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https://www.readbyqxmd.com/read/28742110/evaluation-of-exome-variants-using-the-ion-proton-platform-to-sequence-error-prone-regions
#1
Heewon Seo, Yoomi Park, Byung Joo Min, Myung Eui Seo, Ju Han Kim
The Ion Proton sequencer from Thermo Fisher accurately determines sequence variants from target regions with a rapid turnaround time at a low cost. However, misleading variant-calling errors can occur. We performed a systematic evaluation and manual curation of read-level alignments for the 675 ultrarare variants reported by the Ion Proton sequencer from 27 whole-exome sequencing data but that are not present in either the 1000 Genomes Project and the Exome Aggregation Consortium. We classified positive variant calls into 393 highly likely false positives, 126 likely false positives, and 156 likely true positives, which comprised 58...
2017: PloS One
https://www.readbyqxmd.com/read/28696069/hcc-associated-single-nucleotide-variants-and-deletions-identified-using-genome-wide-high-throughput-analysis-of-hbv
#2
Wen-Chun Liu, I-Chin Wu, Yen-Chien Lee, Chih-Peng Lin, Ji-Hong Cheng, Yih-Jyh Lin, Chia-Jui Yen, Pin-Nan Cheng, Pei-Fu Li, Yi-Ting Cheng, Pei-Wen Cheng, Koun-Tem Sun, Shu-Ling Yan, Jia-Jhen Lin, Jui-Chu Yang, Kung-Chao Chang, Cheng-Hsun Ho, Vincent S Tseng, Bill Chia-Han Chang, Jaw-Ching Wu, Ting-Tsung Chang
This study investigated hepatitis B virus (HBV) single nucleotide variants (SNVs) and deletion mutations linked with hepatocellular carcinoma (HCC). Ninety-three HCC patients and 108 non-HCC patients were enrolled for HBV genome-wide next-generation sequencing (NGS) analysis. Systemic literature review and meta-analysis were performed to validate NGS-defined HCC-associated SNVs and deletions. The experimental results identified 60 NGS-defined HCC-associated SNVs, including 41 novel SNVs, and their pathogenic frequencies...
July 11, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28694211/novel-mutations-in-patients-with-hereditary-red-blood-cell-membrane-disorders-using-next-generation-sequencing
#3
Yunyan He, Siyuan Jia, Roma Kajal Dewan, Ning Liao
To diagnose and investigate the genotype-phenotype relationship in intractable hereditary red blood cell (RBC) membrane cases, we have utilized next-generation sequencing (NGS) to develop a high-throughput, highly sensitive assay. Three unrelated families including 15 individuals were analysed with a panel interrogating 600 genes related to haematopathy disorders. Where possible, inheritance patterns of pathogenic mutations were determined by sequencing the relatives. We identified 2 novel mutations in ANK1 (Y216X and E142X) responsible for hereditary spherocytosis (HS) that were stop-gain single nucleotide variants (SNVs)...
July 7, 2017: Gene
https://www.readbyqxmd.com/read/28694034/insertion-and-deletion-derived-tumour-specific-neoantigens-and-the-immunogenic-phenotype-a-pan-cancer-analysis
#4
Samra Turajlic, Kevin Litchfield, Hang Xu, Rachel Rosenthal, Nicholas McGranahan, James L Reading, Yien Ning S Wong, Andrew Rowan, Nnennaya Kanu, Maise Al Bakir, Tim Chambers, Roberto Salgado, Peter Savas, Sherene Loi, Nicolai J Birkbak, Laurent Sansregret, Martin Gore, James Larkin, Sergio A Quezada, Charles Swanton
BACKGROUND: The focus of tumour-specific antigen analyses has been on single nucleotide variants (SNVs), with the contribution of small insertions and deletions (indels) less well characterised. We investigated whether the frameshift nature of indel mutations, which create novel open reading frames and a large quantity of mutagenic peptides highly distinct from self, might contribute to the immunogenic phenotype. METHODS: We analysed whole-exome sequencing data from 5777 solid tumours, spanning 19 cancer types from The Cancer Genome Atlas...
July 7, 2017: Lancet Oncology
https://www.readbyqxmd.com/read/28691025/protective-and-predisposing-morphological-factors-in-suprascapular-nerve-entrapment-syndrome-a-fundamental-review-based-on-recent-observations
#5
REVIEW
Piotr Łabętowicz, Marek Synder, Mariusz Wojciechowski, Krzysztof Orczyk, Hubert Jezierski, Mirosław Topol, Michał Polguj
Suprascapular nerve entrapment syndrome (SNES) is a neuropathy caused by compression of the nerve along its course. The most common compression sites include the suprascapular notch and the spinoglenoid notch. The aim of this article was to review the anatomical factors influencing the occurrence of SNES in the light of the newest reports. Potential predisposing morphological factors include a V-shaped, narrow, or "deep" suprascapular notch; a band-shaped, bifurcated, or completely ossified superior transverse scapular ligament (STSL); particular arrangements of the suprascapular nerve and vessels at the suprascapular notch...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28685054/single-nucleotide-variant-sequencing-errors-in-whole-exome-sequencing-using-the-ion-proton-system
#6
Shiro Fujita, Katsuhiro Masago, Chiyuki Okuda, Akito Hata, Reiko Kaji, Nobuyuki Katakami, Yukio Hirata
Errors in sequencing are a major obstacle in the interpretation of next-generation sequencing (NGS) results. In the present study, sequencing errors identified from analysis of single nucleotide variants (SNVs) identified during exome sequencing of human germline DNA were studied using the Thermo Fisher Ion Proton System. Two consanguineous cases were selected for sequencing using the AmpliSeq Exome capture kit, and SNVs found in both cases were validated using Sanger sequencing. A total of 98 SNVs detected by NGS were randomly selected for further analysis...
July 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28683819/interpreting-whole-genome-and-exome-sequencing-data-of-individual-gastric-cancer-samples
#7
Daniela Esser, Niklas Holze, Jochen Haag, Stefan Schreiber, Sandra Krüger, Viktoria Warneke, Philip Rosenstiel, Christoph Röcken
BACKGROUND: Gastric cancer is the fourth most common cancer and the second leading cause of cancer death worldwide. In order to understand the genetic background, we sequenced the whole exome and the whole genome of one microsatellite stable as well as one microsatellite unstable tumor and the matched healthy tissue on two different NGS platforms. We here aimed to provide a comparative approach for individual clinical tumor sequencing and annotation using different sequencing technologies and mutation calling algorithms...
July 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28678392/adding-azathioprine-to-remission-induction-glucocorticoids-for-eosinophilic-granulomatosis-with-polyangiitis-microscopic-polyangiitis-or-polyarteritis-nodosa-without-poor-prognosis-factors-a-randomized-controlled-trial
#8
Xavier Puéchal, Christian Pagnoux, Gabriel Baron, Thomas Quémeneur, Antoine Néel, Christian Agard, François Lifermann, Eric Liozon, Marc Ruivard, Pascal Godmer, Nicolas Limal, Arsène Mékinian, Thomas Papo, Anne-Marie Ruppert, Anne Bourgarit, Boris Bienvenu, Loïck Geffray, Jean-Luc Saraux, Elisabeth Diot, Bruno Crestani, Xavier Delbrel, Laurent Sailler, Pascal Cohen, Véronique Le Guern, Benjamin Terrier, Matthieu Groh, Claire Le Jeunne, Luc Mouthon, Philippe Ravaud, Loïc Guillevin
OBJECTIVE: Most patients with nonsevere systemic necrotizing vasculitides (SNVs) achieve remission with glucocorticoids alone but one-third relapse within 2 years. This study aimed to determine whether azathioprine adjunction to glucocorticoids could achieve a higher sustained remission rate of newly diagnosed nonsevere eosinophilic granulomatosis with polyangiitis (EGPA), microscopic polyangiitis (MPA) or polyarteritis nodosa (PAN). METHODS: All patients included in this double-blind trial received glucocorticoids, gradually tapered over 12 months, and were randomized to receive azathioprine or placebo for 12 months, with stratification according to SNV (EGPA or MPA/PAN)...
July 5, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/28609141/factor-11-single-nucleotide-variants-in-women-with-heavy-menstrual-bleeding
#9
Sophie Wiewel-Verschueren, André B Mulder, Karina Meijer, René Mulder
In a previous study it was shown that lower factor XI (FXI) levels in women with heavy menstrual bleeding (HMB). Our aim was to determine the single-nucleotide variants (SNVs) in the F11 gene in women with HMB. In addition, an extensive literature search was performed to determine the clinical significance of each SNV. Patients referred for HMB (PBAC-score >100) were included. With direct sequencing analysis of all 15 exons and flanking introns of the F11 gene, 29 different non-structural SNVs were detected in 49 patients with HMB...
June 13, 2017: Journal of Obstetrics and Gynaecology: the Journal of the Institute of Obstetrics and Gynaecology
https://www.readbyqxmd.com/read/28606096/pan-cancer-analysis-reveals-technical-artifacts-in-tcga-germline-variant-calls
#10
Alexandra R Buckley, Kristopher A Standish, Kunal Bhutani, Trey Ideker, Roger S Lasken, Hannah Carter, Olivier Harismendy, Nicholas J Schork
BACKGROUND: Cancer research to date has largely focused on somatically acquired genetic aberrations. In contrast, the degree to which germline, or inherited, variation contributes to tumorigenesis remains unclear, possibly due to a lack of accessible germline variant data. Here we called germline variants on 9618 cases from The Cancer Genome Atlas (TCGA) database representing 31 cancer types. RESULTS: We identified batch effects affecting loss of function (LOF) variant calls that can be traced back to differences in the way the sequence data were generated both within and across cancer types...
June 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28584450/t-cell-epitopes-predicted-from-the-nucleocapsid-protein-of-sin-nombre-virus-restricted-to-30-hla-alleles-common-to-the-north-american-population
#11
Sathish Sankar, Mageshbabu Ramamurthy, Balaji Nandagopal, Gopalan Sridharan
Hantavirus cardiopulmonary syndrome in North America is caused by Sin Nombre virus (SNV) and poses a public health problem. We identified T-cell epitopes restricted to HLA alleles commonly seen in the N. American population. Nucleocapsid (N) protein is 428 aminoacid in length and binds to RNA and functions also as a key molecule between virus and host cell processes. The predicted epitopes from N protein that bind to class I MHC were analyzed for human proteasomes cleavage, TAP efficiency, immunogenicity and antigenicity...
2017: Bioinformation
https://www.readbyqxmd.com/read/28573565/concentration-estimation-of-heavy-metal-in-soils-from-typical-sewage-irrigation-area-of-shandong-province-china-using-reflectance-spectroscopy
#12
Fei Wang, Chunfang Li, Jining Wang, Wentao Cao, Quanyuan Wu
Since sewage irrigation can markedly disturb the status of heavy metals in soils, a convenient and accurate technique for heavy metal concentration estimation is of utmost importance in the cropland using wastewater for irrigation. This study therefore assessed the feasibility of visible and near infrared reflectance (VINR) spectroscopy for predicting heavy metal contents including Cr, Cu, Ni, Pb, Zn, As, Cd, and Hg in the north plain of Longkou city, Shandong Province, China. A total of 70 topsoil samples were taken for in situ spectra measurement and chemical analysis...
July 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28562428/single-nucleotide-variant-in-nucleoporin-107-may-be-predictive-of-sensitivity-to-chemotherapy-in-patients-with-ovarian-cancer
#13
Shaheen Alanee, Kristin Delfino, Andrew Wilber, Kathy Robinson, Laurent Brard, Assaad Semaan
BACKGROUND: Alterations in nuclear pore complex (NPC) genes have been previously associated with response to chemotherapy. Using agnostic exome sequencing, we envisioned that new alleles in NPC genes, predictive of sensitivity to platinum treatment, could be discovered. METHODS: Twenty-two platinum-sensitive and six platinum-resistant ovarian cancer patients were tested. Platinum sensitivity was defined as disease-free survival greater than 6 months. Next-generation sequencing of exomes was used to compare platinum-sensitive and platinum-resistant patients...
July 2017: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/28539120/comprehensive-whole-genome-sequence-analyses-yields-novel-genetic-and-structural-insights-for-intellectual-disability
#14
Farah R Zahir, Jill C Mwenifumbo, Hye-Jung E Chun, Emilia L Lim, Clara D M Van Karnebeek, Madeline Couse, Karen L Mungall, Leora Lee, Nancy Makela, Linlea Armstrong, Cornelius F Boerkoel, Sylvie L Langlois, Barbara M McGillivray, Steven J M Jones, Jan M Friedman, Marco A Marra
BACKGROUND: Intellectual Disability (ID) is among the most common global disorders, yet etiology is unknown in ~30% of patients despite clinical assessment. Whole genome sequencing (WGS) is able to interrogate the entire genome, providing potential to diagnose idiopathic patients. METHODS: We conducted WGS on eight children with idiopathic ID and brain structural defects, and their normal parents; carrying out an extensive data analyses, using standard and discovery approaches...
May 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28534831/rapidly-simultaneous-determination-of-six-effective-components-in-cistanche-tubulosa-by-near-infrared-spectroscopy
#15
Xinhong Wang, Xiaoguang Wang, Yuhai Guo
Quantitative determination of multiple effective components in a given plant usually requires a very large amount of authentic natural products. In this study, we proposed a rapid and non-destructive method for the simultaneous determination of echinacoside, verbascoside, mannitol, sucrose, glucose and fructose in Cistanche tubulosa by near infrared spectroscopy (NIRS). Near infrared diffuse reflectance spectroscopy (DRS) and high performance liquid chromatography (HPLC) were conducted on 116 batches of C. tubulosa samples...
May 19, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28508493/exome-sequencing-reveals-novel-genetic-loci-influencing-obesity-related-traits-in-hispanic-children
#16
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
#17
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
#18
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
#19
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
#20
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
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