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https://www.readbyqxmd.com/read/29138229/genomic-structural-variations-lead-to-dysregulation-of-important-coding-and-non-coding-rna-species-in-dilated-cardiomyopathy
#1
Jan Haas, Stefan Mester, Alan Lai, Karen S Frese, Farbod Sedaghat-Hamedani, Elham Kayvanpour, Tobias Rausch, Rouven Nietsch, Jes-Niels Boeckel, Avisha Carstensen, Mirko Völkers, Carsten Dietrich, Dietmar Pils, Ali Amr, Daniel B Holzer, Diana Martins Bordalo, Daniel Oehler, Tanja Weis, Derliz Mereles, Sebastian Buss, Eva Riechert, Emil Wirsz, Maximilian Wuerstle, Jan O Korbel, Andreas Keller, Hugo A Katus, Andreas E Posch, Benjamin Meder
The transcriptome needs to be tightly regulated by mechanisms that include transcription factors, enhancers, and repressors as well as non-coding RNAs. Besides this dynamic regulation, a large part of phenotypic variability of eukaryotes is expressed through changes in gene transcription caused by genetic variation. In this study, we evaluate genome-wide structural genomic variants (SVs) and their association with gene expression in the human heart. We detected 3,898 individual SVs affecting all classes of gene transcripts (e...
November 14, 2017: EMBO Molecular Medicine
https://www.readbyqxmd.com/read/29126011/multi-parameters-monitoring-during-traditional-chinese-medicine-concentration-process-with-near-infrared-spectroscopy-and-chemometrics
#2
Ronghua Liu, Qiaofeng Sun, Tian Hu, Lian Li, Lei Nie, Jiayue Wang, Wanhui Zhou, Hengchang Zang
As a powerful process analytical technology (PAT) tool, near infrared (NIR) spectroscopy has been widely used in real-time monitoring. In this study, NIR spectroscopy was applied to monitor multi-parameters of traditional Chinese medicine (TCM) Shenzhiling oral liquid during the concentration process to guarantee the quality of products. Five lab scale batches were employed to construct quantitative models to determine five chemical ingredients and physical change (samples density) during concentration process...
October 28, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29093469/direct-estimation-of-de-novo-mutation-rates-in-a-chimpanzee-parent-offspring-trio-by-ultra-deep-whole-genome-sequencing
#3
Shoji Tatsumoto, Yasuhiro Go, Kentaro Fukuta, Hideki Noguchi, Takashi Hayakawa, Masaki Tomonaga, Hirohisa Hirai, Tetsuro Matsuzawa, Kiyokazu Agata, Asao Fujiyama
Mutations generate genetic variation and are a major driving force of evolution. Therefore, examining mutation rates and modes are essential for understanding the genetic basis of the physiology and evolution of organisms. Here, we aim to identify germline de novo mutations through the whole-genome surveyance of Mendelian inheritance error sites (MIEs), those not inherited through the Mendelian inheritance manner from either of the parents, using ultra-deep whole genome sequences (>150-fold) from a chimpanzee parent-offspring trio...
November 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29080873/-a-bioinformatic-pipeline-for-ngs-data-analysis-and-mutation-calling-in-human-solid-tumors
#4
K Yu Tsukanov, A Yu Krasnenko, D A Plakhina, D O Korostin, A V Churov, O S Druzhilovskaya, D V Rebrikov, V V Ilinsky
We aimed to develop a pipeline for the bioinformatic analysis and interpretation of NGS data and detection of a wide range of single-nucleotide somatic mutations within tumor DNA. Initially, the NGS reads were submitted to a quality control check by the Cutadapt program. Low-quality 3¢-nucleotides were removed. After that the reads were mapped to the reference genome hg19 (GRCh37.p13) by BWA. The SAMtools program was used for exclusion of duplicates. MuTect was used for SNV calling. The functional effect of SNVs was evaluated using the algorithm, including annotation and evaluation of SNV pathogenicity by SnpEff and analysis of such databases as COSMIC, dbNSFP, Clinvar, and OMIM...
October 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/29069899/nucleic-acid-self-assembly-circuitry-aided-by-exonuclease-iii-for-discrimination-of-single-nucleotide-variants
#5
Zhuo Zhang, I-Ming Hsing
Robust and rapid discrimination of one base mutations in nucleic acid sequences is important in clinical applications. Here, we report a hybridization-based assay exploiting nucleic acid self-assembly circuitry and enzyme exonuclease III (Exo III) for the differentiation of single nucleotide variants (SNVs). This one-step approach combines the merits of discrimination power of competitive DNA hybridization probes (probe + sink) with catalytic amplification assisted by Exo III. The phosphorothioate bonds modified on a wild-type (WT) specific sink inhibit the Exo III digestion; thus, subsequent catalytic amplification magnifies only the intended SNV targets...
November 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29061375/evaluation-of-a-next-generation-sequencing-assay-for-brca1-and-brca2-mutation-detection
#6
Gabriele Lorenzo Capone, Anna Laura Putignano, Sharon Trujillo Saavedra, Irene Paganini, Roberta Sestini, Francesca Gensini, Irene De Rienzo, Laura Papi, Berardino Porfirio
The efficiency of a novel targeted next-generation sequencing (NGS) test, the Devyser BRCA kit, for a comprehensive analysis of all 48 coding exons of the high-risk breast/ovarian cancer susceptibility genes BRCA1 and BRCA2 has been assessed. The new assay intended to detect nucleotide substitutions, small deletions/insertions, and large deletions/duplications. To document the false-negative and false-positive rates of the NGS assay in the hands of end-users, 48 samples with previously identified 444 small-size variants and seven gross rearrangements were analyzed, showing 100% concordance with gold standards...
October 20, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29060238/coupling-scatter-correction-with-bandpass-filtering-for-preprocessing-in-the-quantitative-analysis-of-glucose-from-near-infrared-spectra
#7
Osamah Abdulhameed Alrezj, Krishna Chaitanya Patchava, Mohammed Benaissa, S Alshebeili
This paper proposes a novel pre-processing method based on combining bandpass filtering with scatter correction techniques Multiplicative Scatter Correction (MSC) and Standard Normal Variate (SNV) to enhance the prediction capability of the linear regression models Partial Least Squares Regression (PLSR) and Principal Component Regression (PCR) in near infrared (NIR) spectroscopy. The method is implemented into a calibration model, evaluated and then validated for the prediction of the glucose concentration from NIR spectra of an aqueous mixture of human serum albumin and glucose in a solution of distilled water and phosphate buffer...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/29048532/lightning-fast-genome-variant-detection-with-grom
#8
Sean D Smith, Joseph K Kawash, Andrey Grigoriev
Current human whole genome sequencing projects produce massive amounts of data, often creating significant computational challenges. Different approaches have been developed for each type of genome variant and method of its detection, necessitating users to run multiple algorithms to find variants. We present Genome Rearrangement OmniMapper (GROM), a novel comprehensive variant detection algorithm accepting aligned read files as input and finding SNVs, indels, structural variants (SVs), and copy number variants (CNVs)...
October 1, 2017: GigaScience
https://www.readbyqxmd.com/read/29039810/effects-of-moisture-and-particle-size-on-quantitative-determination-of-total-organic-carbon-toc-in-soils-using-near-infrared-spectroscopy
#9
Elena Tamburini, Fabio Vincenzi, Stefania Costa, Paolo Mantovi, Paola Pedrini, Giuseppe Castaldelli
Near-Infrared Spectroscopy is a cost-effective and environmentally friendly technique that could represent an alternative to conventional soil analysis methods, including total organic carbon (TOC). Soil fertility and quality are usually measured by traditional methods that involve the use of hazardous and strong chemicals. The effects of physical soil characteristics, such as moisture content and particle size, on spectral signals could be of great interest in order to understand and optimize prediction capability and set up a robust and reliable calibration model, with the future perspective of being applied in the field...
October 17, 2017: Sensors
https://www.readbyqxmd.com/read/29034124/multi-provincial-salmonellosis-outbreak-related-to-newly-hatched-chicks-and-poults-a-genomics-perspective
#10
Matthew A Croxen, Kimberley A Macdonald, Matthew Walker, Nancy deWith, Erin Zabek, Christy Peterson, Aleisha Reimer, Linda Chui, Lorelee Tschetter, Linda Hoang, Robin K King
BACKGROUND: A multi-provincial outbreak of Salmonella enterica serovar Enteritidis was linked to newly hatched chicks and poults from a single hatchery during the spring of 2015. In total, there were 61 human cases that were epidemiologically confirmed to be linked to the chicks and poults and the outbreak was deemed to have ended in the summer of 2015. METHODS: PulseNet Canada, in coordination with the affected provinces, used genome sequencing of human and agricultural Salmonella Enteritidis isolates to aid in the epidemiological investigation, while also using traditional typing methods such as phagetyping and pulsed-field gel electrophoresis (PFGE)...
August 9, 2017: PLoS Currents
https://www.readbyqxmd.com/read/29032825/line-1-retrotransposon-mediated-dna-transductions-in-endometriosis-associated-ovarian-cancers
#11
Zhouchunyang Xia, Dawn R Cochrane, Michael S Anglesio, Yi Kan Wang, Tayyebeh Nazeran, Basile Tessier-Cloutier, Melissa K McConechy, Janine Senz, Amy Lum, Ali Bashashati, Sohrab P Shah, David G Huntsman
OBJECTIVE: Endometrioid (ENOC) and clear cell ovarian carcinoma (CCOC) share a common precursor lesion, endometriosis, hence the designation endometriosis associated ovarian cancers (EAOC). Long interspersed nuclear element 1 (LINE-1 or L1), is a family of mobile genetic elements activated in many cancers capable of moving neighboring DNA through 3' transductions. Here we investigated the involvement of specific L1-mediated transductions in EAOCs. METHODS: Through whole genome sequencing, we identified active L1-mediated transductions originating within the TTC28 gene in 34% (10/29) of ENOC and 31% (11/35) of CCOC cases...
October 9, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29030403/new-blood-pressure-associated-loci-identified-in-meta-analyses-of-475%C3%A2-000-individuals
#12
Aldi T Kraja, James P Cook, Helen R Warren, Praveen Surendran, Chunyu Liu, Evangelos Evangelou, Alisa K Manning, Niels Grarup, Fotios Drenos, Xueling Sim, Albert Vernon Smith, Najaf Amin, Alexandra I F Blakemore, Jette Bork-Jensen, Ivan Brandslund, Aliki-Eleni Farmaki, Cristiano Fava, Teresa Ferreira, Karl-Heinz Herzig, Ayush Giri, Franco Giulianini, Megan L Grove, Xiuqing Guo, Sarah E Harris, Christian T Have, Aki S Havulinna, He Zhang, Marit E Jørgensen, AnneMari Käräjämäki, Charles Kooperberg, Allan Linneberg, Louis Little, Yongmei Liu, Lori L Bonnycastle, Yingchang Lu, Reedik Mägi, Anubha Mahajan, Giovanni Malerba, Riccardo E Marioni, Hao Mei, Cristina Menni, Alanna C Morrison, Sandosh Padmanabhan, Walter Palmas, Alaitz Poveda, Rainer Rauramaa, Nigel William Rayner, Muhammad Riaz, Ken Rice, Melissa A Richard, Jennifer A Smith, Lorraine Southam, Alena Stančáková, Kathleen E Stirrups, Vinicius Tragante, Tiinamaija Tuomi, Ioanna Tzoulaki, Tibor V Varga, Stefan Weiss, Andrianos M Yiorkas, Robin Young, Weihua Zhang, Michael R Barnes, Claudia P Cabrera, He Gao, Michael Boehnke, Eric Boerwinkle, John C Chambers, John M Connell, Cramer K Christensen, Rudolf A de Boer, Ian J Deary, George Dedoussis, Panos Deloukas, Anna F Dominiczak, Marcus Dörr, Roby Joehanes, Todd L Edwards, Tõnu Esko, Myriam Fornage, Nora Franceschini, Paul W Franks, Giovanni Gambaro, Leif Groop, Göran Hallmans, Torben Hansen, Caroline Hayward, Oksa Heikki, Erik Ingelsson, Jaakko Tuomilehto, Marjo-Riitta Jarvelin, Sharon L R Kardia, Fredrik Karpe, Jaspal S Kooner, Timo A Lakka, Claudia Langenberg, Lars Lind, Ruth J F Loos, Markku Laakso, Mark I McCarthy, Olle Melander, Karen L Mohlke, Andrew P Morris, Colin N A Palmer, Oluf Pedersen, Ozren Polasek, Neil R Poulter, Michael A Province, Bruce M Psaty, Paul M Ridker, Jerome I Rotter, Igor Rudan, Veikko Salomaa, Nilesh J Samani, Peter J Sever, Tea Skaaby, Jeanette M Stafford, John M Starr, Pim van der Harst, Peter van der Meer, Cornelia M van Duijn, Anne-Claire Vergnaud, Vilmundur Gudnason, Nicholas J Wareham, James G Wilson, Cristen J Willer, Daniel R Witte, Eleftheria Zeggini, Danish Saleheen, Adam S Butterworth, John Danesh, Folkert W Asselbergs, Louise V Wain, Georg B Ehret, Daniel I Chasman, Mark J Caulfield, Paul Elliott, Cecilia M Lindgren, Daniel Levy, Christopher Newton-Cheh, Patricia B Munroe, Joanna M M Howson
BACKGROUND: Genome-wide association studies have recently identified >400 loci that harbor DNA sequence variants that influence blood pressure (BP). Our earlier studies identified and validated 56 single nucleotide variants (SNVs) associated with BP from meta-analyses of exome chip genotype data. An additional 100 variants yielded suggestive evidence of association. METHODS AND RESULTS: Here, we augment the sample with 140 886 European individuals from the UK Biobank, in whom 77 of the 100 suggestive SNVs were available for association analysis with systolic BP or diastolic BP or pulse pressure...
October 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/29026651/snvphyl-a-single-nucleotide-variant-phylogenomics-pipeline-for-microbial-genomic-epidemiology
#13
Aaron Petkau, Philip Mabon, Cameron Sieffert, Natalie C Knox, Jennifer Cabral, Mariam Iskander, Mark Iskander, Kelly Weedmark, Rahat Zaheer, Lee S Katz, Celine Nadon, Aleisha Reimer, Eduardo Taboada, Robert G Beiko, William Hsiao, Fiona Brinkman, Morag Graham, Gary Van Domselaar
The recent widespread application of whole-genome sequencing (WGS) for microbial disease investigations has spurred the development of new bioinformatics tools, including a notable proliferation of phylogenomics pipelines designed for infectious disease surveillance and outbreak investigation. Transitioning the use of WGS data out of the research laboratory and into the front lines of surveillance and outbreak response requires user-friendly, reproducible and scalable pipelines that have been well validated...
June 30, 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29020110/comprehensive-benchmarking-of-snv-callers-for-highly-admixed-tumor-data
#14
Regina Bohnert, Sonia Vivas, Gunther Jansen
Precision medicine attempts to individualize cancer therapy by matching tumor-specific genetic changes with effective targeted therapies. A crucial first step in this process is the reliable identification of cancer-relevant variants, which is considerably complicated by the impurity and heterogeneity of clinical tumor samples. We compared the impact of admixture of non-cancerous cells and low somatic allele frequencies on the sensitivity and precision of 19 state-of-the-art SNV callers. We studied both whole exome and targeted gene panel data and up to 13 distinct parameter configurations for each tool...
2017: PloS One
https://www.readbyqxmd.com/read/29018311/de-novo-genome-assembly-and-single-nucleotide-variations-for-soybean-mosaic-virus-using-soybean-seed-transcriptome-data
#15
Yeonhwa Jo, Hoseong Choi, Miah Bae, Sang-Min Kim, Sun-Lim Kim, Bong Choon Lee, Won Kyong Cho, Kook-Hyung Kim
Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by de novo transcriptome assembly followed by blast search...
October 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/29017490/germline-mutation-within-col2a1-associated-with-lethal-chondrodysplasia-in-a-polled-holstein-family
#16
Sina Reinartz, Hartmut Mohwinkel, Christian Sürie, Maren Hellige, Karsten Feige, Deborah Eikelberg, Andreas Beineke, Julia Metzger, Ottmar Distl
BACKGROUND: The bulldog calf syndrome is a lethal form of the inherited congenital chondrodysplasias. Among the progeny of the polled Holstein bull Energy P cases of lethal chondrodysplasia were observed. Pedigrees of the cases and the frequency of 3/8 cases among the offspring of Energy P at our teaching and experimental farm Ruthe (LuFG Ruthe) supported the assumption of a germline mutation with a mosaic of normal and defective sperm. RESULTS: All three malformed calves were examined using necropsy, histopathology and computed tomography scanning...
October 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28990360/effects-of-genetic-variants-on-carboxylesterase-1-gene-expression-and-clopidogrel-pharmacokinetics-and-antiplatelet-effects
#17
Mikko Neuvonen, E Katriina Tarkiainen, Aleksi Tornio, Päivi Hirvensalo, Tuija Tapaninen, Maria Paile-Hyvärinen, Matti K Itkonen, Mikko T Holmberg, Vesa Kärjä, Ville T Männistö, Pertti J Neuvonen, Jussi Pihlajamäki, Janne T Backman, Mikko Niemi
Several single nucleotide variations (SNVs) affect carboxylesterase 1 (CES1) activity, but the effects of genetic variants on CES1 gene expression have not been systematically investigated. Therefore, our aim was to investigate effects of genetic variants on CES1 gene expression in two independent whole blood sample cohorts of 192 (discovery) and 88 (replication) healthy volunteers and in a liver sample cohort of 177 patients. Furthermore, we investigated possible effects of the found variants on clopidogrel pharmacokinetics (n=106) and pharmacodynamics (n=46) in healthy volunteers, who had ingested a single 300 mg or 600 mg dose of clopidogrel...
October 8, 2017: Basic & Clinical Pharmacology & Toxicology
https://www.readbyqxmd.com/read/28984205/the-discrepancy-among-single-nucleotide-variants-detected-by-dna-and-rna-high-throughput-sequencing-data
#18
Yan Guo, Shilin Zhao, Quanhu Sheng, David C Samuels, Yu Shyr
BACKGROUND: High throughput sequencing technology enables the both the human genome and transcriptome to be screened at the single nucleotide resolution. Tools have been developed to infer single nucleotide variants (SNVs) from both DNA and RNA sequencing data. To evaluate how much difference can be expected between DNA and RNA sequencing data, and among tissue sources, we designed a study to examine the single nucleotide difference among five sources of high throughput sequencing data generated from the same individual, including exome sequencing from blood, tumor and adjacent normal tissue, and RNAseq from tumor and adjacent normal tissue...
October 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28980147/adamts13-missense-variants-associated-with-defective-activity-and-secretion-of-adamts13-in-a-patient-with-non-cirrhotic-portal-hypertension
#19
Ashish Goel, V Raghupathy, G J Amirtharaj, Aaron Chapla, Aparna Venkatraman, Banumathi Ramakrishna, Anup Ramachandran, Nihal Thomas, K A Balasubramanian, Ian Mackie, Elwyn Elias, Chundamannil E Eapen
BACKGROUND: Non-cirrhotic intrahepatic portal hypertension (NCIPH) is characterized by thrombotic microangiopathy of the portal venous system, low ADAMTS13 (a disintegrin-like and metalloproteinase with thrombospondin type 1 motifs-13), and high vWF (von Willebrand factor) levels. This study aimed to screen for ADAMTS13 mutations, focusing on the CUB domain, in these patients. METHODS: Prospectively recruited NCIPH patients and healthy volunteers underwent tests for plasma vWF-ADAMTS13 balance...
October 5, 2017: Indian Journal of Gastroenterology: Official Journal of the Indian Society of Gastroenterology
https://www.readbyqxmd.com/read/28977767/evaluating-the-impacts-of-coinfection-on-immune-system-function-of-the-deer-mouse-peromyscus-maniculatus-using-sin-nombre-virus-and-bartonella-as-model-pathogen-systems
#20
Erin M Lehmer, Kathryn Lavengood, Mason Miller, Jacob Rodgers, Steven D Fenster
Simultaneous infections with multiple pathogens can alter the function of the host's immune system, often resulting in additive or synergistic morbidity. We examined how coinfection with the common pathogens Sin Nombre virus (SNV) and Bartonella sp. affected aspects of the adaptive and innate immune responses of wild deer mice (Peromyscus maniculatus). Adaptive immunity was assessed by measuring SNV antibody production; innate immunity was determined by measuring levels of C-reactive protein (CRP) in blood and the complement activity of plasma...
October 4, 2017: Journal of Wildlife Diseases
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