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https://www.readbyqxmd.com/read/28092796/global-open-data-management-in-metabolomics
#1
REVIEW
Kenneth Haug, Reza M Salek, Christoph Steinbeck
Chemical Biology employs chemical synthesis, analytical chemistry and other tools to study biological systems. Recent advances in both molecular biology such as next generation sequencing (NGS) have led to unprecedented insights towards the evolution of organisms' biochemical repertoires. Because of the specific data sharing culture in Genomics, genomes from all kingdoms of life become readily available for further analysis by other researchers. While the genome expresses the potential of an organism to adapt to external influences, the Metabolome presents a molecular phenotype that allows us to asses the external influences under which an organism exists and develops in a dynamic way...
January 13, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28090632/identification-of-highly-selective-mmp-14-inhibitory-fabs-by-deep-sequencing
#2
Tyler Lopez, Dong Hyun Nam, Evan Kaihara, Zahid Mustafa, Xin Ge
Matrix metalloproteinase (MMP)-14 is an important target for cancer treatment due to its critical roles in tumor invasion and metastasis. Previous failures of all compound-based broad-spectrum MMP inhibitors in clinical trials suggest that selectivity is the key for a successful therapy. With inherent high specificity, monoclonal antibodies (mAbs) therefore arise as attractive inhibitors able to target the particular MMP of interest. As a routine screening method, enzyme-linked immunosorbent assays (ELISA) have been applied to panned phage libraries for the isolation of mAbs inhibiting MMP-14...
January 16, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28087426/next-generation-sequencing-of-a-large-gene-panel-in-patients-initially-diagnosed-with-idiopathic-ventricular-fibrillation
#3
Marloes Visser, Dennis Dooijes, Jasper J van der Smagt, Jeroen F van der Heijden, Pieter A Doevendans, Peter Loh, Folkert W Asselbergs, Rutger J Hassink
BACKGROUND: Idiopathic ventricular fibrillation (IVF) is a rare primary cardiac arrhythmia syndrome that is diagnosed in a resuscitated cardiac arrest victim, with documented ventricular fibrillation, in whom no underlying cause is identified after comprehensive clinical evaluation. In some patients causative genetic mutations are detected which facilitate patient treatment and follow-up. The feasibility of next generation sequencing (NGS) has increased with its greater availability and decreasing costs...
January 10, 2017: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/28079900/a-curated-gene-list-for-reporting-results-of-newborn-genomic-sequencing
#4
Ozge Ceyhan-Birsoy, Kalotina Machini, Matthew S Lebo, Tim W Yu, Pankaj B Agrawal, Richard B Parad, Ingrid A Holm, Amy McGuire, Robert C Green, Alan H Beggs, Heidi L Rehm
PURPOSE: Genomic sequencing (GS) for newborns may enable detection of conditions for which early knowledge can improve health outcomes. One of the major challenges hindering its broader application is the time it takes to assess the clinical relevance of detected variants and the genes they impact so that disease risk is reported appropriately. METHODS: To facilitate rapid interpretation of GS results in newborns, we curated a catalog of genes with putative pediatric relevance for their validity based on the ClinGen clinical validity classification framework criteria, age of onset, penetrance, and mode of inheritance through systematic evaluation of published evidence...
January 12, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28078776/performance-of-the-forenseq-tm-dna-signature-prep-kit-on-highly-degraded-samples
#5
Paolo Fattorini, Carlo Previderé, Ilaria Carboni, Giorgio Marrubini, Solange Sorçaburu-Cigliero, Pierangela Grignani, Barbara Bertoglio, Paolo Vatta, Ugo Ricci
Next generation sequencing (NGS) is the emerging technology in forensic genomics laboratories. It offers higher resolution to address most problems of human identification, greater efficiency and potential ability to interrogate very challenging forensic casework samples. In the present study, a trial set of DNA samples was artificially degraded, by progressive aqueous hydrolysis, and analyzed together with the corresponding unmodified DNA sample and control sample 2800M, to test the performance and reliability of the ForenSeq(TM) DNA Signature Prep kit using the MiSeq Sequencer (Illumina)...
January 12, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28078112/molecular-spectrum-of-kras-nras-braf-pik3ca-tp53-and-apc-somatic-gene-mutations-in-arab-patients-with-colorectal-cancer-determination-of-frequency-and-distribution-pattern
#6
Humaid O Al-Shamsi, Jeremy Jones, Yazan Fahmawi, Ibrahim Dahbour, Aziz Tabash, Reham Abdel-Wahab, Ahmed O S Abousamra, Kenna R Shaw, Lianchun Xiao, Manal M Hassan, Benjamin R Kipp, Scott Kopetz, Amr S Soliman, Robert R McWilliams, Robert A Wolff
BACKGROUND: The frequency rates of mutations such as KRAS, NRAS, BRAF, and PIK3CA in colorectal cancer (CRC) differ among populations. The aim of this study was to assess mutation frequencies in the Arab population and determine their correlations with certain clinicopathological features. METHODS: Arab patients from the Arab Gulf region and a population of age- and sex-matched Western patients with CRC whose tumors were evaluated with next-generation sequencing (NGS) were identified and retrospectively reviewed...
December 2016: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28077840/novel-gatad2b-loss-of-function-mutations-cause-intellectual-disability-in-two-unrelated-cases
#7
Xiaomei Luo, Yongyi Zou, Bo Tan, Yue Zhang, Jing Guo, Lanlan Zeng, Rui Zhang, Hu Tan, Xianda Wei, Yiqiao Hu, Yu Zheng, Desheng Liang, Lingqian Wu
GATA zinc finger domain-containing 2B (GATAD2B) is a subunit of the methyl-CpG-binding protein-1 complex (MECP1), which deacetylates methylated nucleosomes and regresses transcriptional activity. Recently, GATAD2B has been elucidated as a candidate gene in patients with intellectual disability (ID). In this study, we identified two novel heterozygous frameshift mutations of GATAD2B in two unrelated ID cases through next-generation sequencing (NGS). Both of the mutations c.80_81insGATGT and c.552_555delGAAA cause truncated proteins that might be detrimental to neurodevelopment...
January 12, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28077647/sensitive-next-generation-sequencing-method-reveals-deep-genetic-diversity-of-hiv-1-in-the-democratic-republic-of-the-congo
#8
M A Rodgers, E Wilkerson, A Vallari, C McArthur, L Sthreshley, C A Brennan, G Cloherty, T de Oliveira
: As the epidemiological epicentre of the human immunodeficiency virus (HIV) pandemic, the Democratic Republic of the Congo (DRC) is a reservoir of circulating HIV strains exhibiting high levels of diversity and recombination. In this study, we characterized HIV specimens collected in two rural areas of the DRC between 2001 and 2003 to identify rare strains of HIV. The env gp41 region was sequenced and characterized for 172 HIV-positive specimens. The env sequences were predominantly subtype A (43...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28077090/gbs-based-single-dosage-markers-for-linkage-and-qtl-mapping-allow-gene-mining-for-yield-related-traits-in-sugarcane
#9
Thiago Willian Almeida Balsalobre, Guilherme da Silva Pereira, Gabriel Rodrigues Alves Margarido, Rodrigo Gazaffi, Fernanda Zatti Barreto, Carina Oliveira Anoni, Cláudio Benício Cardoso-Silva, Estela Araújo Costa, Melina Cristina Mancini, Hermann Paulo Hoffmann, Anete Pereira de Souza, Antonio Augusto Franco Garcia, Monalisa Sampaio Carneiro
BACKGROUND: Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection...
January 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28076841/clonal-evolution-in-therapy-related-neoplasms
#10
Emiliano Fabiani, Giulia Falconi, Luana Fianchi, Marianna Criscuolo, Tiziana Ottone, Laura Cicconi, Stefan Hohaus, Simona Sica, Massimiliano Postorino, Antonino Neri, Marta Lionetti, Giuseppe Leone, Francesco Lo-Coco, Maria Teresa Voso
Therapy-related myeloid neoplasms (t-MN) may occur as a late effect of cytotoxic therapy for a primary malignancy or autoimmune diseases in susceptible individuals. We studied the development of somatic mutations in t-MN, using a collection of follow-up samples from 14 patients with a primary hematologic malignancy, who developed a secondary leukemia (13 t-MN and 1 t-acute lymphoblastic leukemia), at a median latency of 73 months (range 18-108) from primary cancer diagnosis.Using Sanger and next generation sequencing (NGS) approaches we identified 8 mutations (IDH1 R132H, ASXL1 Y591*, ASXL1 S689*, ASXL1 R693*, SRSF2 P95H, SF3B1 K700E, SETBP1 G870R and TP53 Y220C) in seven of thirteen t-MN patients (54%), whereas the t-ALL patient had a t(4,11) translocation, resulting in the KMT2A/AFF1 fusion gene...
January 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28075483/detecting-apc-gene-mutations-in-familial-adenomatous-polyposis-fap
#11
Babi Ramesh Reddy Nallamilli, Madhuri Hegde
Hereditary forms of colorectal cancer (CRC) account for up to 5% of total cases. Familial adenomatous polyposis (FAP) is an autosomal dominant condition affecting nearly 1 in 5000 people and accounts for only about 1% of all CRCs. It is characterized by the progressive development of hundreds to thousands of adenomatous colon polyps. The gene associated with FAP (APC) contains 15 coding exons. The mutation spectrum of the APC gene is broad in that 87% of causative mutations are point mutations (including other sequence variants) and around 10% to 15% are intragenic deletions and duplications...
January 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28074849/genetic-variants-identified-from-epilepsy-of-unknown-etiology-in-chinese-children-by-targeted-exome-sequencing
#12
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/28074712/high-throughput-whole-genome-sequencing-of-porcine-reproductive-and-respiratory-syndrome-virus-from-cell-culture-materials-and-clinical-specimens-using-next-generation-sequencing-technology
#13
Jianqiang Zhang, Ying Zheng, Xiao-Qin Xia, Qi Chen, Sarah A Bade, Kyoung-Jin Yoon, Karen M Harmon, Phillip C Gauger, Rodger G Main, Ganwu Li
Next-generation sequencing (NGS) technologies have increasingly played crucial roles in biological and medical research, but are not yet in routine use in veterinary diagnostic laboratories. We developed and applied a procedure for high-throughput RNA sequencing of Porcine reproductive and respiratory syndrome virus (PRRSV) from cell culture-derived isolates and clinical specimens. Ten PRRSV isolates with known sequence information, 2 mixtures each with 2 different PRRSV isolates, and 51 clinical specimens (19 sera, 16 lungs, and 16 oral fluids) with various PCR threshold cycle (Ct) values were subjected to nucleic acid extraction, cDNA library preparation (24-plexed), and sequencing...
January 2017: Journal of Veterinary Diagnostic Investigation
https://www.readbyqxmd.com/read/28072833/accurate-breakpoint-mapping-in-apparently-balanced-translocation-families-with-discordant-phenotypes-using-whole-genome-mate-pair-sequencing
#14
Constantia Aristidou, Costas Koufaris, Athina Theodosiou, Mads Bak, Mana M Mehrjouy, Farkhondeh Behjati, George Tanteles, Violetta Christophidou-Anastasiadou, Niels Tommerup, Carolina Sismani
Familial apparently balanced translocations (ABTs) segregating with discordant phenotypes are extremely challenging for interpretation and counseling due to the scarcity of publications and lack of routine techniques for quick investigation. Recently, next generation sequencing has emerged as an efficacious methodology for precise detection of translocation breakpoints. However, studies so far have mainly focused on de novo translocations. The present study focuses specifically on familial cases in order to shed some light to this diagnostic dilemma...
2017: PloS One
https://www.readbyqxmd.com/read/28070990/a-targeted-next-generation-sequencing-in-the-molecular-risk-stratification-of-adult-acute-myeloid-leukemia-implications-for-clinical-practice
#15
Po-Han Lin, Huei-Ying Li, Sheng-Chih Fan, Tzu-Hang Yuan, Ming Chen, Yu-Hua Hsu, Yu-Hsuan Yang, Long-Yuan Li, Su-Peng Yeh, Li-Yuan Bai, Yu-Min Liao, Chen-Yuan Lin, Ching-Yun Hsieh, Ching-Chan Lin, Che-Hung Lin, Ming-Yu Lien, Tzu-Ting Chen, Yen-Hsuan Ni, Chang-Fang Chiu
Conventional cytogenetics can categorize patients with acute myeloid leukemia (AML) into favorable, intermediate, and unfavorable-risk groups; however, patients with intermediate-risk cytogenetics represent the major population with variable outcomes. Because molecular profiling can assist with AML prognosis and next-generation sequencing allows simultaneous sequencing of many target genes, we analyzed 260 genes in 112 patients with de novo AML who received standard treatment. Multivariate analysis showed that karyotypes and mutation status of TET2, PHF6, KIT, and NPM1(mutation) /FLT3- internal tandem duplication (ITD)(negative) were independent prognostic factors for the entire cohort...
January 10, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28069593/knime4ngs-a-comprehensive-toolbox-for-next
#16
Maximilian Hastreiter, Tim Jeske, Jonathan Hoser, Michael Kluge, Kaarin Ahomaa, Marie-Sophie Friedl, Sebastian J Kopetzky, Jan-Dominik Quell, H- Werner Mewes, Robert Küffner
: Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis...
January 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28069272/smarcb1-ini1-deficient-sinonasal-carcinoma-shows-methylation-of-rassf1-gene-a-clinicopathological-immunohistochemical-and-molecular-genetic-study-of-a-recently-described-entity
#17
Jan Laco, Marcela Chmelařová, Hana Vošmiková, Kateřina Sieglová, Ivana Bubancová, Pavel Dundr, Kristýna Němejcová, Jaroslav Michálek, Petr Čelakovský, Radovan Mottl, Igor Sirák, Milan Vošmik, Aleš Ryška
The aim of the study was detailed clinicopathological investigation of SMARCB1/INI1-deficient sinonasal carcinomas, including molecular genetic analysis of mutational status and DNA methylation of selected protooncogenes and tumor suppressor genes by means of next generation sequencing (NGS) and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). A total of 4/56 (7%) cases of SMARCB1/INI1-deficient carcinomas were detected among 56 sinonasal carcinomas diagnosed over a 19year period using immunohistochemical screening...
October 25, 2016: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28067828/pharmacogenetic-foundations-of-therapeutic-efficacy-and-adverse-events-of-statins
#18
REVIEW
Elena Arrigoni, Marzia Del Re, Leonardo Fidilio, Stefano Fogli, Romano Danesi, Antonello Di Paolo
BACKGROUND: In the era of precision medicine, more attention is paid to the search for predictive markers of treatment efficacy and tolerability. Statins are one of the classes of drugs that could benefit from this approach because of their wide use and their incidence of adverse events. METHODS: Literature from PubMed databases and bibliography from retrieved publications have been analyzed according to terms such as statins, pharmacogenetics, epigenetics, toxicity and drug-drug interaction, among others...
January 6, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28065512/assessment-of-tuberous-sclerosis-complex-associated-with-renal-lesions-by-targeted-next-generation-sequencing-in-mainland-china
#19
Yi Cai, Hanzhong Li, Yushi Zhang
OBJECTIVE: To identify the TSC1 and TSC2 mutations in patients with tuberous sclerosis complex (TSC) associated with renal lesions, and to explore the relationship between genotypes and phenotypes. MATERIALS AND METHODS: We analyzed 43 individuals affected with TSC accompanied by renal lesions using next-generation sequencing (NGS). We also performed Sanger sequencing to validate the NGS results. RESULTS: We reported a comprehensive mutation analysis of 43 affected individuals with TSC accompanied by renal lesions using NGS...
January 5, 2017: Urology
https://www.readbyqxmd.com/read/28063046/messenger-rna-sequencing-of-rare-cell-populations-in-the-lung-and-lung-draining-lymph-nodes
#20
Alexander Ulges, Edgar Schmitt, Tobias Bopp, Matthias Klein
Next-generation sequencing (NGS) techniques provide unique prospects for in-depth transcriptome analyses. Nevertheless, the emerging and still growing knowledge about the large diversity and heterogeneity of cells that participate in immunological responses in a tissue- and micromilieu-specific manner calls for advanced isolation and sequencing methods for the accurate quantification of gene expression in small cell populations and even individual cells from any organ or tissue. One of the major limitations in performing transcriptome analyses of rare cell populations was and still is quality and quantity of RNA that often limits analyses of complex mixtures of immune cell populations...
2017: Methods in Molecular Biology
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