keyword
MENU ▼
Read by QxMD icon Read
search

Targeted sequencing

keyword
https://www.readbyqxmd.com/read/28750222/assessing-the-relevance-of-a-multiplexed-methodology-for-proteomic-biomarker-measurement-in-the-invertebrate-species-gammarus-fossarum-a-physiological-and-ecotoxicological-study
#1
D Gouveia, A Chaumot, A Charnot, H Queau, J Armengaud, C Almunia, A Salvador, O Geffard
Recently, a protein sequence database was built specifically for the sentinel non-model species Gammarus fossarum using a proteogenomics approach. A quantitative multiplexed targeted proteomics assay (using Selected Reaction Monitoring mass spectrometry) was then developed for a fast and simultaneous quantification of dozens of biomarker peptides specific of this freshwater sentinel crustacean species. In order to assess the relevance of this breakthrough methodology in ecotoxicology, the response patterns of a panel of 26 peptides reporting for 20 proteins from the Gammarus fossarum proteome with putative key functional roles (homeostasis, osmoregulation, nutrition, reproduction, molting,…) were recorded through male and female reproductive cycles and after exposure to environmental concentrations of cadmium and lead in laboratory-controlled conditions...
July 17, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28750119/minimal-residual-disease-in-chronic-lymphocytic-leukemia-in-the-era-of-novel-agents-a-review
#2
Meghan Thompson, Danielle Brander, Chadi Nabhan, Anthony Mato
Importance: The landscape of chronic lymphocytic leukemia (CLL) treatment has changed considerably since the first reported assessment of minimal residual disease (MRD) by flow cytometry in 1992. Chemoimmunotherapy (CIT) combinations have become the standard of care for most patients, and novel targeted agents are rapidly being incorporated into the front-line and relapsed settings. Minimal residual disease status has been shown to be a predictor of both progression-free survival (PFS) and overall survival (OS) at the time of response assessment following CIT, but less is known about the relationship between MRD and outcomes after novel oral therapeutics...
July 27, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28750076/targeted-next-generation-sequencing-detects-novel-gene-phenotype-associations-and-expands-the-mutational-spectrum-in-cardiomyopathies
#3
Cinzia Forleo, Anna Maria D'Erchia, Sandro Sorrentino, Caterina Manzari, Matteo Chiara, Massimo Iacoviello, Andrea Igoren Guaricci, Delia De Santis, Rita Leonarda Musci, Antonino La Spada, Vito Marangelli, Graziano Pesole, Stefano Favale
Cardiomyopathies are a heterogeneous group of primary diseases of the myocardium, including hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), and arrhythmogenic right ventricular cardiomyopathy (ARVC), with higher morbidity and mortality. These diseases are genetically diverse and associated with rare mutations in a large number of genes, many of which overlap among the phenotypes. To better investigate the genetic overlap between these three phenotypes and to identify new genotype-phenotype correlations, we designed a custom gene panel consisting of 115 genes known to be associated with cardiomyopathic phenotypes and channelopathies...
2017: PloS One
https://www.readbyqxmd.com/read/28750054/assisted-design-of-antibody-and-protein-therapeutics-adapt
#4
Victor Vivcharuk, Jason Baardsnes, Christophe Deprez, Traian Sulea, Maria Jaramillo, Christopher R Corbeil, Alaka Mullick, Joanne Magoon, Anne Marcil, Yves Durocher, Maureen D O'Connor-McCourt, Enrico O Purisima
Effective biologic therapeutics require binding affinities that are fine-tuned to their disease-related molecular target. The ADAPT (Assisted Design of Antibody and Protein Therapeutics) platform aids in the selection of mutants that improve/modulate the affinity of antibodies and other biologics. It uses a consensus z-score from three scoring functions and interleaves computational predictions with experimental validation, significantly enhancing the robustness of the design and selection of mutants. The platform was tested on three antibody Fab-antigen systems that spanned a wide range of initial binding affinities: bH1-VEGF-A (44 nM), bH1-HER2 (3...
2017: PloS One
https://www.readbyqxmd.com/read/28750049/genome-target-evaluator-gtevaluator-a-workflow-exploiting-genome-dataset-to-measure-the-sensitivity-and-specificity-of-genetic-markers
#5
Arnaud Felten, Laurent Guillier, Nicolas Radomski, Michel-Yves Mistou, Renaud Lailler, Sabrina Cadel-Six
Most of the bacterial typing methods used to discriminate isolates in medical or food safety microbiology are based on genetic markers used as targets in PCR or hybridization experiments. These DNA typing methods are important tools for studying prevalence and epidemiology, for conducting surveillance, investigations and control of biological hazard sources. In that perspective, it is crucial to insure that the chosen genetic markers have the greatest specificity and sensitivity. The wealth of whole-genome sequences available for many bacterial species offers the opportunity to evaluate the performance of these genetic markers...
2017: PloS One
https://www.readbyqxmd.com/read/28750028/clinical-impact-of-a-targeted-next-generation-sequencing-gene-panel-for-autoinflammation-and-vasculitis
#6
Ebun Omoyinmi, Ariane Standing, Annette Keylock, Fiona Price-Kuehne, Sonia Melo Gomes, Dorota Rowczenio, Sira Nanthapisal, Thomas Cullup, Rodney Nyanhete, Emma Ashton, Claire Murphy, Megan Clarke, Helena Ahlfors, Lucy Jenkins, Kimberly Gilmour, Despina Eleftheriou, Helen J Lachmann, Philip N Hawkins, Nigel Klein, Paul A Brogan
BACKGROUND: Monogenic autoinflammatory diseases (AID) are a rapidly expanding group of genetically diverse but phenotypically overlapping systemic inflammatory disorders associated with dysregulated innate immunity. They cause significant morbidity, mortality and economic burden. Here, we aimed to develop and evaluate the clinical impact of a NGS targeted gene panel, the "Vasculitis and Inflammation Panel" (VIP) for AID and vasculitis. METHODS: The Agilent SureDesign tool was used to design 2 versions of VIP; VIP1 targeting 113 genes, and a later version, VIP2, targeting 166 genes...
2017: PloS One
https://www.readbyqxmd.com/read/28749987/dude-seq-fast-flexible-and-robust-denoising-for-targeted-amplicon-sequencing
#7
Byunghan Lee, Taesup Moon, Sungroh Yoon, Tsachy Weissman
We consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high throughput, but the associated error rates often tend to be high. Denoising in high-throughput sequencing has thus become a crucial process for boosting the reliability of downstream analyses. Our methodology, named DUDE-Seq, is derived from a general setting of reconstructing finite-valued source data corrupted by a discrete memoryless channel and effectively corrects substitution and homopolymer indel errors, the two major types of sequencing errors in most high-throughput targeted amplicon sequencing platforms...
2017: PloS One
https://www.readbyqxmd.com/read/28749938/the-mecillinam-resistome-reveals-a-role-for-peptidoglycan-endopeptidases-in-stimulating-cell-wall-synthesis-in-escherichia-coli
#8
Ghee Chuan Lai, Hongbaek Cho, Thomas G Bernhardt
Bacterial cells are typically surrounded by an net-like macromolecule called the cell wall constructed from the heteropolymer peptidoglycan (PG). Biogenesis of this matrix is the target of penicillin and related beta-lactams. These drugs inhibit the transpeptidase activity of PG synthases called penicillin-binding proteins (PBPs), preventing the crosslinking of nascent wall material into the existing network. The beta-lactam mecillinam specifically targets the PBP2 enzyme in the cell elongation machinery of Escherichia coli...
July 27, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28749613/linked-selection-demography-and-the-evolution-of-correlated-genomic-landscapes-in-birds-and-beyond
#9
Reto Burri
Selection has a deep impact on the distribution of genetic diversity and population differentiation along the genome (the genomic landscapes of diversity and differentiation), reducing diversity and elevating differentiation not only at the sites it targets, but also at linked neutral sites. Fuelled by the high-throughput sequencing revolution, these genomic footprints of selection have been extensively exploited over the past decade with the aim to identify genomic regions involved in adaptation and speciation...
August 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28749585/mir3954-is-a-trigger-of-phasirnas-that-affects-flowering-time-in-citrus
#10
Yuanlong Liu, Lili Ke, Guizhi Wu, Yuantao Xu, Xiaomeng Wu, Rui Xia, Xiuxin Deng, Qiang Xu
In plant, a few 22 nt miRNAs direct cleavages of their targets and trigger the biogenesis of phased small interfering RNAs (phasiRNAs) in plant. In this study, we characterized a miRNA triggering phasiRNAs generation, miR3954, and explored its downstream target genes and potential function. Our results demonstrated that miR3954 showed specific expression in the flowers of citrus species and it targeted a NAC transcription factor (Cs7g22460) and two non-coding RNA transcripts (lncRNAs, Cs1g09600 and Cs1g09635)...
July 27, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28748912/a-novel-allosteric-site-in-casein-kinase-2%C3%AE-discovered-using-combining-bioinformatics-and-biochemistry-methods
#11
Hai-Ming Jiang, Jiang-Kai Dong, Kun Song, Tong-Dan Wang, Wen-Kang Huang, Jing-Miao Zhang, Xiu-Yan Yang, Ying Shen, Jian Zhang
Casein kinase 2 (CK2) is a highly pleiotropic serine-threonine kinase, which catalyzed phosphorylation of more than 300 proteins that are implicated in regulation of many cellular functions, such as signal transduction, transcriptional control, apoptosis and the cell cycle. On the other hand, CK2 is abnormally elevated in a variety of tumors, and is considered as a promising therapeutic target. The currently available ATP-competitive CK2 inhibitors, however, lack selectivity, which has impeded their development in cancer therapy...
July 27, 2017: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/28748849/a-novel-missense-mutation-in-peripheral-myelin-protein-22-causes-charcot-marie-tooth-disease
#12
Li-Xi Li, Hai-Lin Dong, Bao-Guo Xiao, Zhi-Ying Wu
BACKGROUND: Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy. A great number of causative genes have been described in CMT, and among them, the heterozygous duplication of peripheral myelin protein-22 (PMP22) is the major cause. Although the missense mutation in PMP22 is rarely reported, it has been demonstrated to be associated with CMT. This study described a novel missense mutation of PMP22 in a Chinese family with CMT phenotype. METHODS: Targeted next-generation sequencing (NGS) was used to screen the causative genes in a family featured with an autosomal dominant demyelinating form of CMT...
August 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28748739/multiplex-pcr-assay-discriminates-rabbit-rat-and-squirrel-meat-in-food-chain
#13
Mohammad Nasir Uddin Ahamad, Md Eaqub Ali, M A Motalib Hossain, Asing Asing, Sharmin Sultana, M H A Jahurul
Rabbit meat is receiving increasing attention because it contains more proteins and less fat. On the other hand, squirrel meat is served in aristocrat meals in certain countries and so it is sold at higher prices. The other side of the coin is rat meat that has family ties with rabbit and squirrel but possesses huge threats to public health because it is a potential career of several zoonotic organisms. Recently, rat meat was mislabeled and sold as lamb after chemical modification. Thus the chances of rabbit and squirrel meat substitution by rat meat cannot be ruled out...
July 27, 2017: Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment
https://www.readbyqxmd.com/read/28748721/real-world-costs-and-outcomes-in-metastatic-renal-cell-carcinoma-patients-treated-by-targeted-therapies-a-cohort-study-from-the-french-health-insurance-database
#14
Rana Maroun, Laetitia Fleury, Gaelle Nachbaur, Franck Maunoury, Jean-Louis Vanhille, Isabelle Durand-Zaleski
OBJECTIVES: The objective of this study was to describe treatment patterns, survival, healthcare use and costs in patients with metastatic renal cell carcinoma (mRCC) in a real-world setting. RESEARCH DESIGN AND METHODS: We used the National Health Insurance (NHI) claims database for the Ile-de-France region to perform a retrospective cohort analysis of patients with mRCC treated by a first-line targeted therapy. Treatment naïve patients were identified combining the 10(th) revision of the International Classification of Diseases (ICD-10) codes (C64 & C77-C79) and a first prescription of targeted therapies...
July 27, 2017: Current Medical Research and Opinion
https://www.readbyqxmd.com/read/28748648/accurate-template-based-modelling-in-casp12-using-the-intfold4-ts-modfold6-and-refold-methods
#15
Liam J McGuffin, Ahmad N Shuid, Robert Kempster, Ali H A Maghrabi, John O Nealon, Bajuna R Salehe, Jennifer D Atkins, Daniel B Roche
Our aim in CASP12 was to improve our Template Based Modelling (TBM) methods through better model selection, accuracy self-estimate (ASE) scores and refinement. To meet these aims we developed two new automated methods, which we used to score, rank and improve upon the provided server models. Firstly, the ModFOLD6_rank method, for improved global Quality Assessment (QA), model ranking and the detection of local errors. Secondly, the ReFOLD method for fixing errors through iterative QA guided refinement. For our automated predictions we developed the IntFOLD4-TS protocol, which integrates the ModFOLD6_rank method for scoring the multiple-template models that were generated using a number of alternative sequence-structure alignments...
July 27, 2017: Proteins
https://www.readbyqxmd.com/read/28748644/diversity-and-stability-of-coral-endolithic-microbial-communities-at-a-naturally-high-pco2-reef
#16
Vanessa R Marcelino, Kathleen M Morrow, Madeleine J H van Oppen, David G Bourne, Heroen Verbruggen
The health and functioning of reef-building corals is dependent on a balanced association with prokaryotic and eukaryotic microbes. The coral skeleton harbours numerous endolithic microbes, but their diversity, ecological roles and responses to environmental stress, including ocean acidification, are not well characterized. This study tests whether pH affects the diversity and structure of prokaryotic and eukaryotic algal communities associated with skeletons of Porites spp. using targeted amplicon (16S rRNA gene, UPA and tufA) sequencing...
July 27, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28748635/copy-number-changes-identified-using-whole-exome-sequencing-in-nonsyndromic-cleft-lip-and-palate-in-a-honduran-population
#17
Yi Cai, Karynne E Patterson, Frederic Reinier, Sarah E Keesecker, Elizabeth Blue, Michael Bamshad, Joseph Haddad
BACKGROUND: The majority of cleft lip with or without cleft palate cases appear as an isolated, nonsyndromic entity (NSCLP). With the advent of next generation sequencing, whole exome sequencing (WES) has been used to identify single nucleotide variants and insertion/deletions which cause or increase the risk of NSCLP. However, to our knowledge, there are no published studies using WES in NSCLP to investigate copy number changes (CNCs), which are a major component of human genetic variation...
July 27, 2017: Birth defects research
https://www.readbyqxmd.com/read/28748566/application-of-whole-exome-sequencing-to-direct-the-specific-functional-testing-and-diagnosis-of-rare-inherited-bleeding-disorders-in-patients-from-the-%C3%A3-resund-region-scandinavia
#18
Eva Leinøe, Eva Zetterberg, Savvas Kinalis, Olga Østrup, Peter Kampmann, Eva Norström, Nadine Andersson, Jenny Klintman, Klaus Qvortrup, Finn Cilius Nielsen, Maria Rossing
Rare inherited bleeding disorders (IBD) are a common cause of bleeding tendency. To ensure a correct diagnosis, specialized laboratory analyses are necessary. This study reports the results of an upfront diagnostic strategy using targeted whole exome sequencing. In total, 156 patients with a significant bleeding assessment tool score participated in the study, of which a third had thrombocytopenia. Eighty-seven genes specifically associated with genetic predisposition to bleeding were analysed by whole exome sequencing...
July 27, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28748477/chromogenic-in-situ-hybridization-methods-for-microrna-biomarker-monitoring-of-drug-safety-and-efficacy
#19
Barbara R Gould, Tina Damgaard, Boye Schnack Nielsen
Disease research and treatment development have turned to the impact and utility of microRNA. The dynamic and highly specific expression of these molecular regulators can be used to predict and monitor disease progression as well as therapeutic treatment efficacy and safety, thus aiding decisions in patient care. In situ hybridization (ISH) of biopsy material has become a routine clinical pathology procedure for monitoring gene structure, expression, and sample characterization. For ribonucleic acid (RNA), determining cell source and level of expression of these biomarkers gives insight into the cellular function and physiopathology...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28748311/advantages-of-melodic-over-rhythmic-movement-sonification-in-bimanual-motor-skill-learning
#20
J F Dyer, P Stapleton, M W M Rodger
An important question for skill acquisition is whether and how augmented feedback can be designed to improve the learning of complex skills. Auditory information triggered by learners' actions, movement sonification, can enhance learning of a complex bimanual coordination skill, specifically polyrhythmic bimanual shape tracing. However, it is not clear whether the coordination of polyrhythmic sequenced movements is enhanced by auditory-specified timing information alone or whether more complex sound mappings, such as melodic sonification, are necessary...
July 26, 2017: Experimental Brain Research. Experimentelle Hirnforschung. Expérimentation Cérébrale
keyword
keyword
26403
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"