability exhibited by a high number of clones (vegetatively propagated lines of selected mother plants). However, limited information is available for this cultivar at the molecular and genomic levels. The whole-genomes of three 'Nebbiolo' clones (CVT 71, CVT 185 and CVT 423) were re-sequenced and a de novo transcriptome assembly was produced. Important remarks about the genetic peculiarities of 'Nebbiolo' and its intra-varietal variability useful for clonal identification were reported...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29219260/-gene-analysis-for-the-sudden-death-of-hypertrophic-cardiomyopathy-by-whole-exome-sequencing
#9
C C Xu, Y Z Bai, X S Xu, G L Lü, X P Lai, R Chen, H G Lin, W J Kuang
OBJECTIVES: To analyze the related pathogenicity gene mutations in a sudden death of hypertrophic cardiomyopathy (HCM) on whole exome level. METHODS: Whole exome sequencing (WES) was been performed on a sudden death case sample with pathological features of HCM by Illumina® Hiseq 2500 platform. Using hg19 as the reference sequences, the sequencing data were analyzed. Suspicious single nucleotide variants (SNV) were screened, and the conservatism and function were analyzed by the software such as PhyloP, PolyPhen-2, SIFT, etc...
August 2017: Fa Yi Xue za Zhi
https://www.readbyqxmd.com/read/29217820/longitudinal-exome-wide-association-study-to-identify-genetic-susceptibility-loci-for-hypertension-in-a-japanese-population
#10
Yoshiki Yasukochi, Jun Sakuma, Ichiro Takeuchi, Kimihiko Kato, Mitsutoshi Oguri, Tetsuo Fujimaki, Hideki Horibe, Yoshiji Yamada
Genome-wide association studies have identified various genetic variants associated with complex disorders. However, these studies have commonly been conducted in a cross-sectional manner. Therefore, we performed a longitudinal exome-wide association study (EWAS) in a Japanese cohort. We aimed to identify genetic variants that confer susceptibility to hypertension using ~244 000 single-nucleotide variants (SNVs) and physiological data from 6026 Japanese individuals who underwent annual health check-ups for several years...
December 8, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29217587/different-mutational-rates-and-mechanisms-in-human-cells-at-pregastrulation-and-neurogenesis
#11
Taejeong Bae, Livia Tomasini, Jessica Mariani, Bo Zhou, Tanmoy Roychowdhury, Daniel Franjic, Mihovil Pletikos, Reenal Pattni, Bo-Juen Chen, Elisa Venturini, Bridget Riley-Gillis, Nenad Sestan, Alexander E Urban, Alexej Abyzov, Flora M Vaccarino
Somatic mosaicism in the human brain may alter function of individual neurons. We analyzed genomes of single cells from the forebrains of three human fetuses (15 to 21 weeks post-conception) using clonal cell populations. We detected 200-400 single nucleotide variations (SNVs) per cell. SNV patterns resembled those found in cancer cell genomes, indicating a role of background mutagenesis in cancer. SNVs with a frequency of >2% in brain were shared with the spleen, revealing a pregastrulation origin. We reconstructed cell lineages for the first five post-zygotic cleavages and calculated a mutation rate of ~1...
December 7, 2017: Science
https://www.readbyqxmd.com/read/29214199/dataset-of-near-infrared-spectroscopy-measurement-for-amylose-determination-using-pls-algorithms
#12
P Sampaio, A Soares, A Castanho, A S Almeida, J Oliveira, C Brites
In the dataset presented in this article, 168 rice samples comprising sixteen rice varieties (including Indica and Japonica sub species) from a Portuguese Rice Breeding Program obtained from three different sites along four seasons, and 11 standard rice varieties from International Rice Research Institute were characterised. The amylose concentration was evaluated based on iodine method, and the near infrared (NIR) spectra were determined. To assess the advantage of Near infrared spectroscopy, different rice varieties and specific algorithms based on Matlab software such as Standard Normal Variate (SNV), Multiple Scatter Calibration (MSC) and Savitzky-Golay filter were used for NIR spectra pre-processing...
December 2017: Data in Brief
https://www.readbyqxmd.com/read/29212019/pervasive-within-mitochondrion-single-nucleotide-variant-heteroplasmy-as-revealed-by-single-mitochondrion-sequencing
#13
Jacqueline Morris, Young-Ji Na, Hua Zhu, Jae-Hee Lee, Hoa Giang, Alexandra V Ulyanova, Gordon H Baltuch, Steven Brem, H Isaac Chen, David K Kung, Timothy H Lucas, Donald M O'Rourke, John A Wolf, M Sean Grady, Jai-Yoon Sul, Junhyong Kim, James Eberwine
A number of mitochondrial diseases arise from single-nucleotide variant (SNV) accumulation in multiple mitochondria. Here, we present a method for identification of variants present at the single-mitochondrion level in individual mouse and human neuronal cells, allowing for extremely high-resolution study of mitochondrial mutation dynamics. We identified extensive heteroplasmy between individual mitochondrion, along with three high-confidence variants in mouse and one in human that were present in multiple mitochondria across cells...
December 5, 2017: Cell Reports
https://www.readbyqxmd.com/read/29192454/-rapid-prediction-of-the-content-of-polyphyllin-in-various-species-of-paris-by-infrared-spectrometry
#14
Zhe Wu, Ji Zhang, Jin-Yu Zhang, Fu-Rong Xu, Yuan-Zhong Wang
Polyphyllin is the main active constituent in Paris which was a traditional Chinese medicine. In order to evaluate the quality of Paris rapidly and ensure the efficacy in clinical therapy, we quantified the contents of polyphyllin Ⅰ, polyphyllin Ⅱ and polyphyllin Ⅶ using infrared spectroscopy with partial least squares regression(PLSR). The method for evaluating the quality of Paris was established. Infrared spectra of 78 samples from various species in different origins were collected. The contents of polyphyllin Ⅰ, Ⅱ and Ⅶ were determined by high performance liquid chromatography(HPLC)...
September 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29185836/exome-chip-meta-analysis-identifies-association-between-variation-in-ankrd26-and-platelet-aggregation
#15
Ming-Huei Chen, Lisa R Yanek, Joshua D Backman, John D Eicher, Jennifer E Huffman, Yoav Ben-Shlomo, Andrew D Beswick, Laura M Yerges-Armstrong, Alan R Shuldiner, Jeffrey R O'Connell, Rasika A Mathias, Diane M Becker, Lewis C Becker, Joshua P Lewis, Andrew D Johnson, Nauder Faraday
Previous genome-wide association studies (GWAS) have identified several variants associated with platelet function phenotypes; however, the proportion of variance explained by the identified variants is mostly small. Rare coding variants, particularly those with high potential for impact on protein structure/function, may have substantial impact on phenotype but are difficult to detect by GWAS. The main purpose of this study was to identify low frequency or rare variants associated with platelet function using genotype data from the Illumina HumanExome Bead Chip...
November 29, 2017: Platelets
https://www.readbyqxmd.com/read/29181591/post-zygotic-genomic-changes-in-glutamate-and-dopamine-pathway-genes-may-explain-discordance-of-monozygotic-twins-for-schizophrenia
#16
C A Castellani, M G Melka, J L Gui, A J Gallo, R L O'Reilly, S M Singh
BACKGROUND: Monozygotic twins are valuable in assessing the genetic vs environmental contribution to diseases. In the era of complete genome sequences, they allow identification of mutational mechanisms and specific genes and pathways that offer predisposition to the development of complex diseases including schizophrenia. METHODS: We sequenced the complete genomes of two pairs of monozygotic twins discordant for schizophrenia (MZD), including one representing a family tetrad...
November 28, 2017: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/29178823/genetic-relatedness-of-vibrio-cholerae-isolates-within-and-between-households-during-outbreaks-in-dhaka-bangladesh
#17
Christine Marie George, Mahamud Rashid, Mathieu Almeida, K M Saif-Ur-Rahman, Shirajum Monira, Md Sazzadul Islam Bhuyian, Khaled Hasan, Toslim T Mahmud, Shan Li, Jessica Brubaker, Jamie Perin, Zillur Rahman, Munshi Mustafiz, David A Sack, R Bradley Sack, Munirul Alam, O Colin Stine
BACKGROUND: Household contacts of cholera patients have a 100 times higher risk of developing a cholera infection than the general population. To compare the genetic relatedness of clinical and water source Vibrio cholerae isolates from cholera patients' households across three outbreaks, we analyzed these isolates using whole-genome-sequencing (WGS) and multilocus variable-number tandem-repeat analysis (MLVA). RESULTS: The WGS analyses revealed that 80% of households had source water isolates that were more closely related to clinical isolates from the same household than to any other isolates...
November 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29162237/inter-individual-gene-variants-associated-with-trabecular-bone-plasticity-a-step-forward-in-the-personal-genomics-of-degenerative-bone-disease
#18
Enrique Caso, Cristina C Sabiers, Daniel López-Guillén, Jaime Caso, Manuel Toledano, Raquel Osorio, Estrella Osorio, Carmen Lozano, Enrique Guerado
Continuing tissue destruction in osteoarthrosis is maintained by molecular pathways related to an unbalanced chondrocyte metabolism, the loss of reactive oxygen species (ROS) homeostasis, increase catabolism in a degraded matrix and the limited response to growth factors due to cell aging. Rare deleterious gene variants driving relevant molecular pathways may play a key role in the pathogenesis and genetic control of common diseases and may also influence the common gene variants observed in GWAS. We use molecular profiling technologies based on massive sequencing of genes to interrogate clinical samples for a variety of molecules involved in the pathogenesis pathways of OA and also to derive new insights for drug targeting discovery at an early stage of the disease...
November 2017: Injury
https://www.readbyqxmd.com/read/29156912/genetic-biomarkers-associated-with-pain-flare-and-dexamethasone-response-following-palliative-radiotherapy-in-patients-with-painful-bone-metastases
#19
Anthony Furfari, Bo Angela Wan, Keyue Ding, Andrew Wong, Liting Zhu, Andrea Bezjak, Rebecca Wong, Carolyn F Wilson, Carlo DeAngelis, Azar Azad, Edward Chow, George S Charames
BACKGROUND: In patients who receive palliative radiation therapy (RT) for painful bone metastases, 40% experience a transient increase in pain known as a pain flare. Prophylactic dexamethasone has been shown to reduce pain flare incidence to 25%. We aimed to identify DNA biomarkers associated with pain flare and dexamethasone response. METHODS: Daily pain levels were recorded by 81 patients who received a single 8 Gy RT for painful bone metastases, of which 50 also received prophylactic dexamethasone...
September 20, 2017: Annals of Palliative Medicine
https://www.readbyqxmd.com/read/29156910/genetic-biomarkers-associated-with-changes-in-quality-of-life-and-pain-following-palliative-radiotherapy-in-patients-with-bone-metastases
#20
Anthony Furfari, Bo Angela Wan, Keyue Ding, Andrew Wong, Liting Zhu, Andrea Bezjak, Rebecca Wong, Carolyn F Wilson, Carlo DeAngelis, Azar Azad, Edward Chow, George S Charames
BACKGROUND: Patients with bone metastases undergoing palliative radiation therapy (RT) may experience changes in both the functional and symptomatic aspects of quality of life (QOL). The European Organization of Cancer Research and Treatment (EORTC) QOL Questionnaire Core-15 Palliative (QLQ-C15-PAL) is a validated questionnaire employed to assess QOL specifically in palliative patients. Our study aimed to identify single-nucleotide variant (SNV) genetic biomarkers associated with changes in QOL and pain...
September 28, 2017: Annals of Palliative Medicine
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