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https://www.readbyqxmd.com/read/28944914/gene-screening-facilitates-diagnosis-of-complicated-symptoms-a-case-report
#1
Hong Duan, Di Zhang, Jing Cheng, Yu Lu, Huijun Yuan
Gene mutation has an important role in disease pathogenesis; therefore, genetic screening is a useful tool for diagnosis. The present study screened pathogenic genes, ectodysplasin A (EDA) and lamin A/C (LMNA), in a patient with suspected syndromic hearing impairment and various other symptoms including tooth and skin abnormalities. Large‑scale sequencing of 438 deafness‑associated genes and whole‑genome sequencing was also performed. The present findings did not identify copy number variation and mutations in EDA; therefore, excluding the possibility of EDA‑initiated ectodermal dysplasia syndrome...
September 22, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28942070/ryanodine-receptor-and-fk506-binding-protein-1-in-the-atlantic-killifish-fundulus-heteroclitus-a-phylogenetic-and-population-based-comparison
#2
Erika B Holland, Jared V Goldstone, Isaac N Pessah, Andrew Whitehead, Noah M Reid, Sibel I Karchner, Mark E Hahn, Diane E Nacci, Bryan W Clark, John J Stegeman
Non-dioxin-like polychlorinated biphenyls (NDL PCBs) activate ryanodine receptors (RyR), microsomal Ca(2+) channels of broad significance. Teleost fish may be important models for NDL PCB neurotoxicity, and we used sequencing databases to characterize teleost RyR and FK506 binding protein 12 or 12.6kDa (genes FKBP1A; FKBP1B), which promote NDL PCB-triggered Ca(2+) dysregulation. Particular focus was placed on describing genes in the Atlantic killifish (Fundulus heteroclitus) genome and searching available RNA-sequencing datasets for single nucleotide variants (SNV) between PCB tolerant killifish from New Bedford Harbor (NBH) versus sensitive killifish from Scorton Creek (SC), MA...
September 4, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28940478/comprehensive-pharmacogenomic-study-reveals-an-important-role-of-ugt1a3-in-montelukast-pharmacokinetics
#3
Päivi Hirvensalo, Aleksi Tornio, Mikko Neuvonen, Tuija Tapaninen, Maria Paile-Hyvärinen, Vesa Kärjä, Ville T Männistö, Jussi Pihlajamäki, Janne T Backman, Mikko Niemi
To identify genetic basis of interindividual variability in montelukast exposure, we determined its pharmacokinetics and sequenced 379 pharmacokinetic genes in 191 healthy volunteers. An intronic single nucleotide variation (SNV), strongly linked with UGT1A3*2, associated with reduced area under the plasma concentration-time curve (AUC0-∞ ) of montelukast (by 18% per copy of the minor allele; P=1.83 × 10(-10) ). UGT1A3*2 associated with increased AUC0-∞ of montelukast acyl-glucuronide M1 and decreased AUC0-∞ of hydroxymetabolites M5R, M5S, and M6 (P<10(-9) )...
September 23, 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/28919550/improving-the-genotyping-resolution-of-cryptosporidium-hominis-subtype-iba10g2-using-one-step-pcr-based-amplicon-sequencing
#4
Jessica Beser, Björn M Hallström, Abdolreza Advani, Sofia Andersson, Gabriel Östlund, Jadwiga Winiecka-Krusnell, Marianne Lebbad, Erik Alm, Karin Troell, Romanico B G Arrighi
Cryptosporidium hominis gp60 subtype IbA10G2 is a common cause of cryptosporidiosis. This subtype is responsible for many waterborne outbreaks as well as sporadic cases and is considered virulent and highly important in the epidemiology of cryptosporidiosis. Due to low heterogeneity within the genome of C. hominis it has been difficult to identify epidemiological markers with higher resolution than gp60. However, new markers are required in order to improve outbreak investigations and studies of the transmission dynamics of this clinically important subtype...
September 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28910730/pathogenic-and-likely-pathogenic-genetic-alterations-and-polymorphisms-in-growth-hormone-gene-gh1-and-growth-hormone-releasing-hormone-receptor-gene-ghrhr-in-a-cohort-of-isolated-growth-hormone-deficient-ighd-children-in-sri-lanka
#5
Tharmini Sundralingam, Kamani Hemamala Tennekoon, Shamya de Silva, Sumadee De Silva, Asanka Sudeshini Hewage
OBJECTIVE: Genetic alterations in GH1 and GHRHR genes are known to cause isolated growth hormone deficiency (IGHD). Of these, GHRHR codon 72 mutation has been reported to be highly prevalent in the Indian subcontinent, but among Sri Lankans its prevalence was low compared to reports from neighboring countries. The present study was therefore carried out to identify genetic alterations in the GH1 gene and rest of the GHRHR gene in a cohort of Sri Lankan IGHD patients who tested negative for GHRHR codon 72 mutation...
September 5, 2017: Growth Hormone & IGF Research
https://www.readbyqxmd.com/read/28887485/direct-comparison-of-performance-of-single-nucleotide-variant-calling-in-human-genome-with-alignment-based-and-assembly-based-approaches
#6
Leihong Wu, Gokhan Yavas, Huixiao Hong, Weida Tong, Wenming Xiao
Complementary to reference-based variant detection, recent studies revealed that many novel variants could be detected with de novo assembled genomes. To evaluate the effect of reads coverage and the accuracy of assembly-based variant calling, we simulated short reads containing more than 3 million of single nucleotide variants (SNVs) from the whole human genome and compared the efficiency of SNV calling between the assembly-based and alignment-based calling approaches. We assessed the quality of the assembled contig and found that a minimum of 30X coverage of short reads was needed to ensure reliable SNV calling and to generate assembled contigs with a good coverage of genome and genes...
September 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28886757/differentiation-of-bovine-porcine-and-fish-gelatins-by-attenuated-total-reflectance-fourier-transform-infrared-spectroscopy-atr-ftirs-coupled-with-pattern-recognition
#7
Ahmet Kemal Aloglu, Peter de B Harrington
Bovine, porcine, and fish gelatins have been differentiated based on their spectra collected by attenuated total reflectance FTIR spectroscopy (ATR-FTIRS) coupled with pattern recognition. Three tree-based classification methods, a fuzzy rule-building expert system (FuRES), support vector machine classification trees (SVMTreeG and SVMTreeH), and one reference model, super partial least-squares discriminant analysis (sPLS-DA), were evaluated with and without two preprocessing techniques, namely standard normal variate (SNV) and principal component orthogonal signal correction (PC-OSC)...
September 8, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28884721/-a-search-of-target-regions-for-association-studies-between-dna-methylation-and-cognitive-impairment-in-schizophrenia
#8
N V Kondratiev, M V Alfimova, V E Golimbet
AIM: To develop a strategy for the search for candidate genes and targets for epigenetic studies of cognitive impairments in patients with schizophrenia. MATERIAL AND METHODS: A search for literature on epigenetics of schizophrenia and cognitive functions was performed. Single nucleotide polymorphisms (SNPs) that can create or abolish a site for DNA methylation or transcription factor sites were determined using a custom script. RESULTS AND CONCLUSION: Eight candidate genes, including BDNF, COMT, RELN, SNRPN, PSMA4, FAM63B, IL-1RAP, MAD1L1, as well as 750 targets in CpG islands in the linkage regions identified in GWAS of schizophrenia and 406 targets in SNV located within transcription factor binding sites were selected...
2017: Zhurnal Nevrologii i Psikhiatrii Imeni S.S. Korsakova
https://www.readbyqxmd.com/read/28882180/high-performance-of-targeted-next-generation-sequencing-on-variance-detection-in-clinical-tumor-specimens-in-comparison-with-current-conventional-methods
#9
Dan Su, Dadong Zhang, Kaiyan Chen, Jing Lu, Junzhou Wu, Xinkai Cao, Lisha Ying, Qihuang Jin, Yizhou Ye, Zhenghua Xie, Lei Xiong, Weimin Mao, Fugen Li
BACKGROUND: Next generation sequencing (NGS) is being increasingly applied for assisting cancer molecular diagnosis. However, it is still needed to validate NGS accuracy on detection of DNA alternations based on a large number of clinical samples, especially for DNA rearrangements and copy number variations (CNVs). This study is to set up basic parameters of targeted NGS for clinical diagnosis and to understand advantage of targeted NGS in comparison with the conventional methods of molecular diagnosis...
September 7, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28867142/exonic-mosaic-mutations-contribute-risk-for-autism-spectrum-disorder
#10
Deidre R Krupp, Rebecca A Barnard, Yannis Duffourd, Sara A Evans, Ryan M Mulqueen, Raphael Bernier, Jean-Baptiste Rivière, Eric Fombonne, Brian J O'Roak
Genetic risk factors for autism spectrum disorder (ASD) have yet to be fully elucidated. Postzygotic mosaic mutations (PMMs) have been implicated in several neurodevelopmental disorders and overgrowth syndromes. By leveraging whole-exome sequencing data on a large family-based ASD cohort, the Simons Simplex Collection, we systematically evaluated the potential role of PMMs in autism risk. Initial re-evaluation of published single-nucleotide variant (SNV) de novo mutations showed evidence consistent with putative PMMs for 11% of mutations...
September 7, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28866361/targeted-next-generation-sequencing-of-glandular-odontogenic-cyst-a-preliminary-study
#11
Elisa Carvalho de Siqueira, Silvia Ferreira de Sousa, Josiane Alves França, Marina Gonçalves Diniz, Thaís Dos Santos Fontes Pereira, Rennan Garcias Moreira, Pablo Agustin Vargas, Ricardo Santiago Gomez, Carolina Cavalieri Gomes
OBJECTIVE: Glandular odontogenic cyst (GOC) is an uncommon developmental cyst. Its molecular pathogenesis is unclear, and deep sequencing may help identify causative low-frequency variants in tumors. We investigated in GOC mutations in 50 genes commonly altered in human cancers. STUDY DESIGN: Targeted next-generation sequencing was used to interrogate a panel of approximately 2800 mutations in GOC. RESULTS: Six missense single nucleotide variations (SNVs) were reported...
July 26, 2017: Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology
https://www.readbyqxmd.com/read/28859103/myt1l-mutations-cause-intellectual-disability-and-variable-obesity-by-dysregulating-gene-expression-and-development-of-the-neuroendocrine-hypothalamus
#12
Patricia Blanchet, Martina Bebin, Shaam Bruet, Gregory M Cooper, Michelle L Thompson, Benedicte Duban-Bedu, Benedicte Gerard, Amelie Piton, Sylvie Suckno, Charu Deshpande, Virginia Clowes, Julie Vogt, Peter Turnpenny, Michael P Williamson, Yves Alembik, Eric Glasgow, Alisdair McNeill
Deletions at chromosome 2p25.3 are associated with a syndrome consisting of intellectual disability and obesity. The smallest region of overlap for deletions at 2p25.3 contains PXDN and MYT1L. MYT1L is expressed only within the brain in humans. We hypothesized that single nucleotide variants (SNVs) in MYT1L would cause a phenotype resembling deletion at 2p25.3. To examine this we sought MYT1L SNVs in exome sequencing data from 4, 296 parent-child trios. Further variants were identified through a genematcher-facilitated collaboration...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28839369/rapid-detection-of-volatile-oil-in-mentha-haplocalyx-by-near-infrared-spectroscopy-and-chemometrics
#13
Hui Yan, Cheng Guo, Yang Shao, Zhen Ouyang
Near-infrared spectroscopy combined with partial least squares regression (PLSR) and support vector machine (SVM) was applied for the rapid determination of chemical component of volatile oil content in Mentha haplocalyx. The effects of data pre-processing methods on the accuracy of the PLSR calibration models were investigated. The performance of the final model was evaluated according to the correlation coefficient (R) and root mean square error of prediction (RMSEP). For PLSR model, the best preprocessing method combination was first-order derivative, standard normal variate transformation (SNV), and mean centering, which had of 0...
July 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28838314/lack-of-association-between-akap2-and-the-susceptibility-of-adolescent-idiopathic-scoliosis-in-the-chinese-population
#14
Leilei Xu, Chao Xia, Weiguo Zhu, Zhenhua Feng, Xiaodong Qin, Weixiang Sun, Yong Qiu, Zezhang Zhu
BACKGROUND: Adolescent idiopathic scoliosis (AIS) is a well characterized spinal deformity that affects millions of children world-wide. The role of genetic factor in the development of AIS has been of great interest, since obvious hereditary trend has been observed in AIS families. In a recent study of Chinese population, a novel mutation of AKAP2 was observed in a family with AIS, which was believed to play a role in the aetiopathogenesis of AIS. The purpose of this study was to investigate whether genetic variants of AKAP2 are associated with the susceptibility of AIS in Chinese population...
August 24, 2017: BMC Musculoskeletal Disorders
https://www.readbyqxmd.com/read/28837838/single-nucleotide-variations-in-cultured-cancer-cells-effect-of-mismatch-repair
#15
Igor G Panyutin, Irina V Panyutin, Ian Powell-Castilla, Laura Felix, Ronald D Neumann
We assessed single nucleotide variations (SNVs) between individual cells in two cancer cell lines; DU145, from brain metastasis of prostate tumor with deficient mismatch repair; and HT1080, a fibrosarcoma cell line. Clones of individual cells were isolated, and sequenced using Ion Ampliseq comprehensive cancer panel that covered the exomes of 409 oncogenes and tumor suppressor genes. Five clones of DU145 and four clones of HT1080 cells were analyzed. We found from 7 to 12 unique SNVs between DU145 clones, while HT1080 clones showed no more than one unique SNV...
July 27, 2017: Mutation Research
https://www.readbyqxmd.com/read/28835374/low-affinity-binding-in-cis-to-p2y2r-mediates-force-dependent-integrin-activation-during-hantavirus-infection
#16
Virginie Bondu, Chenyu Wu, Wenpeng Cao, Peter C Simons, Jennifer Gillette, Jieqing Zhu, Laurie Erb, X Frank Zhang, Tione Buranda
Pathogenic hantaviruses bind to the Plexin Semaphorin Integrin (PSI) domain of inactive, β3 integrins. Previous studies have implicated a cognate cis interaction between the bent conformation β5/β3 integrins and an RGD sequence in the first extracellular loop of P2Y2R (Erb et al., 2001). With single-molecule atomic force microscopy, we show a cognate interaction between (RGD)P2Y2R and an AFM tip decorated with recombinant αIIbβ3 integrins expressed on cell membranes. Mutation of the RGD sequence to RGE in the P2Y2R removes this interaction...
August 23, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28835080/-high-throughput-targeted-sequencing-panel-for-exploring-radiosensitivity-associated-genes-in-esophageal-squamous-cell-carcinoma
#17
Y Qiao, C X Hu, D A Song, S Q Li, L H Zhou, X D Jiang
Objective: To explore radiosensitivity-associated genes in esophageal squamous cell carcinoma by targeted sequencing panel. Methods: The peripheral blood from 22 esophageal squamous cell carcinoma (ESCC) patients received radiotherapy alone were collected, respectively. The genomic DNA (gDNA) of peripheral blood was extracted and used to create a library of gDNA restriction fragments. The gDNA restriction fragments were hybridized to the HaloPlex probe capture library, which comprises 356 cancer genes selected from the Catalogue of Somatic Mutations in Cancer (Cosmic) database of 2011 updated edition...
August 23, 2017: Zhonghua Zhong Liu za Zhi [Chinese Journal of Oncology]
https://www.readbyqxmd.com/read/28834784/determination-of-fat-content-in-chicken-hamburgers-using-nir-spectroscopy-and-the-successive-projections-algorithm-for-interval-selection-in-pls-regression-ispa-pls
#18
Gabriela Krepper, Florencia Romeo, David Douglas de Sousa Fernandes, Paulo Henrique Gonçalves Dias Diniz, Mário César Ugulino de Araújo, María Susana Di Nezio, Marcelo Fabián Pistonesi, María Eugenia Centurión
Determining fat content in hamburgers is very important to minimize or control the negative effects of fat on human health, effects such as cardiovascular diseases and obesity, which are caused by the high consumption of saturated fatty acids and cholesterol. This study proposed an alternative analytical method based on Near Infrared Spectroscopy (NIR) and Successive Projections Algorithm for interval selection in Partial Least Squares regression (iSPA-PLS) for fat content determination in commercial chicken hamburgers...
August 17, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28832570/accurate-and-comprehensive-analysis-of-single-nucleotide-variants-and-large-deletions-of-the-human-mitochondrial-genome-in-dna-and-single-cells
#19
Filippo Zambelli, Kim Vancampenhout, Dorien Daneels, Daniel Brown, Joke Mertens, Sonia Van Dooren, Ben Caljon, Luca Gianaroli, Karen Sermon, Thierry Voet, Sara Seneca, Claudia Spits
Massive parallel sequencing (MPS) can accurately quantify mitochondrial DNA (mtDNA) single nucleotide variants (SNVs), but no MPS methods are currently validated to simultaneously and accurately establish the breakpoints and frequency of large deletions at low heteroplasmic loads. Here we present the thorough validation of an MPS protocol to quantify the load of very low frequency, large mtDNA deletions in bulk DNA and single cells, along with SNV calling by standard methods. We used a set of well-characterized DNA samples, DNA mixes and single cells to thoroughly control the study...
August 23, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28757019/genomic-comparison-of-virulent-and-non-virulent-serotype-v-st1-streptococcus-agalactiae-in-fish
#20
Rui Wang, Li-Ping Li, Ting Huang, Ai-Ying Lei, Yan Huang, Fu-Guang Luo, Dong-Ying Wang, Wei-Yi Huang, Ming Chen, Jun Huang
Streptococcus agalactiae or Group B Streptococcus (GBS) is the major pathogen causing pneumonia and meningitis in human, mastitis in dairy cows, and streptococcal disease in tilapia. Previous studies have shown that fish GBS strains are correlated with human GBS strains in evolution and might have cross-host infection ability. Although the invasive disease caused by ST1 GBS in non-pregnant adults and cows is increasing worldwide, infection of fish by ST1 GBS has not been reported. The aim of this study was to determine whether ST1 GBS was virulent in fish and to investigate the genomic characteristics of ST1 GBS strains with different pathogenicity in tilapia...
August 2017: Veterinary Microbiology
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