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https://www.readbyqxmd.com/read/28440220/rapid-evolution-of-the-human-mutation-spectrum
#1
Kelley Harris, Jonathan K Pritchard
DNA is a remarkably precise medium for copying and storing biological information. This high fidelity results from the action of hundreds of genes involved in replication, proofreading, and damage repair. Evolutionary theory suggests that in such a system, selection has limited ability to remove genetic variants that change mutation rates by small amounts or in specific sequence contexts. Consistent with this, using SNV variation as a proxy for mutational input, we report here that mutational spectra differ substantially among species, human continental groups and even some closely-related populations...
April 25, 2017: ELife
https://www.readbyqxmd.com/read/28419202/genomic-characterization-of-usa300-mrsa-to-evaluate-intraclass-transmission-and-recurrence-of-ssti-among-high-risk-military-trainees
#2
Eugene V Millar, Gregory K Rice, Emad M Elassal, Carey D Schlett, Jason W Bennett, Cassie L Redden, Deepika Mor, Natasha N Law, David R Tribble, Theron Hamilton, Michael W Ellis, Kimberly A Bishop-Lilly
Background.: Military trainees are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) skin and soft tissue infection (SSTI). Whole genome sequencing (WGS) can refine our understanding of MRSA transmission and microevolution in congregate settings. Methods.: We conducted a prospective case-control study of SSTI among US Army Infantry trainees at Fort Benning, GA from July 2012-December 2014. We identified clusters of USA300 MRSA SSTI within select training classes and performed WGS on clinical isolates...
April 17, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28408367/variability-in-chromatin-architecture-and-associated-dna-repair-at-genomic-positions-containing-somatic-mutations
#3
Byungho Lim, Jihyeob Mun, Yong Sung Kim, Seon-Young Kim
Dynamic chromatin structures result in differential chemical reactivity to mutational processes throughout the genome. To identify chromatin features responsible for mutagenesis, we compared chromatin architecture around single-nucleotide variants (SNV), insertion/deletions (indels) and their context-matched, non-mutated positions. We found epigenetic differences between genomic regions containing missense SNV and those containing frameshift indels across multiple cancer types. Levels active histone marks were higher around frameshift indels than around missense SNV, whereas repressive histone marks exhibited the reverse trend...
April 13, 2017: Cancer Research
https://www.readbyqxmd.com/read/28399151/the-recent-emergence-in-hospitals-of-multidrug-resistant-community-associated-sequence-type-1-and-spa-type-t127-methicillin-resistant-staphylococcus-aureus-investigated-by-whole-genome-sequencing-implications-for-screening
#4
Megan R Earls, Peter M Kinnevey, Gráinne I Brennan, Alexandros Lazaris, Mairead Skally, Brian O'Connell, Hilary Humphreys, Anna C Shore, David C Coleman
Community-associated spa type t127/t922 methicillin-resistant Staphylococcus aureus (MRSA) prevalence increased from 1%-7% in Ireland between 2010-2015. This study tracked the spread of 89 such isolates from June 2013-June 2016. These included 78 healthcare-associated and 11 community associated-MRSA isolates from a prolonged hospital outbreak (H1) (n = 46), 16 other hospitals (n = 28), four other healthcare facilities (n = 4) and community-associated sources (n = 11). Isolates underwent antimicrobial susceptibility testing, DNA microarray profiling and whole-genome sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28398228/quantification-of-lycopene-%C3%AE-carotene-and-total-soluble-solids-in-intact-red-flesh-watermelon-citrullus-lanatus-using-on-line-near-infrared-spectroscopy
#5
Elena Tamburini, Stefania Costa, Irene Rugiero, Paola Pedrini, Maria Gabriella Marchetti
A great interest has recently been focused on lycopene and β-carotene, because of their antioxidant action in the organism. Red-flesh watermelon is one of the main sources of lycopene as the most abundant carotenoid. The use of near-infrared spectroscopy (NIRS) in post-harvesting has permitted us to rapidly quantify lycopene, β-carotene, and total soluble solids (TSS) on single intact fruits. Watermelons, harvested in 2013-2015, were submitted to near-infrared (NIR) radiation while being transported along a conveyor belt system, stationary and in movement, and at different positions on the belt...
April 11, 2017: Sensors
https://www.readbyqxmd.com/read/28392550/comparison-of-ion-personal-genome-machine-platforms-for-the-detection-of-variants-in-brca1-and-brca2
#6
Sang Mee Hwang, Ki Chan Lee, Min Seob Lee, Kyoung Un Park
Purpose: Transition to next generation sequencing (NGS) for BRCA1/BRCA2 analysis in clinical laboratories is ongoing but different platforms and/or data analysis pipelines give different results resulting in difficulties in implementation. We have evaluated the Ion Personal Genome Machine (PGM) Platforms (Ion PGM, Ion PGM Dx, Thermo Fisher Scientific) for the analysis of BRCA1/2. Materials and Methods: The results of Ion PGM with OTG-snpcaller, a pipeline based on Torrent mapping alignment program and Genome Analysis Toolkit, from 75 clinical samples and 14 reference DNA samples were compared with Sanger sequencing for BRCA1/BRCA2...
April 7, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28388474/a-comprehensive-quality-evaluation-method-by-ft-nir-spectroscopy-and-chemometric-fine-classification-and-untargeted-authentication-against-multiple-frauds-for-chinese-ganoderma-lucidum
#7
Haiyan Fu, Qiaobo Yin, Lu Xu, Weizheng Wang, Feng Chen, Tianming Yang
The origins and authenticity against frauds are two essential aspects of food quality. In this work, a comprehensive quality evaluation method by FT-NIR spectroscopy and chemometrics were suggested to address the geographical origins and authentication of Chinese Ganoderma lucidum (GL). Classification for 25 groups of GL samples (7 common species from 15 producing areas) was performed using near-infrared spectroscopy and interval-combination One-Versus-One least squares support vector machine (IC-OVO-LS-SVM)...
April 2, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28369576/a-direct-test-of-selection-in-cell-populations-using-the-diversity-in-gene-expression-within-tumors
#8
Chunyan Li, Yali Hou, Jin Xu, Aiqun Zhang, Zhenzhen Liu, Furong Qi, Zuyu Yang, Ke Chen, Sixue Liu, Huanwei Huang, Qianfei Wang, Jiahong Dong, Chung-I Wu, Xuemei Lu
Although intra-tumor diversity driven by selection has been the prevailing view in cancer biology, recent population genetic analyses have been unable to reject the neutral interpretation. Since the power to reject neutrality in tumors is often low, it will be desirable to have an alternative means to test selection directly. Here, we utilize gene expression data as a surrogate for functional significance in intra- and inter-tumor comparisons. The expression divergence between samples known to be driven by selection (e...
March 27, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28369513/identification-and-characterization-of-aurora-kinase-b-and-c-variants-associated-with-maternal-aneuploidy
#9
Alexandra L Nguyen, Diego Marin, Anbo Zhou, Amanda S Gentilello, Evan M Smoak, Zubing Cao, Anastasia Fedick, Yujue Wang, Deanne Taylor, Richard T Scott, Jinchuan Xing, Nathan Treff, Karen Schindler
STUDY QUESTION: Are single nucleotide variants (SNVs) in Aurora kinases B and C associated with risk of aneuploid conception? SUMMARY ANSWER: Two SNVs were found in patients with extreme aneuploid concepti rates with respect to their age; one variant, AURKC p.I79V, is benign, while another, AURKB p.L39P, is a potential gain-of-function mutant with increased efficiency in promoting chromosome alignment. WHAT IS KNOWN ALREADY: Maternal age does not always predict aneuploidy risk, and rare gene variants can be drivers of disease...
March 25, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28361286/quasispecies-evolution-of-the-prototypical-genotype-1-porcine-reproductive-and-respiratory-syndrome-virus-early-during-in-vivo-infection-is-rapid-and-tissue-specific
#10
Zen H Lu, Xinglong Wang, Alison D Wilson, Daniel L W Dorey-Robinson, Alan L Archibald, Tahar Ait-Ali, Jean-Pierre Frossard
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major infectious threat to the pig industry worldwide. Increasing evidence suggests that microevolution within a quasispecies population can give rise to high sequence heterogeneity in PRRSV; potentially impacting the pathogenicity of the virus. Here, we report on micro-evolutionary events taking place within the viral quasispecies population in lung and lymph node 3 days post infection (dpi) following experimental in vivo infection with the prototypical Lelystad PRRSV (LV)...
March 30, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28358914/analysis-of-single-nucleotide-variants-of-hfe-gene-and-association-to-survival-in-the-cancer-genome-atlas-gbm-data
#11
Sang Y Lee, Junjia Zhu, Anna C Salzberg, Bo Zhang, Dajiang J Liu, Joshua E Muscat, Sara T Langan, James R Connor
Human hemochromatosis protein (HFE) is involved in iron metabolism. Two major HFE polymorphisms, H63D and C282Y, have been associated with an increased risk of cancers. Previously, we reported decreased gender effects in overall survival based on H63D or C282Y HFE polymorphisms patients with glioblastoma multiforme (GBM). However, the effect of other single nucleotide variation (SNV) in the HFE gene on the cancer development and progression has not been systematically studied. To expand our finding in a larger sample, and to identify other HFE SNV, we analyzed the frequency of somatic SNV in HFE gene and its relationship to survival in GBM patients using The Cancer Genome Atlas (TCGA) GBM (Caucasian only) database...
2017: PloS One
https://www.readbyqxmd.com/read/28353203/gene-structure-of-the-pregnancy-associated-glycoprotein-like-pag-l-in-the-eurasian-beaver-castor-fiber-l
#12
Aleksandra Lipka, Marta Majewska, Grzegorz Panasiewicz, Martyna Bieniek-Kobuszewska, Bozena Szafranska
The pregnancy-associated glycoprotein-like family (PAG-L) is a large group of chorionic products, expressed in the pre-placental trophoblast and later in the post-implantational chorionic epithelium, and are involved in proper placenta development and embryo-maternal interaction in eutherians. This study describes identification of the PAG-L family in the genome of the Eurasian beaver (Castor fiber L.), named CfPAG-L. We identified 7657 bp of the CfPAG-L gDNA sequence (Acc. No. KX377932), encompassing nine exons (1-9) and eight introns (A-H)...
March 29, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28340729/development-validation-and-comparison-of-near-infrared-and-raman-spectroscopic-methods-for-fast-characterization-of-tablets-with-amlodipine-and-valsartan
#13
Tibor Casian, Andra Reznek, Andreea Loredana Vonica-Gligor, Jeroen Van Renterghem, Thomas De Beer, Ioan Tomuță
The objective of this study was to develop, validate and compare NIR and Raman spectroscopic methods for fast characterization in terms of API content and tensile strength of fixed-dose combination tablets containing amlodipine and valsartan. For the APIs assay NIR-transmittance and Raman-reflectance methods were considered, whereas for the tensile strength assay Raman spectra were recorded in reflectance configuration and NIR spectra were recorded in both reflectance and transmittance. Multivariate calibration models (PLS) were built by applying different pre-processing methods (SNV, MSC, SD+SNV) on certain spectral regions...
May 15, 2017: Talanta
https://www.readbyqxmd.com/read/28327206/lessons-learned-from-additional-research-analyses-of-unsolved-clinical-exome-cases
#14
Mohammad K Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R Lalani, Christian P Schaaf, Michael F Wangler, Carlos A Bacino, Richard Alan Lewis, Lorraine Potocki, Brett H Graham, John W Belmont, Fernando Scaglia, Jordan S Orange, Shalini N Jhangiani, Theodore Chiang, Harsha Doddapaneni, Jianhong Hu, Donna M Muzny, Fan Xia, Arthur L Beaudet, Eric Boerwinkle, Christine M Eng, Sharon E Plon, V Reid Sutton, Richard A Gibbs, Jennifer E Posey, Yaping Yang, James R Lupski
BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease...
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28298214/climat-het-detecting-subclonal-copy-number-alterations-and-loss-of-heterozygosity-in-heterogeneous-tumor-samples-from-whole-genome-sequencing-data
#15
Zhenhua Yu, Ao Li, Minghui Wang
BACKGROUND: Copy number alterations (CNA) and loss of heterozygosity (LOH) represent a large proportion of genetic structural variations of cancer genomes. These aberrations are continuously accumulated during the procedure of clonal evolution and patterned by phylogenetic branching. This invariably results in the emergence of multiple cell populations with distinct complement of mutational landscapes in tumor sample. With the advent of next-generation sequencing technology, inference of subclonal populations has become one of the focused interests in cancer-associated studies, and is usually based on the assessment of combinations of somatic single-nucleotide variations (SNV), CNA and LOH...
March 15, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28290094/evaluating-the-calling-performance-of-a-rare-disease-ngs-panel-for-single-nucleotide-and-copy-number-variants
#16
P Cacheiro, A Ordóñez-Ugalde, B Quintáns, S Piñeiro-Hermida, J Amigo, M García-Murias, S I Pascual-Pascual, F Grandas, J Arpa, A Carracedo, M J Sobrido
INTRODUCTION: Variant detection protocols for clinical next-generation sequencing (NGS) need application-specific optimization. Our aim was to analyze the performance of single nucleotide variant (SNV) and copy number (CNV) detection programs on an NGS panel for a rare disease. METHODS: Thirty genes were sequenced in 83 patients with hereditary spastic paraplegia. The variant calls obtained with LifeScope, GATK UnifiedGenotyper and GATK HaplotypeCaller were compared with Sanger sequencing...
March 13, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28287619/effects-of-cdh23-single-nucleotide-substitutions-on-age-related-hearing-loss-in-c57bl-6-and-129s1-sv-mice-and-comparisons-with-congenic-strains
#17
Kenneth R Johnson, Cong Tian, Leona H Gagnon, Haiyan Jiang, Dalian Ding, Richard Salvi
A single nucleotide variant (SNV) of the cadherin 23 gene (Cdh23(c.753A)), common to many inbred mouse strains, accelerates age-related hearing loss (AHL) and can worsen auditory phenotypes of other mutations. We used homologous recombination in C57BL/6 NJ (B6N) and 129S1/SvImJ (129S1) embryonic stem cells to engineer mouse strains with reciprocal single base pair substitutions (B6-Cdh23(c.753A>G) and 129S1-Cdh23(c.753G>A)). We compared ABR thresholds and cochlear pathologies of these SNV mice with those of congenic (B6...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28274438/detection-of-unexpected-frauds-screening-and-quantification-of-maleic-acid-in-cassava-starch-by-fourier-transform-near-infrared-spectroscopy
#18
Hai-Yan Fu, He-Dong Li, Lu Xu, Qiao-Bo Yin, Tian-Ming Yang, Chuang Ni, Chen-Bo Cai, Ji Yang, Yuan-Bin She
Fourier transform near-infrared (FT-NIR) spectroscopy and chemometrics were adopted for the rapid analysis of a toxic additive, maleic acid (MA), which has emerged as a new extraneous adulterant in cassava starch (CS). After developing an untargeted screening method for MA detection in CS using one-class partial least squares (OCPLS), multivariate calibration models were subsequently developed using least squares support vector machine (LS-SVM) to quantitatively analyze MA. As a result, the OCPLS model using the second-order derivative (D2) spectra detected 0...
July 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28265118/risk-alleles-of-genes-with-monoallelic-expression-are-enriched-in-gain-of-function-variants-and-depleted-in-loss-of-function-variants-for-neurodevelopmental-disorders
#19
V Savova, S Vinogradova, D Pruss, A A Gimelbrant, L A Weiss
Over 3000 human genes can be expressed from a single allele in one cell, and from the other allele-or both-in neighboring cells. Little is known about the consequences of this epigenetic phenomenon, monoallelic expression (MAE). We hypothesized that MAE increases expression variability, with a potential impact on human disease. Here, we use a chromatin signature to infer MAE for genes in lymphoblastoid cell lines and human fetal brain tissue. We confirm that across clones MAE status correlates with expression level, and that in human tissue data sets, MAE genes show increased expression variability...
March 7, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28258043/whole-genome-single-nucleotide-variant-distribution-on-genomic-regions-and-its-relationship-to-major-depression
#20
Chenglong Yu, Bernhard T Baune, Julio Licinio, Ma-Li Wong
Recent advances in DNA technologies have provided unprecedented opportunities for biological and medical research. In contrast to current popular genotyping platforms which identify specific variations, whole-genome sequencing (WGS) allows for the detection of all private mutations within an individual. Major depressive disorder (MDD) is a chronic condition with enormous medical, social and economic impacts. Genetic analysis, by identifying risk variants and thereby increasing our understanding of how MDD arises, could lead to improved prevention and the development of new and more effective treatments...
February 20, 2017: Psychiatry Research
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