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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
#1
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
#2
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...
February 6, 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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/28106558/validation-of-suspected-somatic-single-nucleotide-variations-in-the-brain-of-alzheimer-s-disease-patients
#9
Alberto Gomez-Ramos, Angel J Picher, Esther García, Patricia Garrido, Felix Hernandez, Eduardo Soriano, Jesús Avila
Next-generation sequencing techniques and genome-wide association study analyses have provided a huge amount of data, thereby enabling the identification of DNA variations and mutations related to disease pathogenesis. New techniques and software tools have been developed to improve the accuracy and reliability of this identification. Most of these tools have been designed to discover and validate single nucleotide variants (SNVs). However, in addition to germ-line mutations, human tissues bear genomic mosaicism, which implies that somatic events are present only in low percentages of cells within a given tissue, thereby hindering the validation of these variations using standard genetic tools...
January 19, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28103211/notes-from-the-field-hantavirus-pulmonary-syndrome-in-a-migrant-farm-worker-colorado-2016
#10
Grace Marx, Kaylan Stinson, Monte Deatrich, Bernadette Albanese
HASH(0x45f1978)
20, 2017: MMWR. Morbidity and Mortality Weekly Report
https://www.readbyqxmd.com/read/28100066/identification-of-eggs-from-different-production-systems-based-on-hyperspectra-and-cs-svm
#11
J Sun, S Cong, H Mao, X Zhou, X Wu, X Zhang
1. To identify the origin of table eggs more accurately, a method based on hyperspectral imaging technology was studied. 2. The hyperspectral data of 200 samples of intensive and extensive eggs were collected. Standard normalised variables (SNV) combined with Savitzky-Golay (SG) were used to eliminate noise, then stepwise regression (SWR) was used for feature selection. Grid search algorithm (GS), genetic search algorithm (GA), particle swarm optimisation algorithm (PSO) and cuckoo search algorithm (CS) were applied by support vector machine (SVM) to establish a SVM identification model with the optimal parameters...
January 19, 2017: British Poultry Science
https://www.readbyqxmd.com/read/28093192/spectrum-of-mutations-in-leiomyosarcomas-identified-by-clinical-targeted-next-generation-sequencing
#12
Paul J Lee, Naomi S Yoo, Ian S Hagemann, John D Pfeifer, Catherine E Cottrell, Haley J Abel, Eric J Duncavage
Recurrent genomic mutations in uterine and non-uterine leiomyosarcomas have not been well established. Using a next generation sequencing (NGS) panel of common cancer-associated genes, 25 leiomyosarcomas arising from multiple sites were examined to explore genetic alterations, including single nucleotide variants (SNV), small insertions/deletions (indels), and copy number alterations (CNA). Sequencing showed 86 non-synonymous, coding region somatic variants within 151 gene targets in 21 cases, with a mean of 4...
January 14, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28074849/genetic-variants-identified-from-epilepsy-of-unknown-etiology-in-chinese-children-by-targeted-exome-sequencing
#13
Yimin Wang, Xiaonan Du, Rao Bin, Shanshan Yu, Zhezhi Xia, Guo Zheng, Jianmin Zhong, Yunjian Zhang, Yong-Hui Jiang, Yi Wang
Genetic factors play a major role in the etiology of epilepsy disorders. Recent genomics studies using next generation sequencing (NGS) technique have identified a large number of genetic variants including copy number (CNV) and single nucleotide variant (SNV) in a small set of genes from individuals with epilepsy. These discoveries have contributed significantly to evaluate the etiology of epilepsy in clinic and lay the foundation to develop molecular specific treatment. However, the molecular basis for a majority of epilepsy patients remains elusive, and furthermore, most of these studies have been conducted in Caucasian children...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28062191/tracking-hcv-protease-population-diversity-during-transmission-and-susceptibility-of-founder-populations-to-antiviral-therapy
#14
Tanvi Khera, Daniel Todt, Koen Vercauteren, C Patrick McClure, Lieven Verhoye, Ali Farhoudi, Sabin Bhuju, Robert Geffers, Thomas F Baumert, Eike Steinmann, Philip Meuleman, Thomas Pietschmann, Richard J P Brown
Due to the highly restricted species-tropism of Hepatitis C virus (HCV) a limited number of animal models exist for pre-clinical evaluation of vaccines and antiviral compounds. The human-liver chimeric mouse model allows heterologous challenge with clinically relevant strains derived from patients. However, to date, the transmission and longitudinal evolution of founder viral populations in this model have not been characterized in-depth using state-of-the-art sequencing technologies. Focusing on NS3 protease encoding region of the viral genome, mutant spectra in a donor inoculum and individual recipient mice were determined via Illumina sequencing and compared, to determine the effects of transmission on founder viral population complexity...
March 2017: Antiviral Research
https://www.readbyqxmd.com/read/28032522/platelet-genomics-the-role-of-platelet-size-and-number-in-health-and-disease
#15
Diane Nugent, Thomas Kunicki
Taken together, there is ample evidence of the association of cardiovascular disease, cerebrovascular, and inflammatory disease with single nucleotide variants (SNV) due to their impact on platelet size, number, and function. With the use of electronic medical record (EMR) or other phenotypic-linked bioinformatics sources, the more important "functional" variants are emerging and provide valuable information on their specific role in promoting early onset of disease or poor response to therapeutic measures...
January 2017: Platelets
https://www.readbyqxmd.com/read/28029147/snp-variants-at-the-map3k1-setd9-locus-5q11-2-associate-with-somatic-pik3ca-variants-in-breast-cancers
#16
Roberto Puzone, Ulrich Pfeffer
Genome-wide association studies have revealed many breast cancer (BC) risk-associated genetic variants that might functionally interact with other molecular determinants of BC. We analysed the association of 21 known risk-associated single-nucleotide variants (SNVs) with recurrent somatic variants in two cohorts of 77 and 754 oestrogen receptor α-positive BCs. Four SNVs located at 5q11.2 were found to be associated with the somatic PIK3CA variant status in the pilot cohort of 77 cases with odds ratio (OR) up to 6...
February 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/27999612/purecn-copy-number-calling-and-snv-classification-using-targeted-short-read-sequencing
#17
Markus Riester, Angad P Singh, A Rose Brannon, Kun Yu, Catarina D Campbell, Derek Y Chiang, Michael P Morrissey
BACKGROUND: Matched sequencing of both tumor and normal tissue is routinely used to classify variants of uncertain significance (VUS) into somatic vs. germline. However, assays used in molecular diagnostics focus on known somatic alterations in cancer genes and often only sequence tumors. Therefore, an algorithm that reliably classifies variants would be helpful for retrospective exploratory analyses. Contamination of tumor samples with normal cells results in differences in expected allelic fractions of germline and somatic variants, which can be exploited to accurately infer genotypes after adjusting for local copy number...
2016: Source Code for Biology and Medicine
https://www.readbyqxmd.com/read/27987181/association-of-snps-in-dopamine-and-serotonin-pathway-genes-and-their-interacting-genes-with-temperament-traits-in-charolais-cows
#18
E Garza-Brenner, A M Sifuentes-Rincón, R D Randel, F A Paredes-Sánchez, G M Parra-Bracamonte, W Arellano Vera, F A Rodríguez Almeida, A Segura Cabrera
Cattle temperament is a complex trait, and molecular studies aimed at defining this trait are scarce. We used an interaction networks approach to identify new genes (interacting genes) and to estimate their effects and those of 19 dopamine- and serotonin-related genes on the temperament traits of Charolais cattle. The genes proopiomelanocortin (POMC), neuropeptide Y (NPY), solute carrier family 18, member 2 (SLC18A2) and FBJ murine osteosarcoma viral oncogene homologue (FOSFBJ) were identified as new candidates...
December 16, 2016: Journal of Applied Genetics
https://www.readbyqxmd.com/read/27986441/silent-genetic-alterations-identified-by-targeted-next-generation-sequencing-in-pheochromocytoma-paraganglioma-a-clinicopathological-correlations
#19
Suja Pillai, Vinod Gopalan, Chung Y Lo, Victor Liew, Robert A Smith, Alfred King Y Lam
AIMS: The goal of this pilot study was to develop a customized, cost-effective amplicon panel (Ampliseq) for target sequencing in a cohort of patients with sporadic phaeochromocytoma/paraganglioma. METHODS: Phaeochromocytoma/paragangliomas from 25 patients were analysed by targeted next-generation sequencing approach using an Ion Torrent PGM instrument. Primers for 15 target genes (NF1, RET, VHL, SDHA, SDHB, SDHC, SDHD, SDHAF2, TMEM127, MAX, MEN1, KIF1Bβ, EPAS1, CDKN2 & PHD2) were designed using ion ampliseq designer...
December 13, 2016: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/27964748/non-coding-single-nucleotide-variants-affecting-estrogen-receptor-binding-and-activity
#20
Amir Bahreini, Kevin Levine, Lucas Santana-Santos, Panayiotis V Benos, Peilu Wang, Courtney Andersen, Steffi Oesterreich, Adrian V Lee
BACKGROUND: Estrogen receptor (ER) activity is critical for the development and progression of the majority of breast cancers. It is known that ER is differentially bound to DNA leading to transcriptomic and phenotypic changes in different breast cancer models. We investigated whether single nucleotide variants (SNVs) in ER binding sites (regSNVs) contribute to ER action through changes in the ER cistrome, thereby affecting disease progression. Here we developed a computational pipeline to identify SNVs in ER binding sites using chromatin immunoprecipitation sequencing (ChIP-seq) data from ER+ breast cancer models...
December 13, 2016: Genome Medicine
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