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https://www.readbyqxmd.com/read/29774841/novel-focus-of-sin-nombre-virus-in-peromyscus-eremicus-mice-death-valley-national-park-california-usa
#1
Joseph E Burns, Marco E Metzger, Sharon Messenger, Curtis L Fritz, Inger-Marie E Vilcins, Barryett Enge, Lawrence R Bronson, Vicki L Kramer, Renjie Hu
The deer mouse (Peromyscus maniculatus) is the primary reservoir for Sin Nombre virus (SNV) in the western United States. Rodent surveillance for hantavirus in Death Valley National Park, California, USA, revealed cactus mice (P. eremicus) as a possible focal reservoir for SNV in this location. We identified SNV antibodies in 40% of cactus mice sampled.
June 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29767709/double-hits-in-schizophrenia
#2
Jacob A S Vorstman, Loes M Olde Loohuis, René S Kahn, Roel A Ophoff
The co-occurrence of a Copy Number Variant (CNV) and a functional variant on the other allele may be a relevant genetic mechanism in schizophrenia. We hypothesized that the cumulative burden of such double hits - in particular those composed of a deletion and a coding single nucleotide variation (SNV) - is increased in patients with schizophrenia.We combined CNV data with coding variants data in 795 patients with schizophrenia and 474 controls. To limit false CNV-detection, only CNVs called only by two algorithms we included...
May 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29756748/%C3%AE-opioid-receptor-genetic-polymorphisms-and-duration-of-epidural-fentanyl-analgesia-during-early-labor
#3
Nathalie K Zgheib, Marie T Aouad, Samar K Taha, Anwar H Nassar, Riwa F Masri, Mira Y Khoury, Maha H Makki, Sahar M Siddik-Sayyid
BACKGROUND: Epidural fentanyl is commonly used for initiation of early labor analgesia. The aim of this prospective study is to test the hypothesis that duration of epidural fentanyl analgesia differs in nulliparous women requesting epidural analgesia in early labor who are variant allele carriers of the OPRM1 SNVs 118A>G rs1799971, IVS2+31G>A rs9479757, and IVS2+691G>C rs2075572. METHODS: Two hundred and twenty parturients who received epidural analgesia with fentanyl were included in the 118A>G analysis, and a 196 subcohort was included in the IVS2+31G>A and IVS2+691G>C exploratory analysis...
May 14, 2018: Minerva Anestesiologica
https://www.readbyqxmd.com/read/29748622/genomic-features-of-renal-cell-carcinoma-with-venous-tumor-thrombus
#4
Gregor Warsow, Daniel Hübschmann, Kortine Kleinheinz, Cathleen Nientiedt, Martina Heller, Laura Van Coile, Yanis Tolstov, Lukas Trennheuser, Kathrin Wieczorek, Carine Pecqueux, Claudia Gasch, Timur Kuru, Joanne Nyarangi-Dix, Gencay Hatiboglu, Dogu Teber, Sven Perner, Albrecht Stenzinger, Wilfried Roth, Boris Hadaschik, Sascha Pahernik, Dirk Jäger, Carsten Grüllich, Anette Duensing, Roland Eils, Matthias Schlesner, Holger Sültmann, Markus Hohenfellner, Stefan Duensing
A venous tumor thrombus (VTT) is a potentially lethal complication of renal cell carcinoma (RCC) but virtually nothing is known about the underlying natural history. Based on our observation that venous thrombi contain significant numbers of viable tumor cells, we applied multiregion whole exome sequencing to a total of 37 primary tumor and VTT samples including normal tissue specimens from five consecutive patients. Our findings demonstrate mutational heterogeneity between primary tumor and VTT with 106 of 483 genes (22%) harboring functional SNVs and/or indels altered in either primary tumor or thrombus...
May 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29743119/profiling-microbial-strains-in-urban-environments-using-metagenomic-sequencing-data
#5
Moreno Zolfo, Francesco Asnicar, Paolo Manghi, Edoardo Pasolli, Adrian Tett, Nicola Segata
BACKGROUND: The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially important for human health, but have received less attention than those of other environments. Ongoing efforts started to target urban microbiomes at a large scale, but the most recent computational methods to profile these metagenomes have never been applied in this context...
May 9, 2018: Biology Direct
https://www.readbyqxmd.com/read/29730524/mortality-in-systemic-necrotizing-vasculitides-a-retrospective-analysis-of-the-french-vasculitis-study-group-registry
#6
REVIEW
Sabine Jardel, Xavier Puéchal, Alain Le Quellec, Christian Pagnoux, Mohamed Hamidou, François Maurier, Olivier Aumaitre, Achille Aouba, Thomas Quemeneur, Jean-François Subra, Vincent Cottin, Jean Sibilia, Pascal Godmer, Patrice Cacoub, Anne Laure Fauchais, Eric Hachulla, Delphine Maucort-Boulch, Loïc Guillevin, Jean-Christophe Lega
OBJECTIVE: The aim of the study was to describe the evolution of mortality and cause-specific mortality over time in patients with systemic necrotizing vasculitides (SNV), including polyarteritis nodosa (PAN), granulomatosis with polyangiitis (GPA), microscopic polyangiitis (MPA), and eosinophilic granulomatosis with polyangiitis (EGPA). METHODS: Patients with SNV from the French Vasculitis Study Group registry were divided into 5 groups according to the date of diagnosis: <1980, 1980-1989, 1990-1999, 2000-2010, and ≥ 2010...
May 3, 2018: Autoimmunity Reviews
https://www.readbyqxmd.com/read/29726922/macaron-a-python-framework-to-identify-and-re-annotate-multi-base-affected-codons-in-whole-genome-exome-sequence-data
#7
Waqasuddin Khan, Ganapathi Varma- Saripella, Thomas Ludwig, Tania Cuppens, Florian Thibord, Emmanuelle Génin, Jean-Francois Deleuze, David-Alexandre Trégouët
Summary: Predicted deleteriousness of coding variants is a frequently used criterion to filter out variants detected in next-generation sequencing projects and to select candidates impacting on the risk of human diseases. Most available dedicated tools implement a base-to-base annotation approach that could be biased in presence of several variants in the same genetic codon. We here proposed the MACARON program that, from a standard VCF file, identifies, re-annotates and predicts the amino acid change resulting from multiple single nucleotide variants (SNVs) within the same genetic codon...
May 3, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29706646/comprehensive-genomic-analysis-of-patients-with-disorders-of-cerebral-cortical-development
#8
Wojciech Wiszniewski, Pawel Gawlinski, Tomasz Gambin, Monika Bekiesinska-Figatowska, Ewa Obersztyn, Dorota Antczak-Marach, Zeynep Hande Coban Akdemir, Tamar Harel, Ender Karaca, Marta Jurek, Katarzyna Sobecka, Beata Nowakowska, Malgorzata Kruk, Iwona Terczynska, Alicja Goszczanska-Ciuchta, Mariola Rudzka-Dybala, Ewa Jamroz, Antoni Pyrkosz, Anna Jakubiuk-Tomaszuk, Piotr Iwanowski, Dorota Gieruszczak-Bialek, Malgorzata Piotrowicz, Maria Sasiadek, Iwona Kochanowska, Barbara Gurda, Barbara Steinborn, Mateusz Dawidziuk, Jennifer Castaneda, Pawel Wlasienko, Natalia Bezniakow, Shalini N Jhangiani, Dorota Hoffman-Zacharska, Jerzy Bal, Elzbieta Szczepanik, Eric Boerwinkle, Richard A Gibbs, James R Lupski
Malformations of cortical development (MCDs) manifest with structural brain anomalies that lead to neurologic sequelae, including epilepsy, cerebral palsy, developmental delay, and intellectual disability. To investigate the underlying genetic architecture of patients with disorders of cerebral cortical development, a cohort of 54 patients demonstrating neuroradiologic signs of MCDs was investigated. Individual genomes were interrogated for single-nucleotide variants (SNV) and copy number variants (CNV) with whole-exome sequencing and chromosomal microarray studies...
April 30, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29703152/analysis-of-theileria-orientalis-draft-genome-sequences-reveals-potential-species-level-divergence-of-the-ikeda-chitose-and-buffeli-genotypes
#9
Daniel R Bogema, Melinda L Micallef, Michael Liu, Matthew P Padula, Steven P Djordjevic, Aaron E Darling, Cheryl Jenkins
BACKGROUND: Theileria orientalis (Apicomplexa: Piroplasmida) has caused clinical disease in cattle of Eastern Asia for many years and its recent rapid spread throughout Australian and New Zealand herds has caused substantial economic losses to production through cattle deaths, late term abortion and morbidity. Disease outbreaks have been linked to the detection of a pathogenic genotype of T. orientalis, genotype Ikeda, which is also responsible for disease outbreaks in Asia. Here, we sequenced and compared the draft genomes of one pathogenic (Ikeda) and two apathogenic (Chitose, Buffeli) isolates of T...
April 27, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29687626/dissemination-of-clostridium-difficile-spores-between-environment-and-households-dog-paws-and-shoes
#10
Sandra Janezic, Sabina Mlakar, Maja Rupnik
Clostridium difficile is an anaerobic, spore-forming bacterium that causes intestinal infections. Although C. difficile is still predominantly considered as a nosocomial pathogen, there has been an increase in the number of community-associated infections. Since C. difficile is ubiquitous and can be isolated from nearly any environment, one of the possibilities for community acquisition could be exposure to spores in the domestic environment. The aim of this study was to evaluate the presence of C. difficile spores on shoes, slippers and on dog paws and to explore the importance of these surfaces as vectors for the dissemination of C...
April 23, 2018: Zoonoses and Public Health
https://www.readbyqxmd.com/read/29676123/-data-fusion-and-multi-components-quantitative-analysis-for-identification-and-quality-evaluation-of-gentiana-rigescens-from-different-geographical-origins
#11
Qin-Qin Wang, Tao Shen, Zhi-Tian Zuo, Heng-Yu Huang, Yuan-Zhong Wang
The accumulation of secondary metabolites of traditional Chinese medicine (TCM) is closely related to its origins. The identification of origins and multi-components quantitative evaluation are of great significance to ensure the quality of medicinal materials. In this study, the identification of Gentiana rigescens from different geographical origins was conducted by data fusion of Fourier transform infrared (FTIR) spectroscopy and high performance liquid chromatography (HPLC) in combination of partial least squares discriminant analysis; meanwhile quantitative analysis of index components was conducted to provide an accurate and comprehensive identification and quality evaluation strategy for selecting the best production areas of G...
March 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29675612/complement-receptor-1-gene-cr1-intragenic-duplication-and-risk-of-alzheimer-s-disease
#12
Ezgi Kucukkilic, Keeley Brookes, Imelda Barber, Tamar Guetta-Baranes, Kevin Morgan, Edward J Hollox
Single nucleotide variants (SNVs) within and surrounding the complement receptor 1 (CR1) gene show some of the strongest genome-wide association signals with late-onset Alzheimer's disease. Some studies have suggested that this association signal is due to a duplication allele (CR1-B) of a low copy repeat (LCR) within the CR1 gene, which increases the number of complement C3b/C4b-binding sites in the mature receptor. In this study, we develop a triplex paralogue ratio test assay for CR1 LCR copy number allowing large numbers of samples to be typed with a limited amount of DNA...
April 19, 2018: Human Genetics
https://www.readbyqxmd.com/read/29669011/annotsv-an-integrated-tool-for-structural-variations-annotation
#13
Véronique Geoffroy, Yvan Herenger, Arnaud Kress, Corinne Stoetzel, Amélie Piton, Hélène Dollfus, Jean Muller
Summary: Structural Variations (SV) are a major source of variability in the human genome that shaped its actual structure during evolution. Moreover, many human diseases are caused by SV, highlighting the need to accurately detect those genomic events but also to annotate them and assist their biological interpretation. Therefore, we developed AnnotSV that compiles functionally, regulatory and clinically relevant information and aims at providing annotations useful to i) interpret SV potential pathogenicity and ii) filter out SV potential false positive...
April 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29626196/mutation-methylation-and-gene-expression-profiles-in-dup-1q-positive-pediatric-b-cell-precursor-acute-lymphoblastic-leukemia
#14
Rebeqa Gunnarsson, Sebastian Dilorenzo, Kristina B Lundin-Ström, Linda Olsson, Andrea Biloglav, Henrik Lilljebjörn, Marianne Rissler, Per Wahlberg, Anders Lundmark, Anders Castor, Mikael Behrendtz, Thoas Fioretos, Kajsa Paulsson, Anders Isaksson, Bertil Johansson
High-throughput sequencing was applied to investigate the mutation/methylation patterns on 1q and gene expression profiles in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL) with/without (w/wo) dup(1q). Sequencing of the breakpoint regions and all exons on 1q in seven dup(1q)-positive cases revealed non-synonymous somatic single nucleotide variants (SNVs) in BLZF1, FMN2, KCNT2, LCE1C, NES, and PARP1. Deep sequencing of these in a validation cohort w (n = 17)/wo (n = 94) dup(1q) revealed similar SNV frequencies in the two groups (47% vs...
March 12, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/29622186/non-targeted-detection-of-paprika-adulteration-using-mid-infrared-spectroscopy-and-one-class-classification-is-it-data-preprocessing-that-makes-the-performance
#15
Bettina Horn, Susanne Esslinger, Michael Pfister, Carsten Fauhl-Hassek, Janet Riedl
A method for the non-targeted detection of paprika adulteration was developed using Fourier transform mid-infrared (FT-MIR) spectroscopy and one-class soft independent modelling of class analogy (OCSIMCA). One-class models based on commercially available paprika powders were developed and optimised to provide >80% sensitivity by external validation. The performances of the established models for adulteration detection were tested by predicting spiked paprika samples with various types of fraudulent material and levels of adulterations including 1% (w/w) Sudan I, 1% (w/w) Sudan IV, 3% (w/w) lead chromate, 3% (w/w) lead oxide, 5% (w/w) silicon dioxide, 10% (w/w) polyvinyl chloride, and 10% (w/w) gum arabic...
August 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29621242/comparison-of-phasing-strategies-for-whole-human-genomes
#16
Yongwook Choi, Agnes P Chan, Ewen Kirkness, Amalio Telenti, Nicholas J Schork
Humans are a diploid species that inherit one set of chromosomes paternally and one homologous set of chromosomes maternally. Unfortunately, most human sequencing initiatives ignore this fact in that they do not directly delineate the nucleotide content of the maternal and paternal copies of the 23 chromosomes individuals possess (i.e., they do not 'phase' the genome) often because of the costs and complexities of doing so. We compared 11 different widely-used approaches to phasing human genomes using the publicly available 'Genome-In-A-Bottle' (GIAB) phased version of the NA12878 genome as a gold standard...
April 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29618732/kovariome-korean-national-standard-reference-variome-database-of-whole-genomes-with-comprehensive-snv-indel-cnv-and-sv-analyses
#17
Jungeun Kim, Jessica A Weber, Sungwoong Jho, Jinho Jang, JeHoon Jun, Yun Sung Cho, Hak-Min Kim, Hyunho Kim, Yumi Kim, OkSung Chung, Chang Geun Kim, HyeJin Lee, Byung Chul Kim, Kyudong Han, InSong Koh, Kyun Shik Chae, Semin Lee, Jeremy S Edwards, Jong Bhak
High-coverage whole-genome sequencing data of a single ethnicity can provide a useful catalogue of population-specific genetic variations, and provides a critical resource that can be used to more accurately identify pathogenic genetic variants. We report a comprehensive analysis of the Korean population, and present the Korean National Standard Reference Variome (KoVariome). As a part of the Korean Personal Genome Project (KPGP), we constructed the KoVariome database using 5.5 terabases of whole genome sequence data from 50 healthy Korean individuals in order to characterize the benign ethnicity-relevant genetic variation present in the Korean population...
April 4, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29616087/identification-of-potential-key-genes-and-high-frequency-mutant-genes-in-prostate-cancer-by-using-rna-seq-data
#18
Ze Zhang, He Wu, Hong Zhou, Yunhe Gu, Yufeng Bai, Shiliang Yu, Ruihua An, Jiping Qi
The aim of the present study was to identify potential key genes and single nucleotide variations (SNVs) in prostate cancer. RNA sequencing (RNA-seq) data, GSE22260, were downloaded from the Gene Expression Omnibus database, including 4 prostate cancer samples and 4 normal tissues samples. RNA-Seq reads were processed using Tophat and differentially-expressed genes (DEGs) were identified using the Cufflinks package. Gene Ontology enrichment analysis of DEGs was performed. Subsequently, Seqpos was used to identify the potential upstream regulatory elements of DEGs...
April 2018: Oncology Letters
https://www.readbyqxmd.com/read/29608398/a-high-throughput-flow-cytometry-screen-identifies-molecules-that-inhibit-hantavirus-cell-entry
#19
Tione Buranda, Catherine Gineste, Yang Wu, Virginie Bondu, Dominique Perez, Kaylin R Lake, Bruce S Edwards, Larry A Sklar
Hantaviruses cause hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS), which infects more than 200,000 people worldwide. Sin Nombre virus (SNV) and Andes virus (ANDV) cause the most severe form of HCPS, with case fatality ratios of 30%-40%. There are no specific therapies or vaccines for SNV. Using high-throughput flow cytometry, we screened the Prestwick Chemical Library for small-molecule inhibitors of the binding interaction between UV-inactivated and fluorescently labeled SNVR18 particles, and decay-accelerating factor (DAF) expressed on Tanoue B cells...
April 1, 2018: SLAS Discovery
https://www.readbyqxmd.com/read/29600428/cbl-mutation-and-mefv-single-nucleotide-variant-are-important-genetic-predictors-of-tumor-reduction-in-glucocorticoid-treated-patients-with-chronic-myelomonocytic-leukemia
#20
Junichi Watanabe, Ken Sato, Yukiko Osawa, Toshikatsu Horiuchi, Shoichiro Kato, Reina Hikota-Saga, Takaaki Maekawa, Takeshi Yamamura, Ayako Kobayashi, Shinichi Kobayashi, Fumihiko Kimura
Glucocorticoid (GC) therapy occasionally relieves tumor-related fever and promotes tumor reduction in patients with chronic myelomonocytic leukemia (CMML). A mutation analysis of 24 patients with CMML revealed the relationship of GC effectiveness, defined as a monocyte reduction of > 50% within 3 days of methylprednisolone administration, with the MEFV single-nucleotide variant (SNV) and CBL mutation. Lipopolysaccharide-stimulated monocytes harboring MEFV E148Q produced greater amounts of IL-1β and TNF-α than did wild-type monocytes; this was effectively suppressed by GC...
March 29, 2018: International Journal of Hematology
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