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https://www.readbyqxmd.com/read/28508493/exome-sequencing-reveals-novel-genetic-loci-influencing-obesity-related-traits-in-hispanic-children
#1
Aniko Sabo, Pamela Mishra, Shannon Dugan-Perez, V Saroja Voruganti, Jack W Kent, Divya Kalra, Shelley A Cole, Anthony G Comuzzie, Donna M Muzny, Richard A Gibbs, Nancy F Butte
OBJECTIVE: To perform whole exome sequencing in 928 Hispanic children and identify variants and genes associated with childhood obesity. METHODS: Single-nucleotide variants (SNVs) were identified from Illumina whole exome sequencing data using integrated read mapping, variant calling, and an annotation pipeline (Mercury). Association analyses of 74 obesity-related traits and exonic variants were performed using SeqMeta software. Rare autosomal variants were analyzed using gene-based association analyses, and common autosomal variants were analyzed at the SNV level...
May 16, 2017: Obesity
https://www.readbyqxmd.com/read/28502728/technical-validation-of-a-next-generation-sequencing-assay-for-detecting-clinically-relevant-levels-of-breast-cancer-related-single-nucleotide-variants-and-copy-number-variants-using-simulated-cell-free-dna
#2
Xin Yang, Yuxing Chu, Rui Zhang, Yanxi Han, Lucheng Zhang, Yu Fu, Dan Li, Rongxue Peng, Dongdong Li, Jiansheng Ding, Ziyang Li, Meiru Zhao, Kuo Zhang, Tian Lu, Lang Yi, Qisheng Wu, Guigao Lin, Jiehong Xie, Tao Liu, Ling Yang, Xin Yi, Jinming Li
Next-generation sequencing (NGS) is commonly used in a clinical setting for diagnostic and prognostic testing of genetic mutations to select optimal targeted therapies. Herein, we describe the development of a custom NGS assay for detecting single-nucleotide variants (SNVs) and copy number variations (CNVs) in a panel of 51 genes related to breast cancer. We designed and implemented a validation strategy in accordance with principles and guidelines developed by the Next-Generation Sequencing: Standardization of Clinical Testing work group using artificial, cell-free DNA (cfDNA) with mutant fragments prepared in a simple, rapid, and cost-effective manner...
May 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28482034/phd-snpg-a-webserver-and-lightweight-tool-for-scoring-single-nucleotide-variants
#3
Emidio Capriotti, Piero Fariselli
One of the major challenges in human genetics is to identify functional effects of coding and non-coding single nucleotide variants (SNVs). In the past, several methods have been developed to identify disease-related single amino acid changes but only few tools are able to score the impact of non-coding variants. Among the most popular algorithms, CADD and FATHMM predict the effect of SNVs in non-coding regions combining sequence conservation with several functional features derived from the ENCODE project data...
May 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28475866/down-the-rabbit-hole-of-single-cell-genome-analysis
#4
James Eberwine
Chen et al. (2017) demonstrate whole-genome amplification of single-cell genomic DNA using linear nucleic acid amplification. This provides reliable single-nucleotide variation (SNV) detection across the single-cell genome, facilitating an understanding of cell-to-cell similarities and distinctions.
May 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28473326/reduced-carboxylesterase-1-is-associated-with-endothelial-injury-in-methamphetamine-induced-pulmonary-arterial-hypertension
#5
Mark E Orcholski, Artyom Khurshudyan, Elya A Shamskhou, Ke Yuan, Ian Y Chen, Sean D Kodani, Christophe Morisseau, Bruce D Hammock, Ellen M Hong, Ludmila Alexandrova, Tero-Pekka Alastalo, Gerald Berry, Roham T Zamanian, Vinicio A de Jesus Perez
Pulmonary arterial hypertension is a complication of methamphetamine use (METH-PAH) but the pathogenic mechanisms are unknown. Given that cytochrome P450 2D6 (CYP2D6) and carboxylesterase 1 (CES1) are involved in metabolism of METH and other amphetamine-like compounds, we postulated that loss of function variants could contribute to METH-PAH. While no difference in CYP2D6 expression was seen by lung immunofluorescence, CES1 expression was significantly reduced in endothelium of METH-PAH microvessels. Mass spectrometry analysis showed that healthy pulmonary microvascular endothelial cells (PMVECs) have the capacity to both internalize and metabolize METH...
May 4, 2017: American Journal of Physiology. Lung Cellular and Molecular Physiology
https://www.readbyqxmd.com/read/28465312/a-comparative-analysis-of-whole-genome-sequencing-of-oesophageal-adenocarcinoma-pre-and-post-chemotherapy
#6
Ayesha Noorani, Jan Bornschein, Andy G Lynch, Maria Secrier, Achilleas Achilleos, Matthew Eldridge, Lawrence Bower, Jamie M J Weaver, Jason Crawte, Chin-Ann Ong, Nicholas Shannon, Shona MacRae, Nicola Grehan, Barbara Nutzinger, Maria O'Donovan, Richard Hardwick, Simon Tavaré, Rebecca C Fitzgerald, Rachael Fels Elliott, Paul A W Edwards, Xiaodun Li, Hamza Chettouh, Gianmarco Contini, Eleanor Gregson, Sebastian Zeki, Laura Smith, Zarah Abdullahi, Rachel de la Rue, Ahmad Miremadi, Shalini Malhotra, Mike L Smith, Jim Davies, Charles Crichton, Nick Carroll, Peter Safranek, Andrew Hindmarsh, Vijayendran Sujendran, Richard Turkington, Stephen J Hayes, Yeng Ang, Shaun R Preston, Sarah Oakes, Izhar Bagwan, Vicki Save, Richard J E Skipworth, Ted R Hupp, J Robert O'Neill, Olga Tucker, Andrew Beggs, Philippe Taniere, Timothy J Underwood, Fergus Noble, Jack Owsley, Hugh Barr, Neil Shepherd, Oliver Old, Jesper Lagergren, James Gossage, Andrew Davies, Fuju Chang, Janine Zylstra, Grant Sanders, Richard Berrisford, Catherine Harden, David Bunting, Mike Lewis, Ed Cheong, Bhaskar Kumar, Simon L Parsons, Irshad Soomro, Philip Kaye, Laurence Lovat, Rehan Haidry, Victor Eneh, Laszlo Igali, Michael Scott, Shamila Sothi, Sari Suortamo, Suzy Lishman
The scientific community has avoided using tissue samples from patients that have been exposed to systemic chemotherapy to infer the genomic landscape of a given cancer. Esophageal adenocarcinoma is a heterogeneous, chemoresistant tumor for which the availability and size of pretreatment endoscopic samples are limiting. This study compares whole-genome sequencing data obtained from chemo-naive and chemo-treated samples. The quality of whole-genomic sequencing data is comparable across all samples regardless of chemotherapy status...
May 2, 2017: Genome Research
https://www.readbyqxmd.com/read/28456592/whole-exome-sequencing-of-sporadic-patients-with-currarino-syndrome-a-report-of-three-trios
#7
Ingunn Holm, Mari Spildrejorde, Barbro Stadheim, Kristin L Eiklid, Pubudu S Samarakoon
Currarino Syndrome is a rare congenital malformation syndrome described as a triad of anorectal, sacral and presacral anomalies. Currarino Syndrome is reported to be both familial and sporadic. Familial CS is today known as an autosomal dominant disorder caused by mutations in the transcription factor MNX1. The aim of this study was to look for genetic causes of Currarino Syndrome in sporadic patients after ruling out other causes, like chromosome aberrations, disease-causing variants in possible MNX1 cooperating transcription factors and aberrant methylation in the promoter of the MNX1 gene...
April 26, 2017: Gene
https://www.readbyqxmd.com/read/28452169/melanoma-patient-response-to-nivolumab-treatment-for-metastatic-lung-lesions-multi-omics-analysis-in-project-hope
#8
Yoshio Kiyohara, Shusuke Yoshikawa, Masaki Otsuka, Ryota Kondou, Akira Iizuka, Chizu Nonomura, Keiichi Ohshima, Kenichi Urakami, Masatoshi Kusuhara, Takeshi Nagashima, Takashi Sugino, Ken Yamaguchi, Yasuto Akiyama
A 70-year-old woman was diagnosed with a malignant melanoma of the occipital skin which was resected; however, multiple lung metastases were detected. Nivolumab therapy was initiated and partial response was obtained. However, the patient was diagnosed with grade 2 interstitial pneumonitis. Prednisolone administration was initiated and the interstitial pneumonitis shadow disappeared. However, then a right rib metastasis was noticed and given radiation therapy. After progressive disease was obtained, the metastatic lesion was resected, and no relapse occurred until skeletal muscle metastasis was found...
April 28, 2017: Journal of Dermatology
https://www.readbyqxmd.com/read/28450240/correlation-of-fcgrt-genomic-structure-with-serum-immunoglobulin-albumin-and-farletuzumab-pharmacokinetics-in-patients-with-first-relapsed-ovarian-cancer
#9
Daniel J O'Shannessy, Katie Bendas, Charles Schweizer, Wenquan Wang, Earl Albone, Elizabeth B Somers, Susan Weil, Rhonda K Meredith, Jason Wustner, Luigi Grasso, Mark Landers, Nicholas C Nicolaides
Farletuzumab (FAR) is a humanized monoclonal antibody (mAb) that binds to folate receptor alpha. A Ph3 trial in ovarian cancer patients treated with carboplatin/taxane plus FAR or placebo did not meet the primary statistical endpoint. Subgroup analysis demonstrated that subjects with high FAR exposure levels (Cmin>57.6μg/mL) showed statistically significant improvements in PFS and OS. The neonatal Fc receptor (fcgrt) plays a central role in albumin/IgG stasis and mAb pharmacokinetics (PK). Here we evaluated fcgrt sequence and association of its promoter variable number tandem repeats (VNTR) and coding single nucleotide variants (SNV) with albumin/IgG levels and FAR PK in the Ph3 patients...
April 24, 2017: Genomics
https://www.readbyqxmd.com/read/28440220/rapid-evolution-of-the-human-mutation-spectrum
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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)...
July 5, 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
#17
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
#18
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
#19
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
#20
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
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