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https://www.readbyqxmd.com/read/28736571/evaluation-of-quality-assessment-protocols-for-high-throughput-genome-resequencing-data
#1
REVIEW
Matteo Chiara, Giulio Pavesi
Large-scale initiatives aiming to recover the complete sequence of thousands of human genomes are currently being undertaken worldwide, concurring to the generation of a comprehensive catalog of human genetic variation. The ultimate and most ambitious goal of human population scale genomics is the characterization of the so-called human "variome," through the identification of causal mutations or haplotypes. Several research institutions worldwide currently use genotyping assays based on Next-Generation Sequencing (NGS) for diagnostics and clinical screenings, and the widespread application of such technologies promises major revolutions in medical science...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28736530/identification-and-expression-profiling-of-chemosensory-genes-in-dendrolimus-punctatus-walker
#2
Su-Fang Zhang, Hui-Hui Liu, Xiang-Bo Kong, Hong-Bin Wang, Fu Liu, Zhen Zhang
Dendrolimus punctatus Walker is a serious pest affecting conifers in southern China. As extensive pesticide spraying is currently required to control D. punctatus, new control strategies are urgently needed. Chemosensory genes represent potential molecular targets for development of alternative pest control strategies, and the expression characteristics of these genes provide an indication of their function. To date, little information is available regarding chemosensory genes in D. punctatus or their expression profiles at different development stages and in various tissues...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28736296/a-new-targeted-cftr-mutation-panel-based-on-next-generation-sequencing-technology
#3
Marco Lucarelli, Luigi Porcaro, Alice Biffignandi, Lucy Costantino, Valentina Giannone, Luisella Alberti, Sabina Maria Bruno, Carlo Corbetta, Erminio Torresani, Carla Colombo, Manuela Seia
Searching for mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) is a key step in the diagnosis of and neonatal and carrier screening for cystic fibrosis (CF), and it has implications for prognosis and personalized therapy. The large number of mutations and genetic and phenotypic variability make this search a complex task. Herein, we tested the clinical and laboratory validity of an extended search for mutations in CFTR using a next-generation sequencing-based method, with a panel of 188 CFTR mutations customized for the Italian population...
July 19, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28736295/digital-multiplex-ligation-dependent-probe-amplification-for-detection-of-key-copy-number-alterations-in-t-and-b-cell-lymphoblastic-leukemia
#4
Anne Benard-Slagter, Ilse Zondervan, Karel de Groot, Farzaneh Ghazavi, Virinder Sarhadi, Pieter Van Vlierberghe, Barbara De Moerloose, Claire Schwab, Kim Vettenranta, Christine J Harrison, Sakari Knuutila, Jan Schouten, Tim Lammens, Suvi Savola
Recurrent and clonal genetic alterations are characteristic of different subtypes of T- and B-cell lymphoblastic leukemia (ALL), and several subtypes are strong independent predictors of patient outcome. A next-generation sequencing-based multiplex ligation-dependent probe amplification variant (digitalMLPA) has been developed enabling simultaneous detection of copy number alterations (CNAs) of up to 1000 target sequences. This novel digitalMLPA assay was designed and optimized to detect CNAs of 56 key target genes and regions in ALL...
July 19, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28735489/a-zebrafish-model-for-evaluating-the-function-of-human-leukemic-gene-idh1-and-its-mutation
#5
Alvin C H Ma, Xiangguo Shi, Bai-Liang He, Yuhan Guo, Anskar Y H Leung
The recent advent of next-generation sequencing (NGS) has greatly accelerated identification of gene mutations in myeloid malignancies at unprecedented speed that will soon outpace their functional validation by conventional laboratory techniques and animal models. A high-throughput whole-organism model is useful for the functional validation of new mutations. We recently reported the use of zebrafish to evaluate the hematopoietic function of isocitrate dehydrogenase 1 (IDH1) and the effects of expressing human IDH1-R132H that is frequently identified in human acute myeloid leukemia (AML), in myelopoiesis, with a view to develop zebrafish as a model of AML...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735487/targeted-next-generation-sequencing-of-acute-leukemia
#6
Eric Konnick, Christina M Lockwood, David Wu
Mutation profiling of acute leukemias is a valuable tool for identifying genetic mutations with prognostic, predictive, therapeutic, and diagnostic utility. Technological advances, such as massively parallel sequencing, have allowed laboratories to assess for variation across dozens or hundreds of genes simultaneously with relatively low cost per target.Here, we describe a procedure for designing and using a TruSeq Custom Amplicon assay targeting genes involved in acute leukemias. This method is a fully customizable, amplicon-based assay for targeted resequencing, allowing interrogation of selected genomic regions of interest...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735477/molecular-malfeasance-mediating-myeloid-malignancies-the-genetics-of-acute-myeloid-leukemia
#7
Rebecca L King, Adam Bagg
A remarkable number of different, but recurrent, structural cytogenetic abnormalities have been observed in AML, and the 2016 WHO AML classification system incorporates numerous distinct entities associated with translocations or inversions, as well as others associated with single gene mutations into a category entitled "AML with recurrent genetic abnormalities." The AML classification is heavily reliant on cytogenetic and molecular information based on conventional genetic techniques (including karyotype, fluorescence in situ hybridization, reverse transcriptase polymerase chain reaction, single gene sequencing), but large-scale next generation sequencing is now identifying novel mutations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735410/rhizosphere-sampling-protocols-for-microbiome-16s-18s-its-rrna-library-preparation-and-enrichment-for-the-isolation-of-drought-tolerance-promoting-microbes
#8
Venkatachalam Lakshmanan, Prasun Ray, Kelly D Craven
Natural plant microbiomes are abundant and have a remarkably robust composition, both as epiphytes on the plant surface and as endophytes within plant tissues. Microbes in the former "habitat" face limited nutrients and harsh environmental conditions, while those in the latter likely lead a more sheltered existence. The most populous and diverse of these microbiomes are associated with the zone around the plant roots, commonly referred to as the rhizosphere. A majority of recent studies characterize these plant-associated microbiomes by community profiling of bacteria and fungi, using amplicon-based marker genes and next-generation sequencing (NGS)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735394/detection-of-differential-dna-methylation-under-stress-conditions-using-bisulfite-sequence-analysis
#9
Ibtisam Al Harrasi, Rashid Al-Yahyai, Mahmoud W Yaish
DNA methylation is the most important epigenetic change affecting gene expression in plants grown under normal as well as under stress conditions. Therefore, researchers study differential DNA methylation under distinct environmental conditions and their relationship with transcriptome abundance. Up to date, more than 25 methods and techniques are available to detect DNA methylation based on different principles. Bisulfite sequencing method is considered as a gold standard since it is able to distinguish 5-methylcytosine from cytosine using the bisulfite treatment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28734945/the-epigenomic-revolution-in-breast-cancer-from-single-gene-to-genome-wide-next-generation-approaches
#10
REVIEW
Veronica Davalos, Anna Martinez-Cardus, Manel Esteller
From the first identification of aberrant DNA methylation in primary human tumors more than three decades ago, exponential progress in cancer epigenetics research has been made. For many years, cancer epigenetics studies relied on identification of DNA methylation and histone modifications at specific genes. These studies laid the foundation for the field and revealed the epigenetic alterations as hallmark of cancer, as well as the crucial role of epigenetic mechanisms in tumorigenesis. The introduction of next-generation sequencing and array-based technologies for analyzing epigenetic states has accelerated our understanding about cancer and nowadays have become potent tools in our fight against the disease...
July 19, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28734944/triple-negative-breast-cancer-next-generation-sequencing-for-target-identification
#11
REVIEW
Jonathan D Marotti, Francine B de Abreu, Wendy A Wells, Gregory J Tsongalis
Our ability to now study disease at the most fundamental molecular level has led to a reclassification of human cancers into numerous subtypes that vary in disease progression and response to therapy. Like most solid tumors, breast cancer is a heterogeneous disease with considerable variation in histological and biological features. Triple negative breast cancer (TNBC) is a subtype of breast cancer in which estrogen receptor and progesterone receptor are not expressed, and human epidermal growth factor receptor 2 is not amplified or overexpressed...
July 19, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28734796/clonal-composition-of-human-ovarian-cancer-based-on-copy-number-analysis-reveals-a-reciprocal-relation-with-oncogenic-mutation-status
#12
Kazuko Sakai, Masayo Ukita, Jeanette Schmidt, Longyang Wu, Marco De Velasco, Alan Roter, Luis Jevons, Kazuto Nishio, Masaki Mandai
Intratumoral heterogeneity of cancer cells remains largely unexplored. Here we investigated the composition of ovarian cancer and its biological relevance. A whole-genome single nucleotide polymorphism array was applied to detect the clonal composition of 24 formalin-fixed, paraffin-embedded samples of human ovarian cancer. Genome-wide segmentation data consisting of the log2 ratio (log2R) and B allele frequency (BAF) were used to calculate an estimate of the clonal composition number (CC number) for each tumor...
July 19, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28733652/deficient-glutamate-biosynthesis-triggers-a-concerted-upregulation-of-ribosomal-protein-genes-in-arabidopsis
#13
Tamara Muñoz-Nortes, José Manuel Pérez-Pérez, Raquel Sarmiento-Mañús, Héctor Candela, José Luis Micol
Biomass production requires the coordination between growth and metabolism. In a large-scale screen for mutants affected in leaf morphology, we isolated the orbiculata1 (orb1) mutants, which exhibit a pale green phenotype and reduced growth. The combination of map-based cloning and next-generation sequencing allowed us to establish that ORB1 encodes the GLUTAMATE SYNTHASE 1 (GLU1) enzyme, also known as FERREDOXIN-DEPENDENT GLUTAMINE OXOGLUTARATE AMINOTRANSFERASE 1 (Fd-GOGAT1). We performed an RNA-seq analysis to identify global gene expression changes in the orb1-3 mutant...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733441/molecular-screening-for-cancer-treatment-optimization-moscato-01-in-pediatric-patients-a-single-institutional-prospective-molecular-stratification-trial
#14
Anne Catherine Harttrampf, Ludovic Lacroix, Marc Deloger, Frederic Deschamps, Stéphanie Puget, Nathalie Auger, Philippe Vielh, Pascale Varlet, Zsofia Balogh, Samuel Abbou, Adrien Allorant, Dominique Valteau-Couanet, Sabine Sarnacki, Louise Galmiche, Guillaume Meurice, Véronique Minard-Colin, Jacques Grill, Laurence Brugières, Christelle Dufour, Nathalie Gaspar, Stefan Michiels, Gilles Vassal, Jean-Charles Soria, Birgit Geoerger
This single institutional feasibility study prospectively characterized genomic alterations in recurrent or refractory solid tumors of pediatric patients in order to select a targeted therapy.<br /><br />Experimental Design: Following treatment failure patients with signed consent and aged above 6 months, underwent tumor biopsy or surgical resection of primary or metastatic tumor site.  These newly acquired samples were analyzed by comparative genomic hybridization array, next generation sequencing for 75 target genes, whole exome and RNA sequencing...
July 21, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28732364/a-novel-heterozygous-germline-deletion-in-msh2-gene-in-a-five-generation-chinese-family-with-lynch-syndrome
#15
Bin Wu, Wuyang Ji, Shengran Liang, Chao Ling, Yan You, Lai Xu, Min-Er Zhong, Yi Xiao, Hui-Zhong Qiu, Jun-Yang Lu, Santasree Banerjee
Lynch syndrome (LS) is one of the most common familial forms of colorectal cancer predisposing syndrome with an autosomal dominant mode of inheritance. LS is caused by the germline mutations in DNA mismatch repair (MMR) genes including MSH2, MLH1, MSH6and PMS2. Clinically, LS is characterized by high incidence of early-onset colorectal cancer as well as endometrial, small intestinal and urinary tract cancers, usually occur in the third to fourth decade of the life. Here we describe a five generation Chinese family with LS clinically diagnosed according to the Amsterdam II criteria...
July 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28732357/profiling-cancer-related-gene-mutations-in-oral-squamous-cell-carcinoma-from-japanese-patients-by-targeted-amplicon-sequencing
#16
Takafumi Nakagaki, Miyuki Tamura, Kenta Kobashi, Ryota Koyama, Hisayo Fukushima, Tomoko Ohashi, Masashi Idogawa, Kazuhiro Ogi, Hiroyoshi Hiratsuka, Takashi Tokino, Yasushi Sasaki
Somatic mutation analysis is a standard practice in the study of human cancers to identify mutations that cause therapeutic sensitization and resistance. We performed comprehensive genomic analyses that used PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Forty-seven oral squamous cell carcinoma (OSCC) samples and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverage of the entire coding regions of 409 cancer-related genes (covered regions: 95...
July 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28732356/the-circrna-interactome-innovative-hallmarks-of-the-intra-and-extracellular-radiation-response
#17
Valerie Bríd O'Leary, Jan Smida, Martina Matjanovski, Corinna Brockhaus, Klaudia Winkler, Simone Moertl, Saak Victor Ovsepian, Michael John Atkinson
Generated by Quaking (QKI), circular RNAs (circRNAs) are newly recognised non-coding RNA (ncRNA) members characterised by tissue specificity, increased stability and enrichment within exosomes. Studies have shown that ionizing radiation (IR) can influence ncRNA transcription. However, it is unknown whether circRNAs or indeed QKI are regulated by IR. Microarray circRNA profiling and next generation sequencing revealed that circRNA expression was altered by low and medium dose exposure sourced predominantly from genes influencing the p53 pathway...
July 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28732043/investigation-of-horizontal-gene-transfer-of-pathogenicity-islands-in-escherichia-coli-using-next-generation-sequencing
#18
Maxim Messerer, Wolfgang Fischer, Sören Schubert
Horizontal gene transfer (HGT) contributes to the evolution of bacteria. All extraintestinal pathogenic Escherichia coli (ExPEC) harbour pathogenicity islands (PAIs), however relatively little is known about the acquisition of these PAIs. Due to these islands, ExPEC have properties to colonize and invade its hosts efficiently. Even though these PAIs are known to be acquired by HGT, only very few PAIs do carry mobilization and transfer genes required for the transmission by HGT. In this study, we apply for the first time next-generation sequencing (NGS) and in silico analyses in combination with in vitro experiments to decipher the mechanisms of PAI acquisition in ExPEC...
2017: PloS One
https://www.readbyqxmd.com/read/28731464/trophoblast-survival-signaling-during-human-placentation-requires-hsp70-activation-of-mmp2-mediated-hbegf-shedding
#19
Chandni V Jain, Philip Jessmon, Charbel T Barrak, Alan D Bolnick, Brian A Kilburn, Michael Hertz, D Randall Armant
Survival of trophoblast cells in the low oxygen environment of human placentation requires metalloproteinase-mediated shedding of HBEGF and downstream signaling. A matrix metalloproteinase (MMP) antibody array and quantitative RT-PCR revealed upregulation of MMP2 post-transcriptionally in human first trimester HTR-8/SVneo trophoblast cells and placental villous explants exposed to 2% O2. Specific MMP inhibitors established the requirement for MMP2 in HBEGF shedding and upregulation. Because α-amanitin inhibited the upregulation of HBEGF, differentially expressed genes were identified by next-generation sequencing of RNA from trophoblast cells cultured at 2% O2 for 0, 1, 2 and 4 h...
July 21, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28731050/genomic-abnormalities-in-invasive-endocervical-adenocarcinoma-correlate-with-pattern-of-invasion-biologic-and-clinical-implications
#20
Anjelica Hodgson, Yutaka Amemiya, Arun Seth, Matthew Cesari, Bojana Djordjevic, Carlos Parra-Herran
The pattern-based classification system for HPV-related endocervical adenocarcinoma, which classifies tumors based on the destructiveness of stromal invasion, is predictive of the risk of nodal metastases and adverse outcome. Previous studies have demonstrated clinically important molecular alterations in endocervical adenocarcinoma, including KRAS and PIK3CA mutations; however, correlation between the molecular landscape and pathological variables including pattern of invasion has not been thoroughly explored...
July 21, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
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