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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/28254523/transcriptomic-analysis-and-plasma-metabolomics-in-aldh16a1-null-mice-reveals-a-potential-role-of-aldh16a1-in-renal-function
#9
Georgia Charkoftaki, Ying Chen, Ming Han, Monica Sandoval, Xiaoqing Yu, Hongyu Zhao, David J Orlicky, David C Thompson, Vasilis Vasiliou
ALDH16A1 is a novel member of the ALDH superfamily that is enzymatically-inactive and highly expressed in the kidney. Recent studies identified an association between a rare missense single nucleotide variant (SNV) in the ALDH16A1 gene and elevated serum uric acid levels and gout. The present study explores the mechanisms by which ALDH16A1 influences uric acid homeostasis in the kidney. We generated and validated a mouse line with global disruption of the Aldh16a1 gene through gene targeting and performed RNA-seq analyses in the kidney of wild-type (WT) and Aldh16a1 knockout (KO) mice, along with plasma metabolomics...
February 28, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28242600/the-susceptibility-gene-screening-in-a-chinese-high-altitude-pulmonary-edema-family-by-whole-exome-sequencing
#10
Yang Yingzhong, Wang Yaping, Xu Jin, Ge Rili
High-altitude pulmonary edema (HAPE) is one of idiopathic mountain sicknesses that occur in healthy lowlanders when they quickly ascend to altitudes exceeding 2500 m above sea levels within 1-7 days. Growing evidence suggests that genetics plays an important role in the risk of HAPE. In this study, we recruited a Chinese HAPE family and screened genetic variations in the 7 family members (including 6 family members with a medical history of HAPE and the propositus's mother) by whole-exome sequencing. The results showed 18 genetic variations (9 SNVs and 9 Indels) were related to HAPE...
February 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28224495/hidden-markov-models-in-bioinformatics-snv-inference-from-next-generation-sequence
#11
Jiawen Bian, Xiaobo Zhou
The rapid development of next generation sequencing (NGS) technology provides a novel avenue for genomic exploration and research. Hidden Markov models (HMMs) have wide applications in pattern recognition as well as Bioinformatics such as transcription factor binding sites and cis-regulatory modules detection. An application of HMM is introduced in this chapter with the in-deep developing of NGS. Single nucleotide variants (SNVs) inferred from NGS are expected to reveal gene mutations in cancer. However, NGS has lower sequence coverage and poor SNV detection capability in the regulatory regions of the genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28213210/comparison-of-sensitivity-to-artificial-spectral-errors-and-multivariate-lod-in-nir-spectroscopy-determining-the-performance-of-miniaturizations-on-melamine-in-milk-powder
#12
Raphael Henn, Christian G Kirchler, Maria-Elisabeth Grossgut, Christian W Huck
This study compared three commercially available spectrometers - whereas two of them were miniaturized - in terms of prediction ability of melamine in milk powder (infant formula). Therefore all spectra were split into calibration- and validation-set using Kennard Stone and Duplex algorithm in comparison. For each instrument the three best performing PLSR models were constructed using SNV and Savitzky Golay derivatives. The best RMSEP values were 0.28g/100g, 0.33g/100g and 0.27g/100g for the NIRFlex N-500, the microPHAZIR and the microNIR2200 respectively...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28192086/variant-call-concordance-between-two-laboratory-developed-solid-tumor-targeted-genomic-profiling-assays-using-distinct-workflows-and-sequencing-instruments
#13
Ken J Hampel, Francine B de Abreu, Nikoletta Sidiropoulos, Jason D Peterson, Gregory J Tsongalis
Targeted genomic profiling (TGP) using massively parallel DNA sequencing is becoming the standard methodology in clinical laboratories for detecting somatic variants in solid tumors. The variety of methodologies and sequencing platforms in the marketplace for TGP has resulted in a variety of clinical TGP laboratory developed tests (LDT). The variability of LDTs is a challenge for test-to-test and laboratory-to-laboratory reliability. At the University of Vermont Medical Center (UVMMC), we validated a TGP assay for solid tumors which utilizes DNA hybridization capture and complete exon and selected intron sequencing of 29 clinically actionable genes...
February 10, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28190458/detection-of-imprinted-genes-by-single-cell-allele-specific-gene-expression
#14
Federico A Santoni, Georgios Stamoulis, Marco Garieri, Emilie Falconnet, Pascale Ribaux, Christelle Borel, Stylianos E Antonarakis
Genomic imprinting results in parental-specific gene expression. Imprinted genes are involved in the etiology of rare syndromes and have been associated with common diseases such as diabetes and cancer. Standard RNA bulk cell sequencing applied to whole-tissue samples has been used to detect imprinted genes in human and mouse models. However, lowly expressed genes cannot be detected by using RNA bulk approaches. Here, we report an original and robust method that combines single-cell RNA-seq and whole-genome sequencing into an optimized statistical framework to analyze genomic imprinting in specific cell types and in different individuals...
March 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28176830/distribution-bias-analysis-of-germline-and-somatic-single-nucleotide-variations-that-impact-protein-functional-site-and-neighboring-amino-acids
#15
Yang Pan, Cheng Yan, Yu Hu, Yu Fan, Qing Pan, Quan Wan, John Torcivia-Rodriguez, Raja Mazumder
Single nucleotide variations (SNVs) can result in loss or gain of protein functional sites. We analyzed the effects of SNVs on enzyme active sites, ligand binding sites, and various types of post translational modification (PTM) sites. We found that, for most types of protein functional sites, the SNV pattern differs between germline and somatic mutations as well as between synonymous and non-synonymous mutations. From a total of 51,138 protein functional site affecting SNVs (pfsSNVs), a pan-cancer analysis revealed 142 somatic pfsSNVs in five or more cancer types...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28122645/a-variant-by-any-name-quantifying-annotation-discordance-across-tools-and-clinical-databases
#16
Jennifer L Yen, Sarah Garcia, Aldrin Montana, Jason Harris, Stephen Chervitz, Massimo Morra, John West, Richard Chen, Deanna M Church
BACKGROUND: Clinical genomic testing is dependent on the robust identification and reporting of variant-level information in relation to disease. With the shift to high-throughput sequencing, a major challenge for clinical diagnostics is the cross-identification of variants called on their genomic position to resources that rely on transcript- or protein-based descriptions. METHODS: We evaluated the accuracy of three tools (SnpEff, Variant Effect Predictor, and Variation Reporter) that generate transcript and protein-based variant nomenclature from genomic coordinates according to guidelines by the Human Genome Variation Society (HGVS)...
January 26, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28118013/domino-c-f-bond-activation-of-the-cf3-group-synthesis-of-fluorinated-dibenzo-a-c-7-annulenes-from-2-trifluoromethyl-1-alkenes-and-2-2-diceriobiaryls
#17
Takeshi Fujita, Marina Takazawa, Kazuki Sugiyama, Naoto Suzuki, Junji Ichikawa
The construction of ring-fluorinated seven-membered carbocycles was readily achieved via the domino SN2'-type/SNV reaction between 2-(trifluoromethyl)-1-alkenes and 1,4-carbodianions. The SN2'-type reaction of 2-(trifluoromethyl)-1-alkenes with 2,2'-diceriobiaryls generated the intermediary 1,1-difluoro-1-alkenes bearing a monoceriobiaryl moiety, which in turn underwent intramolecular SNV reaction to afford fluorinated 5H-dibenzo[a,c][7]annulenes.
January 24, 2017: Organic Letters
https://www.readbyqxmd.com/read/28117402/whole-exome-sequencing-of-228-patients-with-sporadic-parkinson-s-disease
#18
Cynthia Sandor, Frantisek Honti, Wilfried Haerty, Konrad Szewczyk-Krolikowski, Paul Tomlinson, Sam Evetts, Stephanie Millin, Thomas Keane, Shane A McCarthy, Richard Durbin, Kevin Talbot, Michele Hu, Caleb Webber, Chris P Ponting, Richard Wade-Martins
Parkinson's disease (PD) is the most common neurodegenerative movement disorder, affecting 1% of the population over 65 years characterized clinically by both motor and non-motor symptoms accompanied by the preferential loss of dopamine neurons in the substantia nigra pars compacta. Here, we sequenced the exomes of 244 Parkinson's patients selected from the Oxford Parkinson's Disease Centre Discovery Cohort and, after quality control, 228 exomes were available for analyses. The PD patient exomes were compared to 884 control exomes selected from the UK10K datasets...
January 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28113701/super-normal-vector-for-human-activity-recognition-with-depth-cameras
#19
Xiaodong Yang, YingLi Tian
The advent of cost-effectiveness and easy-operation depth cameras has facilitated a variety of visual recognition tasks including human activity recognition. This paper presents a novel framework for recognizing human activities from video sequences captured by depth cameras. We extend the surface normal to polynormal by assembling local neighboring hypersurface normals from a depth sequence to jointly characterize local motion and shape information. We then propose a general scheme of super normal vector (SNV) to aggregate the low-level polynormals into a discriminative representation, which can be viewed as a simplified version of the Fisher kernel representation...
May 10, 2016: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28109504/mutational-analysis-of-gsc-hoxa2-and-prkra-in-106-chinese-patients-with-microtia
#20
Shaojuan Hao, Lei Jin, Chenlong Li, Huijun Wang, Fengyun Zheng, Duan Ma, Tianyu Zhang
OBJECTIVE: Microtia is defined as a developmental malformation characterized by a small, abnormal shaped auricle, with atresia or stenosis of the auditory canal. Genes responsible for nonsyndromic microtia have remained elusive. We therefore report a mutational analysis of GSC, HOXA2 and PRKRA in 106 congenital microtia patients without any combined malformation to explore the relationship between GSC, HOXA2, PRKRA and nonsyndromic microtia. METHODS: A total of 106 patients with a clinical diagnosis of congenital microtia and a control group (100 unaffected controls) were recruited through the Eye and ENT Hospital of Fudan University in China...
February 2017: International Journal of Pediatric Otorhinolaryngology
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