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https://www.readbyqxmd.com/read/28609141/factor-11-single-nucleotide-variants-in-women-with-heavy-menstrual-bleeding
#1
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
#2
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
#3
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
#4
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...
June 1, 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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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-esophageal-adenocarcinoma-pre-and-post-chemotherapy
#13
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
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...
June 2017: Genome Research
https://www.readbyqxmd.com/read/28456592/whole-exome-sequencing-of-sporadic-patients-with-currarino-syndrome-a-report-of-three-trios
#14
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...
August 15, 2017: Gene
https://www.readbyqxmd.com/read/28452169/melanoma-patient-response-to-nivolumab-treatment-for-metastatic-lung-lesions-multi-omics-analysis-in-project-hope
#15
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
#16
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
#17
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
#18
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
#19
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, nonmutated positions. We found epigenetic differences between genomic regions containing missense SNVs and those containing frameshift indels across multiple cancer types. Levels of 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
#20
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
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