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Next generation sequencing

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https://www.readbyqxmd.com/read/29240080/reinterpretation-of-sequence-variants-one-diagnostic-laboratory-s-experience-and-the-need-for-standard-guidelines
#1
Caitlin Chisholm, Hussein Daoud, Mahdi Ghani, Gabrielle Mettler, Jean McGowan-Jordan, Liz Sinclair-Bourque, Amanda Smith, Olga Jarinova
PurposeThe advent of next-generation sequencing resulted in substantial increases in the number of variants detected, interpreted, and reported by molecular genetics diagnostic laboratories. Recent publications have provided standards for the interpretation of sequence variants, but there are currently no standards regarding reinterpretation of these variants. Recognizing that significant changes in variant classification may occur over time, many genetics diagnostic laboratories have independently developed practices for variant reinterpretation...
December 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29239811/the-wnt-%C3%AE-catenin-pathway-is-deregulated-in-cemento-ossifying-fibromas
#2
Thaís Dos Santos Fontes Pereira, Marina Gonçalves Diniz, Josiane Alves França, Rennan Garcias Moreira, Grazielle Helena Ferreira de Menezes, Sílvia Ferreira de Sousa, Wagner Henriques de Castro, Carolina Cavaliéri Gomes, Ricardo Santiago Gomez
OBJECTIVE: The molecular pathogenesis of cemento ossifying fibroma (COF) is unclear. The purpose of this study was to investigate mutations in 50 oncogenes and tumor suppressor genes, including APC and CTNNB1, in which mutations in COF have been previously reported. In addition, we assessed the transcriptional levels of the Wnt/β-catenin pathway genes in COF. STUDY DESIGN: We used a quantitative polymerase chain reaction array to evaluate the transcriptional levels of 44 Wnt/β-catenin pathway genes in 6 COF samples, in comparison with 6 samples of healthy jaws...
November 24, 2017: Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology
https://www.readbyqxmd.com/read/29239354/an-electric-eel-inspired-soft-power-source-from-stacked-hydrogels
#3
Thomas B H Schroeder, Anirvan Guha, Aaron Lamoureux, Gloria VanRenterghem, David Sept, Max Shtein, Jerry Yang, Michael Mayer
Progress towards the integration of technology into living organisms requires electrical power sources that are biocompatible, mechanically flexible, and able to harness the chemical energy available inside biological systems. Conventional batteries were not designed with these criteria in mind. The electric organ of the knifefish Electrophorus electricus (commonly known as the electric eel) is, however, an example of an electrical power source that operates within biological constraints while featuring power characteristics that include peak potential differences of 600 volts and currents of 1 ampere...
December 13, 2017: Nature
https://www.readbyqxmd.com/read/29238890/real-time-detection-of-braf-v600e-mutation-from-archival-hairy-cell-leukemia-ffpe-tissue-by-nanopore-sequencing
#4
Davide Vacca, Valeria Cancila, Alessandro Gulino, Giosuè Lo Bosco, Beatrice Belmonte, Arianna Di Napoli, Ada Maria Florena, Claudio Tripodo, Walter Arancio
The MinION is a miniaturized high-throughput next generation sequencing platform of novel conception. The use of nucleic acids derived from formalin-fixed paraffin-embedded samples is highly desirable, but their adoption for molecular assays is hurdled by the high degree of fragmentation and by the chemical-induced mutations stemming from the fixation protocols. In order to investigate the suitability of MinION sequencing on formalin-fixed paraffin-embedded samples, the presence and frequency of BRAF c.1799T > A mutation was investigated in two archival tissue specimens of Hairy cell leukemia and Hairy cell leukemia Variant...
December 13, 2017: Molecular Biology Reports
https://www.readbyqxmd.com/read/29238598/breeding-next-generation-tree-fruits-technical-and-legal-challenges
#5
REVIEW
Lorenza Dalla Costa, Mickael Malnoy, Ivana Gribaudo
The new plant breeding technologies (NPBTs) have recently emerged as powerful tools in the context of 'green' biotechnologies. They have wide potential compared to classical genetic engineering and they are attracting the interest of politicians, stakeholders and citizens due to the revolutionary impact they may have on agriculture. Cisgenesis and genome editing potentially allow to obtain pathogen-resistant plants or plants with enhanced qualitative traits by introducing or disrupting specific genes in shorter times compared to traditional breeding programs and by means of minimal modifications in the plant genome...
2017: Horticulture Research
https://www.readbyqxmd.com/read/29238535/a-workflow-of-massive-identification-and-application-of-intron-markers-using-snakes-as-a-model
#6
Jiang-Ni Li, Chong He, Peng Guo, Peng Zhang, Dan Liang
Relative to the commonly used mitochondrial and nuclear protein-coding genes, the noncoding intron sequences are a promising source of informative markers that have the potential to resolve difficult phylogenetic nodes such as rapid radiations and recent divergences. Yet many issues exist in the use of intron markers, which prevent their extensive application as conventional markers. We used the diverse group of snakes as an example to try paving the way for massive identification and application of intron markers...
December 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29237785/mcr-3-and-mcr-4-variants-in-carbapenemase-producing-clinical-enterobacteriaceae-do-not-confer-phenotypic-polymyxin-resistance
#7
Jeanette W P Teo, Marimuthu Kalisvar, Indumathi Venkatachalam, Ng Oon Tek, Raymond T P Lin, Sophie Octavia
The world-wide distribution of plasmid-mediated colistin resistance determinants (mcr-1, mcr-2, mcr-3 and mcr-4) coupled to an emerging observation that colistin resistance is more prevalent in carbapenem-resistant Enterobacteriaceae (CRE) (1, 2) present a daunting challenge in combatting antimicrobial resistance. Undoubtedly, next-generation sequencing approaches have expedited the discovery of mobile colistin resistance determinants (3).….
December 13, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29237689/technical-advances-for-the-clinical-genomic-evaluation-of-sudden-cardiac-death-verification-of-next-generation-sequencing-panels-for-hereditary-cardiovascular-conditions-using-formalin-fixed-paraffin-embedded-tissues-and-dried-blood-spots
#8
Linnea M Baudhuin, Charles Leduc, Laura J Train, Rajeswari Avula, Michelle L Kluge, Katrina E Kotzer, Peter T Lin, Michael J Ackerman, Joseph J Maleszewski
BACKGROUND: Postmortem genetic testing for heritable cardiovascular (CV) disorders is often lacking because ideal specimens (ie, whole blood) are not retained routinely at autopsy. Formalin-fixed paraffin-embedded tissue (FFPET) is ubiquitously collected at autopsy, but DNA quality hampers its use with traditional sequencing methods. Targeted next-generation sequencing may offer the ability to circumvent such limitations, but a method has not been previously described. The primary aim of this study was to develop and evaluate the use of FFPET for heritable CV disorders via next-generation sequencing...
December 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/29237676/familial-ebstein-anomaly-whole-exome-sequencing-identifies-novel-phenotype-associated-with-flna
#9
Catherine L Mercer, Gaia Andreoletti, Aisling Carroll, Anthony P Salmon, I Karen Temple, Sarah Ennis
BACKGROUND: Familial Ebstein anomaly is a rare form of congenital heart disease. We report 7 individuals among 2 generations of 1 family with Ebstein anomaly. This family was first reported in 1991 by Balaji et al in which family members were also reported to have a mild skeletal phenotype. The most likely mechanism of inheritance was concluded to be autosomal dominant. We sought to identify the genetic pathogenesis in this family using a next generation sequencing approach. METHODS AND RESULTS: Whole exome sequencing was performed in 2 cousins in this family using the Agilent SureSelect Human all Exon 51 Mb version 5 capture kit...
December 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/29237063/spectrum-of-pig-a-mutations-in-t-lymphocytes-of-rats-treated-with-procarbazine
#10
Javier Revollo, Javed A Bhalli, Cameron Tebbe, Jessica Noteboom, Demetria Thomas, Page McKinzie, Nicholas Felton, Mason G Pearce, Vasily N Dobrovolsky
Procarbazine is a primary component of antineoplastic combination chemotherapy often used for the treatment of Hodgkin's lymphoma. It is believed that cytostatic and cytotoxic properties of procarbazine are mediated via its interaction with genomic DNA. Procarbazine is a carcinogen in animal models; it is classified as Group 2A compound by IARC. Also it is known as an in vitro and in vivo mutagen and genotoxicant. However, the molecular mechanism by which procarbazine induces mutations is not thoroughly understood and the spectrum of procarbazine-induced in vivo mutations is described insufficiently...
December 8, 2017: Mutagenesis
https://www.readbyqxmd.com/read/29236923/whole-genome-sequencing-of-leptospira-interrogans-from-southern-brazil-genetic-features-of-a-highly-virulent-strain
#11
Sérgio Jorge, Frederico Schmitt Kremer, Natasha Rodrigues de Oliveira, Gabrielle de Oliveira Sanches Valerio Navarro, Amanda Munari Guimarães, Christian Domingues Sanchez, Rafael Danelon Dos Santos Woloski, Karine Forster Ridieri, Vinícius Farias Campos, Luciano da Silva Pinto, Odir Antônio Dellagostin
BACKGROUND Leptospirosis is the most widespread zoonotic disease. It is caused by infection with pathogenic Leptospira species, of which over 300 serovars have been described. The accurate identification of the causative Leptospira spp. is required to ascertain the pathogenic status of the local isolates. OBJECTIVES This study aimed to obtain the complete genome sequence of a virulent Leptospira interrogans strain isolated from southern Brazil and to describe its genetic features. METHODS The whole genome was sequenced by next-generation sequencing (Ion Torrent)...
February 2018: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/29236770/association-between-preoperative-peripheral-blood-mononuclear-cell-gene-expression-profiles-early-postoperative-organ-function-recovery-potential-and-long-term-survival-in-advanced-heart-failure-patients-undergoing-mechanical-circulatory-support
#12
Galyna Bondar, Ryan Togashi, Martin Cadeiras, Joanna Schaenman, Richard K Cheng, Lindsay Masukawa, Josephine Hai, Tra-Mi Bao, Desai Chu, Eleanor Chang, Maral Bakir, Sophie Kupiec-Weglinski, Victoria Groysberg, Tristan Grogan, Joseph Meltzer, Murray Kwon, Maura Rossetti, David Elashoff, Elaine Reed, Pei Pei Ping, Mario C Deng
BACKGROUND: Multiorgan dysfunction syndrome contributes to adverse outcomes in advanced heart failure (AdHF) patients after mechanical circulatory support (MCS) implantation and is associated with aberrant leukocyte activity. We tested the hypothesis that preoperative peripheral blood mononuclear cell (PBMC) gene expression profiles (GEP) can predict early postoperative improvement or non-improvement in patients undergoing MCS implantation. We believe this information may be useful in developing prognostic biomarkers...
2017: PloS One
https://www.readbyqxmd.com/read/29236254/integration-of-encode-rnaseq-and-eclip-data-sets
#13
Jorge Boucas
During the last decade, the study of mRNA decay has largely benefited from an increasing number of high-throughput assays that emerged from developments in next generation sequencing (NGS) technologies as well as mass spectrometry. While assay-specific data analysis is often reported and software made available many researchers struggle with the overwhelming challenge of integrating data from diverse assays, different sources, and of different formats.We here use Python, R, and bash to analyze and integrate RNAseq and eCLIP data publicly available from ENCODE...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236251/par-clip-for-discovering-target-sites-of-rna-binding-proteins
#14
Aitor Garzia, Pavel Morozov, Marcin Sajek, Cindy Meyer, Thomas Tuschl
RNA-binding proteins (RBPs) establish posttranscriptional gene regulation (PTGR) by coordinating the maturation, editing, transport, stability, and translation of cellular RNAs. A variety of experimental approaches have been developed to characterize the RNAs associated with RBPs in vitro as well as in vivo. Our laboratory developed Photoactivatable-Ribonucleoside-Enhanced Cross-Linking and Immunoprecipitation (PAR-CLIP), which in combination with next-generation sequencing enables the identification of RNA targets of RBPs at a nucleotide-level resolution...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236234/assessment-of-the-functional-impact-of-germline-brca1-2-variants-located-in-non-coding-regions-in-families-with-breast-and-or-ovarian-cancer-predisposition
#15
E Santana Dos Santos, S M Caputo, L Castera, M Gendrot, A Briaux, M Breault, S Krieger, P K Rogan, E J Mucaki, L J Burke, I Bièche, C Houdayer, D Vaur, D Stoppa-Lyonnet, M A Brown, F Lallemand, E Rouleau
PURPOSE: The molecular mechanism of breast and/or ovarian cancer susceptibility remains unclear in the majority of patients. While germline mutations in the regulatory non-coding regions of BRCA1 and BRCA2 genes have been described, screening has generally been limited to coding regions. The aim of this study was to evaluate the contribution of BRCA1/2 non-coding variants. METHODS: Four BRCA1/2 non-coding regions were screened using high-resolution melting analysis/Sanger sequencing or next-generation sequencing on DNA extracted from index cases with breast and ovarian cancer predisposition (3926 for BRCA1 and 3910 for BRCA2)...
December 13, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29236161/genetic-analysis-of-adults-heterozygous-for-alpl-mutations
#16
Agnès Taillandier, Christelle Domingues, Annika Dufour, Françoise Debiais, Pascal Guggenbuhl, Christian Roux, Catherine Cormier, Bernard Cortet, Valérie Porquet-Bordes, Fabienne Coury, David Geneviève, Jean Chiesa, Thierry Colin, Elaine Fletcher, Agnès Guichet, Rose-Marie Javier, Michel Laroche, Michael Laurent, Ekkehart Lausch, Bruno LeHeup, Cédric Lukas, Georg Schwabe, Ineke van der Burgt, Christine Muti, Brigitte Simon-Bouy, Etienne Mornet
Hypophosphatasia (HPP) is a rare inherited metabolic bone disease due to a deficiency of the tissue nonspecific alkaline phosphatase isoenzyme (TNSALP) encoded by the ALPL gene. Patients have consistently low serum alkaline phosphatase (AP), so that this parameter is a good hallmark of the disease. Adult HPP is heterogeneous, and some patients present only mild nonpathognomonic symptoms which are also common in the general population such as joint pain, osteomalacia and osteopenia, chondrocalcinosis, arthropathy and musculoskeletal pain...
December 13, 2017: Journal of Bone and Mineral Metabolism
https://www.readbyqxmd.com/read/29235881/prediction-of-pancreatic-cancer-risk-and-therapeutic-response-with-next-generation-sequencing
#17
Ioannis D Kyrochristos, Demosthenes E Ziogas, Georgios K Glantzounis, Dimitrios H Roukos
No abstract text is available yet for this article.
December 13, 2017: Biomarkers in Medicine
https://www.readbyqxmd.com/read/29234950/the-evolution-of-endometrial-carcinoma-classification-through-application-of-immunohistochemistry-and-molecular-diagnostics-past-present-and-future
#18
REVIEW
Emily A Goebel, August Vidal, Xavier Matias-Guiu, C Blake Gilks
Uterine cancer was first subclassified based on anatomic site, separating those tumours arising from the endometrium from cervical cancers. There was then further subclassification of endometrial cancers based on cell type, and this correlated with the Type I and Type II categories identified through the epidemiological studies of Bokhman, with endometrioid carcinoma corresponding (approximately) to Type I and serous carcinoma to Type II. These histotypes are not clearly separable in practice, however, with considerable interobserver variability in histotype diagnosis, especially for high-grade tumours...
December 12, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/29234666/technical-advances-to-study-extracellular-vesicles
#19
REVIEW
Paula Carpintero-Fernández, Juan Fafián-Labora, Ana O'Loghlen
Extracellular vesicles are a heterogeneous and dynamic group of lipid bilayer membrane nanoparticles that can be classified into three different groups depending on their cellular origin: exosomes, microvesicles, and apoptotic bodies. They are produced by different cell types and can be isolated from almost all body fluids. EVs contain a variety of proteins, lipids, nucleic acids, and metabolites which regulate a number of biological and pathological scenarios both locally and systemically. Different techniques have been described in order to determine EV isolation, release, uptake, and cargo...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/29234329/neoantigens-generated-by-individual-mutations-and-their-role-in-cancer-immunity-and-immunotherapy
#20
REVIEW
Mirjana Efremova, Francesca Finotello, Dietmar Rieder, Zlatko Trajanoski
Recent preclinical and clinical studies have proved the long-standing hypothesis that tumors elicit adaptive immune responses and that the antigens driving effective T-cell response are neoantigens, i.e., peptides that are generated from somatically mutated genes. Hence, the characterization of neoantigens and the identification of the immunogenic ones are of utmost importance for improving cancer immunotherapy and broadening its efficacy to a larger fraction of patients. In this review, we first introduce the methods used for the quantification of neoantigens using next-generation sequencing data and then summarize results obtained using these tools to characterize the neoantigen landscape in solid cancers...
2017: Frontiers in Immunology
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