keyword
MENU ▼
Read by QxMD icon Read
search

NGS sequencing

keyword
https://www.readbyqxmd.com/read/29040360/elucidating-the-editome-bioinformatics-approaches-for-rna-editing-detection
#1
Maria Angela Diroma, Loredana Ciaccia, Graziano Pesole, Ernesto Picardi
RNA editing is a widespread co/posttranscriptional mechanism affecting primary RNAs by specific nucleotide modifications, which plays relevant roles in molecular processes including regulation of gene expression and/or the processing of noncoding RNAs. In recent years, the detection of editing sites has been improved through the availability of high-throughput RNA sequencing (RNA-Seq) technologies. Accurate bioinformatics pipelines are essential for the analysis of next-generation sequencing (NGS) data to ensure the correct identification of edited sites...
October 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29040274/a-quadratically-regularized-functional-canonical-correlation-analysis-for-identifying-the-global-structure-of-pleiotropy-with-ngs-data
#2
Nan Lin, Yun Zhu, Ruzong Fan, Momiao Xiong
Investigating the pleiotropic effects of genetic variants can increase statistical power, provide important information to achieve deep understanding of the complex genetic structures of disease, and offer powerful tools for designing effective treatments with fewer side effects. However, the current multiple phenotype association analysis paradigm lacks breadth (number of phenotypes and genetic variants jointly analyzed at the same time) and depth (hierarchical structure of phenotype and genotypes). A key issue for high dimensional pleiotropic analysis is to effectively extract informative internal representation and features from high dimensional genotype and phenotype data...
October 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29036818/a-9-microrna-signature-in-serum-serves-as-a-noninvasive-biomarker-in-early-diagnosis-of-alzheimer-s-disease
#3
Rui Guo, Gang Fan, Jian Zhang, Chunxiao Wu, Yifeng Du, Hui Ye, Zhang Li, Lili Wang, Zhihui Zhang, Lu Zhang, Yueran Zhao, Zhiming Lu
Alzheimer's disease (AD) is the most common type of age-related neurodegenerative disorder; nevertheless, nowadays there are no reliable biomarkers or non-invasive techniques available for its early detection. Recent studies have indicated that the circulating level profiles of microRNAs (miRNAs) have the potential to be used as valuable biomarkers for diagnosis, staging, and progress monitoring of various diseases. Here we report a novel 9-miRNA signature (hsa-miR-26a-5p, hsa-miR-181c-3p, hsa-miR-126-5p, hsa-miR-22-3p, hsa-miR-148b-5p, hsa-miR-106b-3p, hsa-miR-6119-5p, hsa-miR-1246, and hsa-miR-660-5p) that can be utilized as biomarker for detecting AD...
October 12, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/29036546/crocoblast-running-blast-efficiently-in-the-age-of-next-generation-sequencing
#4
Ravi José Tristão Ramos, Allan Cézar de Azevedo Martins, Gabrielle da Silva Delgado, Crina-Maria Ionescu, Turán Peter Ürményi, Rosane Silva, Jaroslav Koca
Summary: CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29035575/hetfhmm-a-novel-approach-to-infer-tumor-heterogeneity-using-factorial-hidden-markov-models
#5
Mohammad S Rahman, Ann E Nicholson, Gholamreza Haffari
Cancer arises from successive rounds of mutations, resulting in tumor cells with different somatic mutations known as clones. Drug responsiveness and therapeutics of cancer depend on the accurate detection of clones in a tumor sample. Recent research has considered inferring clonal composition of a tumor sample using computational models based on short read data of the sample generated using next-generation sequencing (NGS) technology. Short reads (segmented DNA parts of different tumor cells) are noisy; therefore, inferring the clones and their mutations from the data is a difficult and complex problem...
October 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29033976/conffuse-high-confidence-fusion-gene-detection-across-tumor-entities
#6
Zhiqin Huang, David T W Jones, Yonghe Wu, Peter Lichter, Marc Zapatka
Background: Fusion genes play an important role in the tumorigenesis of many cancers. Next-generation sequencing (NGS) technologies have been successfully applied in fusion gene detection for the last several years, and a number of NGS-based tools have been developed for identifying fusion genes during this period. Most fusion gene detection tools based on RNA-seq data report a large number of candidates (mostly false positives), making it hard to prioritize candidates for experimental validation and further analysis...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29033905/a-review-on-the-applications-of-next-generation-sequencing-technologies-as-applied-to-food-related-microbiome-studies
#7
REVIEW
Yu Cao, Séamus Fanning, Sinéad Proos, Kieran Jordan, Shabarinath Srikumar
The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29032884/the-genetics-underlying-idiopathic-ventricular-fibrillation-a-special-role-for-catecholaminergic-polymorphic-ventricular-tachycardia
#8
Jaakko T Leinonen, Lia Crotti, Aurora Djupsjöbacka, Silvia Castelletti, Nella Junna, Alice Ghidoni, Annukka M Tuiskula, Carla Spazzolini, Federica Dagradi, Matti Viitasalo, Kimmo Kontula, Maria-Christina Kotta, Elisabeth Widén, Heikki Swan, Peter J Schwartz
BACKGROUND: Ventricular fibrillation (VF) is a major cause of sudden cardiac death. In some cases clinical investigations fail to identify the underlying cause and the event is classified as idiopathic (IVF). Since mutations in arrhythmia-associated genes frequently determine arrhythmia susceptibility, screening for disease-predisposing variants could improve IVF diagnostics. METHODS AND RESULTS: The study included 76 Finnish and Italian patients with a mean age of 31...
October 5, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/29032542/borrelia-burgdorferi-transcriptome-analysis-by-rna-sequencing
#9
M Lybecker, K C Henderson
Next-Generation Sequencing (NGS) has revolutionized transcriptomics studies in the last decade. Transcriptome analysis experiments using NGS-based RNA-sequencing have several advantages over DNA microarray analysis. Novel unannotated transcripts and transcriptional start sites can be identified. Differential gene expression can be determined on novel and annotated transcripts simultaneously, whereas DNA microarray analysis can only quantify changes of known genes. In the protocol below we describe an Illumina compatible ligation-based method for generating stranded cDNA libraries for total RNA and small RNA transcriptomes in Borrelia burgdorferi...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29032017/editorial-next-generation-sequencing-technology-a-new-tool-for-killer-cell-immunoglobulin-like-receptor-allele-typing-in-hematopoietic-stem-cell-transplantation
#10
B Maniangou, C Retière, K Gagne
Killer cell Immunoglobulin-like Receptor (KIR) genes are a family of genes located together within the leukocyte receptor cluster on human chromosome 19q13.4. To date, 17 KIR genes have been identified including nine inhibitory genes (2DL1/L2/L3/L4/L5A/L5B, 3DL1/L2/L3), six activating genes (2DS1/S2/S3/S4/S5, 3DS1) and two pseudogenes (2DP1, 3DP1) classified into group A (KIR A) and group B (KIR B) haplotypes. The number and the nature of KIR genes vary between the individuals. In addition, these KIR genes are known to be polymorphic at allelic level (907 alleles described in July 2017)...
October 11, 2017: Transfusion Clinique et Biologique: Journal de la Société Française de Transfusion Sanguine
https://www.readbyqxmd.com/read/29031844/alternative-polyadenylation-methods-findings-and-impacts
#11
REVIEW
Wei Chen, Qi Jia, Yifan Song, Haihui Fu, Gang Wei, Ting Ni
Alternative polyadenylation (APA), a phenomenon that RNA molecules with different 3' ends originate from distinct polyadenylation sites of a single gene, is emerging as a mechanism widely used to regulate gene expression. In the present review, we first summarized various methods prevalently adopted in APA study, mainly focused on the next-generation sequencing (NGS)-based techniques specially designed for APA identification, the related bioinformatics methods, and the strategies for APA study in single cells...
October 11, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29030838/cloning-and-identification-of-recombinant-argonaute-bound-small-rnas-using-next-generation-sequencing
#12
Pooja Gangras, Daniel M Dayeh, Justin W Mabin, Kotaro Nakanishi, Guramrit Singh
Argonaute proteins (AGOs) are loaded with small RNAs as guides to recognize target mRNAs. Since the target specificity heavily depends on the base complementarity between two strands, it is important to identify small guide and long target RNAs bound to AGOs. For this purpose, next-generation sequencing (NGS) technologies have extended our appreciation truly to the nucleotide level. However, the identification of RNAs via NGS from scarce RNA samples remains a challenge. Further, most commercial and published methods are compatible with either small RNAs or long RNAs, but are not equally applicable to both...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29030829/review-diagnosing-common-variable-immunodeficiency-disorder-in-the-era-of-genome-sequencing
#13
REVIEW
Rohan Ameratunga, Klaus Lehnert, See-Tarn Woon, David Gillis, Vanessa L Bryant, Charlotte A Slade, Richard Steele
Common variable immunodeficiency disorders (CVID) are an enigmatic group of often heritable conditions, which may manifest for the first time in early childhood or as late as the eighth decade of life. In the last 5 years, next generation sequencing (NGS) has revolutionised identification of genetic disorders. However, despite the best efforts of researchers around the globe, CVID conditions have been slow to yield their molecular secrets. We have previously described the many clinical advantages of identifying the genetic basis of primary immunodeficiency disorders (PIDs)...
October 14, 2017: Clinical Reviews in Allergy & Immunology
https://www.readbyqxmd.com/read/29030741/the-role-of-next-generation-sequencing-in-sarcomas-evolution-from-light-microscope-to-molecular-microscope
#14
REVIEW
Roman Groisberg, Jason Roszik, Anthony Conley, Shreyaskumar R Patel, Vivek Subbiah
PURPOSE OF REVIEW: Sarcomas are rare, heterogeneous group of soft tissue and bone tumors. Precise diagnosis of specific subtypes is challenging using conventional methods. Herein, we review the role of next-generation sequencing (NGS) technology that is used for rapid sequencing of DNA and RNA. RECENT FINDINGS: Recent sarcoma specific studies recommend that molecular genetic testing should be added at diagnosis for appropriate clinical management in addition to diagnosis by expert pathologists...
October 13, 2017: Current Oncology Reports
https://www.readbyqxmd.com/read/29029728/software-dedicated-to-virus-sequence-analysis-bioinformatics-goes-viral
#15
Martin Hölzer, Manja Marz
Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research. The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance. The power of new genome sequencing technologies, associated with new tools to handle "big data", provides unprecedented opportunities to address fundamental questions in virology. Here, we present an overview of the current technologies, challenges, and advantages of Next-Generation Sequencing (NGS) in relation to the field of virology...
2017: Advances in Virus Research
https://www.readbyqxmd.com/read/29029725/bluetongue-virus-from-btv-1-to-btv-27
#16
Guillaume Belbis, Stéphan Zientara, Emmanuel Bréard, Corinne Sailleau, Grégory Caignard, Damien Vitour, Houssam Attoui
Bluetongue virus (BTV) is the type species of genus Orbivirus within family Reoviridae. Bluetongue virus is transmitted between its ruminant hosts by the bite of Culicoides spp. midges. Severe BT cases are characterized by symptoms including hemorrhagic fever, particularly in sheep, loss of productivity, and death. To date, 27 BTV serotypes have been documented. These include novel isolates of atypical BTV, which have been almost fully characterized using deep sequencing technologies and do not rely on Culicoides vectors for their transmission among hosts...
2017: Advances in Virus Research
https://www.readbyqxmd.com/read/29029145/blood-meal-source-characterization-using-illumina-sequencing-in-the-chagas-disease-vector-rhodnius-pallescens-hemiptera-reduviidae-in-panam%C3%A3
#17
Troy J Kieran, Nicole L Gottdenker, Christina P Varian, Azael Saldaña, Nicolas Means, Darlisha Owens, Jose E Calzada, Travis C Glenn
Accurate blood meal identification is critical to understand hematophagous vector-host relationships. This study describes a customizable Next-Generation Sequencing (NGS) approach to identify blood meals from Rhodnius pallescens (Hemiptera: Reduviidae) triatomines using multiple barcoded primers and existing software to pick operational taxonomic units and match sequences for blood meal identification. We precisely identified all positive control samples using this method and further examined 74 wild-caught R...
October 4, 2017: Journal of Medical Entomology
https://www.readbyqxmd.com/read/29028885/hotresdb-host-transcriptional-response-database-for-viral-hemorrhagic-fevers
#18
Jonathan Lo, Deric Zhang, Emily Speranza, Jose A Negron, John H Connor
Summary: High-throughput screening of the host transcriptional response to various viral infections provides a wealth of data but utilization of microarray and next generation sequencing (NGS) data for analysis can be difficult. The Host Transcriptional Response DataBase (HoTResDB), allows visitors to access already processed microarray and NGS data from non-human primate models of viral hemorrhagic fever to better understand the host transcriptional response. Availability: HoTResDB is freely available at http://hotresdb...
September 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29027916/a-next-generation-sequencing-approach-uncovers-viral-transcripts-incorporated-in-poxvirus-virions
#19
Marica Grossegesse, Joerg Doellinger, Berit Haldemann, Lars Schaade, Andreas Nitsche
Transcripts are known to be incorporated in particles of DNA viruses belonging to the families of Herpesviridae and Mimiviridae, but the presence of transcripts in other DNA viruses, such as poxviruses, has not been analyzed yet. Therefore, we first established a next-generation-sequencing (NGS)-based protocol, enabling the unbiased identification of transcripts in virus particles. Subsequently, we applied our protocol to analyze RNA in an emerging zoonotic member of the Poxviridae family, namely Cowpox virus...
October 13, 2017: Viruses
https://www.readbyqxmd.com/read/29027470/next-generation-sequencing-applications-for-cardiovascular-disease
#20
Samira Kalayinia, Hamidreza Goodarzynejad, Majid Maleki, Nejat Mahdieh
The Human Genome Project (HGP), as the primary sequencing of the human genome, lasted more than one decade to be completed using the traditional Sanger's method. At present, next-generation sequencing (NGS) technology could provide the genome sequence data in hours. NGS has also decreased the expense of sequencing; therefore, nowadays it is possible to carry out both whole-genome (WGS) and whole-exome sequencing (WES) for the variations detection in patients with rare genetic diseases as well as complex disorders such as common cardiovascular diseases (CVDs)...
October 13, 2017: Annals of Medicine
keyword
keyword
65993
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"