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https://www.readbyqxmd.com/read/28109504/mutational-analysis-of-gsc-hoxa2-and-prkra-in-106-chinese-patients-with-microtia
#1
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
#2
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
#3
Grace Marx, Kaylan Stinson, Monte Deatrich, Bernadette Albanese
HASH(0x3401678)
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
#4
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
#5
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 13, 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
#6
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
#7
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...
January 3, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28032522/platelet-genomics-the-role-of-platelet-size-and-number-in-health-and-disease
#8
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
#9
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...
December 28, 2016: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/27999612/purecn-copy-number-calling-and-snv-classification-using-targeted-short-read-sequencing
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/27918147/genome-analysis-of-a-hyper-acetone-butanol-ethanol-abe-producing-clostridium-acetobutylicum-bkm19
#14
Changhee Cho, Donghui Choe, Yu-Sin Jang, Kyung-Jin Kim, Won Jun Kim, Byung-Kwan Cho, E Terry Papoutsakis, George N Bennett, Do Young Seung, Sang Yup Lee
We previously reported development of a hyper acetone-butanol-ethanol (ABE) producing Clostridium acetobutylicum BKM19 strain capable of producing 30.5% more total solvent by random mutagenesis of its parental strain PJC4BK, which is a buk mutant C. acetobutylicum ATCC 824 strain. Here BKM19 and PJC4BK strains were re-sequenced by a high-throughput sequencing technique to understand the mutations responsible for enhanced solvent production. In comparison with the C. acetobutylicum PJC4BK, 13 single nucleotide variants (SNVs), 1 deletion and 1 back mutation SNV were identified in the C...
December 5, 2016: Biotechnology Journal
https://www.readbyqxmd.com/read/27897270/trueprime-is-a-novel-method-for-whole-genome-amplification-from-single-cells-based-on-tthprimpol
#15
Ángel J Picher, Bettina Budeus, Oliver Wafzig, Carola Krüger, Sara García-Gómez, María I Martínez-Jiménez, Alberto Díaz-Talavera, Daniela Weber, Luis Blanco, Armin Schneider
Sequencing of a single-cell genome requires DNA amplification, a process prone to introducing bias and errors into the amplified genome. Here we introduce a novel multiple displacement amplification (MDA) method based on the unique DNA primase features of Thermus thermophilus (Tth) PrimPol. TthPrimPol displays a potent primase activity preferring dNTPs as substrates unlike conventional primases. A combination of TthPrimPol's unique ability to synthesize DNA primers with the highly processive Phi29 DNA polymerase (Φ29DNApol) enables near-complete whole genome amplification from single cells...
November 29, 2016: Nature Communications
https://www.readbyqxmd.com/read/27881071/genome-wide-analyses-of-chitin-synthases-identify-horizontal-gene-transfers-towards-bacteria-and-allow-a-robust-and-unifying-classification-into-fungi
#16
Isabelle R Gonçalves, Sophie Brouillet, Marie-Christine Soulié, Simonetta Gribaldo, Catherine Sirven, Noémie Charron, Martine Boccara, Mathias Choquer
BACKGROUND: Chitin, the second most abundant biopolymer on earth after cellulose, is found in probably all fungi, many animals (mainly invertebrates), several protists and a few algae, playing an essential role in the development of many of them. This polysaccharide is produced by type 2 glycosyltransferases, called chitin synthases (CHS). There are several contradictory classifications of CHS isoenzymes and, as regards their evolutionary history, their origin and diversity is still a matter of debate...
November 24, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27874022/in-depth-comparison-of-somatic-point-mutation-callers-based-on-different-tumor-next-generation-sequencing-depth-data
#17
Lei Cai, Wei Yuan, Zhou Zhang, Lin He, Kuo-Chen Chou
Four popular somatic single nucleotide variant (SNV) calling methods (Varscan, SomaticSniper, Strelka and MuTect2) were carefully evaluated on the real whole exome sequencing (WES, depth of ~50X) and ultra-deep targeted sequencing (UDT-Seq, depth of ~370X) data. The four tools returned poor consensus on candidates (only 20% of calls were with multiple hits by the callers). For both WES and UDT-Seq, MuTect2 and Strelka obtained the largest proportion of COSMIC entries as well as the lowest rate of dbSNP presence and high-alternative-alleles-in-control calls, demonstrating their superior sensitivity and accuracy...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27863959/transmission-of-staphylococcus-aureus-between-health-care-workers-the-environment-and-patients-in-an-intensive-care-unit-a-longitudinal-cohort-study-based-on-whole-genome-sequencing
#18
James R Price, Kevin Cole, Andrew Bexley, Vasiliki Kostiou, David W Eyre, Tanya Golubchik, Daniel J Wilson, Derrick W Crook, A Sarah Walker, Timothy E A Peto, Martin J Llewelyn, John Paul
BACKGROUND: Health-care workers have been implicated in nosocomial outbreaks of Staphylococcus aureus, but the dearth of evidence from non-outbreak situations means that routine health-care worker screening and S aureus eradication are controversial. We aimed to determine how often S aureus is transmitted from health-care workers or the environment to patients in an intensive care unit (ICU) and a high-dependency unit (HDU) where standard infection control measures were in place. METHODS: In this longitudinal cohort study, we systematically sampled health-care workers, the environment, and patients over 14 months at the ICU and HDU of the Royal Sussex County Hospital, Brighton, England...
November 15, 2016: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/27826616/development-and-validation-of-an-ultra-high-sensitive-next-generation-sequencing-assay-for-molecular-diagnosis-of-clinical-oncology
#19
Jiao Liang, Yaoguang She, Jiaqi Zhu, Longgang Wei, Lanying Zhang, Lianju Gao, Yan Wang, Jing Xing, Yang Guo, Xuehong Meng, Peiyu Li
Dramatic improvements in the understanding of oncogenes have spurred the development of molecular target therapies, which created an exigent need for comprehensive and rapid clinical genotyping. Next-generation sequencing (NGS) assay with increased performance and decreased cost is becoming more widely used in clinical diagnosis. However, the optimization and validation of NGS assay remain a challenge, especially for the detection of somatic variants at low mutant allele fraction (MAF). In the present study, we developed and validated the Novogene Comprehensive Panel (NCP) based on targeted capture for NGS analysis...
November 2016: International Journal of Oncology
https://www.readbyqxmd.com/read/27822544/multiplexed-metagenomic-deep-sequencing-to-analyze-the-composition-of-high-priority-pathogen-reagents
#20
Michael R Wilson, Greg Fedewa, Mark D Stenglein, Judith Olejnik, Linda J Rennick, Sham Nambulli, Friederike Feldmann, W Paul Duprex, John H Connor, Elke Mühlberger, Joseph L DeRisi
Laboratories studying high-priority pathogens need comprehensive methods to confirm microbial species and strains while also detecting contamination. Metagenomic deep sequencing (MDS) inventories nucleic acids present in laboratory stocks, providing an unbiased assessment of pathogen identity, the extent of genomic variation, and the presence of contaminants. Double-stranded cDNA MDS libraries were constructed from RNA extracted from in vitro-passaged stocks of six viruses (La Crosse virus, Ebola virus, canine distemper virus, measles virus, human respiratory syncytial virus, and vesicular stomatitis virus)...
July 2016: MSystems
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