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Next generation sequencing

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https://www.readbyqxmd.com/read/29036818/a-9-microrna-signature-in-serum-serves-as-a-noninvasive-biomarker-in-early-diagnosis-of-alzheimer-s-disease
#1
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/29036653/mircarta-a-central-repository-for-collecting-mirna-candidates
#2
Christina Backes, Tobias Fehlmann, Fabian Kern, Tim Kehl, Hans-Peter Lenhof, Eckart Meese, Andreas Keller
The continuous increase of available biological data as consequence of modern high-throughput technologies poses new challenges for analysis techniques and database applications. Especially for miRNAs, one class of small non-coding RNAs, many algorithms have been developed to predict new candidates from next-generation sequencing data. While the amount of publications describing novel miRNA candidates keeps steadily increasing, the current gold standard database for miRNAs - miRBase - has not been updated since June 2014...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036644/roles-of-female-and-male-genotype-in-post-mating-responses-in-drosophila-melanogaster-roles-of-female-and-male-genotype-in-female-drosophila-melanogaster-transcriptional-physiological-and-behavioral-responses-to-mating
#3
Sofie Y N Delbare, Clement Y Chow, Mariana F Wolfner, Andrew G Clark
Mating induces a multitude of changes in female behavior, physiology and gene expression. Interactions between female and male genotype lead to variation in post-mating phenotypes and reproductive success. So far, few female molecules responsible for these interactions have been identified. Here, we used Drosophila melanogaster from five geographically dispersed populations to investigate such female x male genotypic interactions at the female transcriptomic and phenotypic levels. Females from each line were singly-mated to males from the same five lines, for a total of 25 combinations...
October 4, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036614/identification-of-a-candidate-mutation-in-the-col1a2-gene-of-a-chow-chow-with-osteogenesis-imperfecta
#4
E M Quist, R Doan, R R Pool, B F Porter, D L Bannasch, S V Dindot
Osteogenesis imperfecta (OI) is a genetic disease that occurs in humans and animals. Individuals with OI exhibit signs of extreme bone fragility and osteopenia with frequent fractures and perinatal lethality in severe cases. In this study, we report the clinical diagnosis of OI in a dog and the use targeted next-generation sequencing to identify a candidate autosomal dominant mutation in the COL1A2 gene. A five-month old male Chow Chow was examined with a fractured left humerus and resolving, bilateral femoral fractures...
September 19, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036601/arrhythmogenic-right-ventricular-cardiomyopathy-implications-of-next-generation-sequencing-and-of-mirnas-regulation-in-appropriate-understanding-and-treatment
#5
Salvatore Patanè, Francesco Patanè
No abstract text is available yet for this article.
October 4, 2017: Europace: European Pacing, Arrhythmias, and Cardiac Electrophysiology
https://www.readbyqxmd.com/read/29036546/crocoblast-running-blast-efficiently-in-the-age-of-next-generation-sequencing
#6
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/29036527/isyte-2-0-a-database-for-expression-based-gene-discovery-in-the-eye
#7
Atul Kakrana, Andrian Yang, Deepti Anand, Djordje Djordjevic, Deepti Ramachandruni, Abhyudai Singh, Hongzhan Huang, Joshua W K Ho, Salil A Lachke
Although successful in identifying new cataract-linked genes, the previous version of the database iSyTE (integrated Systems Tool for Eye gene discovery) was based on expression information on just three mouse lens stages and was functionally limited to visualization by only UCSC-Genome Browser tracks. To increase its efficacy, here we provide an enhanced iSyTE version 2.0 (URL: http://research.bioinformatics.udel.edu/iSyTE) based on well-curated, comprehensive genome-level lens expression data as a one-stop portal for the effective visualization and analysis of candidate genes in lens development and disease...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036298/myvcf-a-desktop-application-for-high-throughput-mutations-data-management
#8
Alessandro Pietrelli, Luca Valenti
Summary: Next-generation sequencing technologies have become the most powerful tool to discover genetic variants associated with human diseases. Although the dramatic reductions in the costs facilitate the use in the wet-lab and clinics, the huge amount of data generated renders their management by non-expert researchers and physicians extremely difficult. Therefore, there is an urgent need of novel approaches and tools aimed at getting the 'end-users' closer to the sequencing data, facilitating the access by non-bioinformaticians, and to speed-up the functional interpretation of genetic variants...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036232/rare-and-common-variants-of-apob-and-pcsk9-in-korean-patients-with-extremely-low-low-density-lipoprotein-cholesterol-levels
#9
Chan Joo Lee, Yunbeom Lee, Sungha Park, Seok-Min Kang, Yangsoo Jang, Ji Hyun Lee, Sang-Hak Lee
BACKGROUND: Screening of variants, related to lipid metabolism in patients with extreme cholesterol levels, is a tool used to identify targets affecting cardiovascular outcomes. The aim of this study was to examine the prevalence and characteristics of rare and common variants of APOB and PCSK9 in Korean patients with extremely low low-density lipoprotein-cholesterol (LDL-C) levels. METHODS: Among 13,545 participants enrolled in a cardiovascular genome cohort, 22 subjects, whose LDL-C levels without lipid-lowering agents were ≤1 percentile (48 mg/dL) of Korean population, were analyzed...
2017: PloS One
https://www.readbyqxmd.com/read/29036181/juvenile-myasthenia-gravis-in-norway-hla-drb1-04-04-is-positively-associated-with-prepubertal-onset
#10
T H Popperud, M K Viken, E Kerty, B A Lie
BACKGROUND: Juvenile myasthenia gravis (MG) is a rare autoantibody mediated autoimmune disorder targeting the neuromuscular endplate. The clinical hallmark is muscle weakness and fatigability. Disease aetiology is complex, including both genetic and environmental factors. The involvement of genes in the human leukocyte antigen (HLA) is well established in adult MG. However, HLA associations in European juvenile MG have not been studied. This case-control study aimed to investigate and characterize genetic risk factors in prepubertal and postpubertal onset juvenile MG...
2017: PloS One
https://www.readbyqxmd.com/read/29035575/hetfhmm-a-novel-approach-to-infer-tumor-heterogeneity-using-factorial-hidden-markov-models
#11
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/29035510/crispri-and-crispra-screens-in-mammalian-cells-for-precision-biology-and-medicine
#12
Martin Kampmann
Next-generation DNA sequencing technologies have led to a massive accumulation of genomic and transcriptomic data from patients and healthy individuals. The major challenge ahead is to understand the functional significance of the elements of the human genome and transcriptome, and implications for diagnosis and treatment. Genetic screens in mammalian cells are a powerful approach to systematically elucidate gene function in health and disease states. In particular, recently developed CRISPR/Cas9-based screening approaches have enormous potential to uncover mechanisms and therapeutic strategies for human diseases...
October 16, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29033976/conffuse-high-confidence-fusion-gene-detection-across-tumor-entities
#13
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/29033962/unveiling-chloroplast-rna-editing-events-using-next-generation-small-rna-sequencing-data
#14
Nureyev F Rodrigues, Ana P Christoff, Guilherme C da Fonseca, Franceli R Kulcheski, Rogerio Margis
Organellar RNA editing involves the modification of nucleotide sequences to maintain conserved protein functions, mainly by reverting non-neutral codon mutations. The loss of plastid editing events, resulting from mutations in RNA editing factors or through stress interference, leads to developmental, physiological and photosynthetic alterations. Recently, next generation sequencing technology has generated the massive discovery of sRNA sequences and expanded the number of sRNA data. Here, we present a method to screen chloroplast RNA editing using public sRNA libraries from Arabidopsis, soybean and rice...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29033917/newly-isolated-bacteriophages-from-the-podoviridae-siphoviridae-and-myoviridae-families-have-variable-effects-on-putative-novel-dickeya-spp
#15
Špela Alič, Tina Naglič, Magda Tušek-Žnidarič, Maja Ravnikar, Nejc Rački, Matjaž Peterka, Tanja Dreo
Soft rot pathogenic bacteria from the genus Dickeya cause severe economic losses in orchid nurseries worldwide, and there is no effective control currently available. In the last decade, the genus Dickeya has undergone multiple changes as multiple new taxa have been described, and just recently a new putative Dickeya species was reported. This study reports the isolation of three bacteriophages active against putative novel Dickeya spp. isolates from commercially produced infected orchids that show variable host-range profiles...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29033905/a-review-on-the-applications-of-next-generation-sequencing-technologies-as-applied-to-food-related-microbiome-studies
#16
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/29033053/identification-and-characterization-of-a-novel-recessive-kcnq1-mutation-associated-with-romano-ward-long-qt-syndrome-in-two-iranian-families
#17
Zahra Zafari, Mohammad Dalili, Sirus Zeinali, Siamak Saber, Amir Farjam Fazeli Far, Mohammad Taghi Akbari
BACKGROUND: One of the foremost causes of sudden cardiac death in the young is an inherent cardiac arrhythmia known as Long-QT syndrome (LQTS). Whereas heterozygous mutations typically lead to the Romano-Ward type of LQTS, We have provided a further evidence for the recessive transmission of a novel KCNQ1 gene mutation in two consanguineous families for the first time in Iran. METHODS: Next generation sequencing, DNA Sanger sequencing and haplotype analysis were performed for genotype determination...
July 12, 2017: Journal of Electrocardiology
https://www.readbyqxmd.com/read/29032884/the-genetics-underlying-idiopathic-ventricular-fibrillation-a-special-role-for-catecholaminergic-polymorphic-ventricular-tachycardia
#18
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/29032825/line-1-retrotransposon-mediated-dna-transductions-in-endometriosis-associated-ovarian-cancers
#19
Zhouchunyang Xia, Dawn R Cochrane, Michael S Anglesio, Yi Kan Wang, Tayyebeh Nazeran, Basile Tessier-Cloutier, Melissa K McConechy, Janine Senz, Amy Lum, Ali Bashashati, Sohrab P Shah, David G Huntsman
OBJECTIVE: Endometrioid (ENOC) and clear cell ovarian carcinoma (CCOC) share a common precursor lesion, endometriosis, hence the designation endometriosis associated ovarian cancers (EAOC). Long interspersed nuclear element 1 (LINE-1 or L1), is a family of mobile genetic elements activated in many cancers capable of moving neighboring DNA through 3' transductions. Here we investigated the involvement of specific L1-mediated transductions in EAOCs. METHODS: Through whole genome sequencing, we identified active L1-mediated transductions originating within the TTC28 gene in 34% (10/29) of ENOC and 31% (11/35) of CCOC cases...
October 9, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29032547/genome-wide-mutagenesis-in-borrelia-burgdorferi
#20
Tao Lin, Lihui Gao
Signature-tagged mutagenesis (STM) is a functional genomics approach to identify bacterial virulence determinants and virulence factors by simultaneously screening multiple mutants in a single host animal, and has been utilized extensively for the study of bacterial pathogenesis, host-pathogen interactions, and spirochete and tick biology. The signature-tagged transposon mutagenesis has been developed to investigate virulence determinants and pathogenesis of Borrelia burgdorferi. Mutants in genes important in virulence are identified by negative selection in which the mutants fail to colonize or disseminate in the animal host and tick vector...
2018: Methods in Molecular Biology
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