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https://www.readbyqxmd.com/read/28617221/identification-of-cancer-specific-motifs-in-mimotope-profiles-of-serum-antibody-repertoire
#1
Ekaterina Gerasimov, Alex Zelikovsky, Ion Măndoiu, Yurij Ionov
BACKGROUND: For fighting cancer, earlier detection is crucial. Circulating auto-antibodies produced by the patient's own immune system after exposure to cancer proteins are promising bio-markers for the early detection of cancer. Since an antibody recognizes not the whole antigen but 4-7 critical amino acids within the antigenic determinant (epitope), the whole proteome can be represented by a random peptide phage display library. This opens the possibility to develop an early cancer detection test based on a set of peptide sequences identified by comparing cancer patients' and healthy donors' global peptide profiles of antibody specificities...
June 7, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28529006/validation-of-a-next-generation-sequencing-pipeline-for-the-molecular-diagnosis-of-multiple-inherited-cancer-predisposing-syndromes
#2
Paula Paulo, Pedro Pinto, Ana Peixoto, Catarina Santos, Carla Pinto, Patrícia Rocha, Isabel Veiga, Gabriela Soares, Catarina Machado, Fabiana Ramos, Manuel R Teixeira
Despite the growing knowledge of the genetic background behind the cancers that occur in a context of hereditary predisposition, personal or family cancer history may not be clear enough to support directional gene testing. Defined targeted next-generation sequencing gene panels allow identification of the causative disease mutations of multigene syndromes and differential diagnosis for syndromes with phenotypically overlapping characteristics. Herein, we established a next-generation sequencing analysis pipeline for the molecular diagnosis of multiple inherited cancer predisposing syndromes using the commercially available target sequencing panel TruSight Cancer...
May 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28499414/hlascan-genotyping-of-the-hla-region-using-next-generation-sequencing-data
#3
Sojeong Ka, Sunho Lee, Jonghee Hong, Yangrae Cho, Joohon Sung, Han-Na Kim, Hyung-Lae Kim, Jongsun Jung
BACKGROUND: Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, however, no method with sufficient read depth has completely solved the allele phasing issue. In this study, we developed a new method (HLAscan) for HLA genotyping using NGS data. RESULTS: HLAscan performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28492066/progression-inference-for-somatic-mutations-in-cancer
#4
Leif E Peterson, Tatiana Kovyrshina
Computational methods were employed to determine progression inference of genomic alterations in commonly occurring cancers. Using cross-sectional TCGA data, we computed evolutionary trajectories involving selectivity relationships among pairs of gene-specific genomic alterations such as somatic mutations, deletions, amplifications, downregulation, and upregulation among the top 20 driver genes associated with each cancer. Results indicate that the majority of hierarchies involved TP53, PIK3CA, ERBB2, APC, KRAS, EGFR, IDH1, VHL, etc...
April 2017: Heliyon
https://www.readbyqxmd.com/read/28422718/validation-and-optimization-of-the-ion-torrent-s5-xl-sequencer-and-oncomine-workflow-for-brca1-and-brca2-genetic-testing
#5
Saeam Shin, Yoonjung Kim, Seoung Chul Oh, Nae Yu, Seung-Tae Lee, Jong Rak Choi, Kyung-A Lee
In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA)...
May 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28388427/the-nextgen-genetic-association-studies-consortium-a-foray-into-in%C3%A2-vitro-population-genetics
#6
Curtis R Warren, Cashell E Jaquish, Chad A Cowan
The National Heart, Lung, and Blood Institute's Next Generation Genetic Association Studies Consortium has used induced pluripotent stem cell technology to study the effects of common genetic variants in vitro. This issue of Cell Stem Cell and affiliated journals include several manuscripts describing the results of the consortium's efforts.
April 6, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28388420/ipscs-meet-gwas-the-nextgen-consortium
#7
EDITORIAL
Deborah J Sweet
No abstract text is available yet for this article.
April 6, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28324502/telomeres-and-nextgen-co-fish-directional-genomic-hybridization-telo-dgh%C3%A2
#8
Miles J McKenna, Erin Robinson, Edwin H Goodwin, Michael N Cornforth, Susan M Bailey
The cytogenomics-based methodology of Directional Genomic Hybridization (dGH™) emerged from the concept of strand-specific hybridization, first made possible by Chromosome Orientation FISH (CO-FISH), the utility of which was demonstrated in a variety of early applications, often involving telomeres. Similar to standard whole chromosome painting (FISH), dGH™ is capable of identifying inter-chromosomal rearrangements (translocations between chromosomes), but its distinctive strength stems from its ability to detect intra-chromosomal rearrangements (inversions within chromosomes), and to do so at higher resolution than previously possible...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28306751/peptidomic-and-transcriptomic-profiling-of-four-distinct-spider-venoms
#9
Vera Oldrati, Dominique Koua, Pierre-Marie Allard, Nicolas Hulo, Miriam Arrell, Wolfgang Nentwig, Frédérique Lisacek, Jean-Luc Wolfender, Lucia Kuhn-Nentwig, Reto Stöcklin
Venom based research is exploited to find novel candidates for the development of innovative pharmacological tools, drug candidates and new ingredients for cosmetic and agrochemical industries. Moreover, venomics, as a well-established approach in systems biology, helps to elucidate the genetic mechanisms of the production of such a great molecular biodiversity. Today the advances made in the proteomics, transcriptomics and bioinformatics fields, favor venomics, allowing the in depth study of complex matrices and the elucidation even of minor compounds present in minute biological samples...
2017: PloS One
https://www.readbyqxmd.com/read/28290981/case-report-of-clinical-vignette-osteopetrosis
#10
John B Moore, Thanh D Hoang, Alfred F Shwayhat
INTRODUCTION: Osteopetrosis is a connective tissue disorder resulting from abnormally dense bone predisposing patients to fracture. The clinical pattern of fractures across time and space as well as suggestive radiographic findings usually raises diagnostic suspicion. Multiple genetic mutations resulting in dysfunctional osteoclasts have been implicated in the pathogenesis of osteopetrosis with variable inheritance patterns. In severe cases, usually inherited in an autosomal recessive pattern, the medullary cavity important in the production of normal blood cell progenitors is replaced by defective endochondral bone, leading to pancytopenia and consequential extramedullary hematopoiesis...
March 2017: Military Medicine
https://www.readbyqxmd.com/read/28249565/statistical-method-to-compare-massive-parallel-sequencing-pipelines
#11
M H Elsensohn, N Leblay, S Dimassi, A Campan-Fournier, A Labalme, F Roucher-Boulez, D Sanlaville, G Lesca, C Bardel, P Roy
BACKGROUND: Today, sequencing is frequently carried out by Massive Parallel Sequencing (MPS) that cuts drastically sequencing time and expenses. Nevertheless, Sanger sequencing remains the main validation method to confirm the presence of variants. The analysis of MPS data involves the development of several bioinformatic tools, academic or commercial. We present here a statistical method to compare MPS pipelines and test it in a comparison between an academic (BWA-GATK) and a commercial pipeline (TMAP-NextGENe®), with and without reference to a gold standard (here, Sanger sequencing), on a panel of 41 genes in 43 epileptic patients...
March 1, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28111279/a-comprehensive-ethnically-diverse-library-of-sickle-cell-disease-specific-induced-pluripotent-stem-cells
#12
Seonmi Park, Andreia Gianotti-Sommer, Francisco Javier Molina-Estevez, Kim Vanuytsel, Nick Skvir, Amy Leung, Sarah S Rozelle, Elmutaz Mohammed Shaikho, Isabelle Weir, Zhihua Jiang, Hong-Yuan Luo, David H K Chui, Maria Stella Figueiredo, Abdulraham Alsultan, Amein Al-Ali, Paola Sebastiani, Martin H Steinberg, Gustavo Mostoslavsky, George J Murphy
Sickle cell anemia affects millions of people worldwide and is an emerging global health burden. As part of a large NIH-funded NextGen Consortium, we generated a diverse, comprehensive, and fully characterized library of sickle-cell-disease-specific induced pluripotent stem cells (iPSCs) from patients of different ethnicities, β-globin gene (HBB) haplotypes, and fetal hemoglobin (HbF) levels. iPSCs stand to revolutionize the way we study human development, model disease, and perhaps eventually, treat patients...
April 11, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28065881/an-integrated-transcriptomics-guided-genome-wide-promoter-analysis-and-next-generation-proteomics-approach-to-mine-factor-s-regulating-cellular-differentiation
#13
Kamal Mandal, Samuel L Bader, Pankaj Kumar, Dipankar Malakar, David S Campbell, Bhola Shankar Pradhan, Rajesh K Sarkar, Neerja Wadhwa, Souvik Sensharma, Vaibhav Jain, Robert L Moritz, Subeer S Majumdar
Differential next-generation-omics approaches aid in the visualization of biological processes and pave the way for divulging important events and/or interactions leading to a functional output at cellular or systems level. To this end, we undertook an integrated Nextgen transcriptomics and proteomics approach to divulge differential gene expression of infant and pubertal rat Sertoli cells (Sc).Unlike, pubertal Sc, infant Sc are immature and fail to support spermatogenesis. We found exclusive association of 14 and 19 transcription factor binding sites to infantile and pubertal states of Sc, respectively, using differential transcriptomics-guided genome-wide computational analysis of relevant promoters employing 220 Positional Weight Matrices from the TRANSFAC database...
January 8, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27977123/profiling-protease-specificity-combining-yeast-er-sequestration-screening-yess-with-next-generation-sequencing
#14
Qing Li, Li Yi, Kam Hon Hoi, Peter Marek, George Georgiou, Brent L Iverson
An enzyme engineering technology involving yeast endoplasmic reticulum (ER) sequestration screening (YESS) has been recently developed. Here, a new method is established, in which the YESS platform is combined with NextGen sequencing (NGS) to enable a comprehensive survey of protease specificity. In this approach, a combinatorial substrate library is targeted to the yeast ER and transported through the secretory pathway, interacting with any protease(s) residing in the ER. Multicolor FACS screening is used to isolate cells labeled with fluorophore-conjugated antibodies, followed by NGS to profile the cleaved substrates...
January 3, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/27957521/dataset-of-the-absorption-emission-and-excitation-spectra-and-fluorescence-intensity-graphs-of-fluorescent-cyanine-dyes-for-the-quantification-of-low-amounts-of-dsdna
#15
Brigitte Bruijns, Roald Tiggelaar, Han Gardeniers
This article describes data related to a research article entitled "Fluorescent cyanine dyes for the quantification of low amounts of dsDNA" (B. Bruijns, R. Tiggelaar, J. Gardeniers, 2016) [1]. Six cyanine dsDNA dyes - EvaGreen, SYBR Green, PicoGreen, AccuClear, AccuBlue NextGen and YOYO-1 - are investigated and in this article the absorption spectra, as well as excitation and emission spectra, for all six researched cyanine dyes are given, all recorded under exactly identical experimental conditions. The intensity graphs, with the relative fluorescence in the presence of low amounts of dsDNA, are also provided...
February 2017: Data in Brief
https://www.readbyqxmd.com/read/27936855/evaluating-probe-techniques-and-a-situated-theory-of-situation-awareness
#16
Dan Chiappe, Corey A Morgan, Joshua Kraut, Jason Ziccardi, Lindsay Sturre, Thomas Z Strybel, Kim-Phuong L Vu
Probe techniques for measuring situation awareness (SA) vary in whether scenarios are paused and displays visible while questions are presented. We examined which technique is least intrusive on workload and performance in air traffic control, and which is most sensitive at capturing differences in SA when automation varies. We also tested predictions from the situated SA theory, which holds that operators offload specific and low-priority information onto displays to limit internal processing. To accomplish these goals, Experiments 1 and 2 manipulated whether radar displays were visible and scenarios paused during queries...
December 2016: Journal of Experimental Psychology. Applied
https://www.readbyqxmd.com/read/27928018/expression-of-the-antisense-to-latency-transcript-long-noncoding-rna-in-kaposi-s-sarcoma-associated-herpesvirus
#17
Jason M Schifano, Kathleen Corcoran, Hemant Kelkar, Dirk P Dittmer
The regulation of latency is central to herpesvirus biology. Recent transcriptome-wide surveys have uncovered evidence for promiscuous transcription across the entirety of the Kaposi's sarcoma-associated herpesvirus (KSHV) genome and postulated the existence of multiple viral long noncoding RNAs (lncRNAs). Next-generation sequencing studies are highly dependent on the specific experimental approach and particular algorithms of analysis and therefore benefit from independent confirmation of the results. The antisense-to-latency transcript (ALT) lncRNA was discovered by genome-tiling microarray (Chandriani et al...
February 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/27920089/world-endometriosis-society-consensus-on-the-classification-of-endometriosis
#18
Neil P Johnson, Lone Hummelshoj, G David Adamson, Jörg Keckstein, Hugh S Taylor, Mauricio S Abrao, Deborah Bush, Ludwig Kiesel, Rulla Tamimi, Kathy L Sharpe-Timms, Luk Rombauts, Linda C Giudice
STUDY QUESTION: What is the global consensus on the classification of endometriosis that considers the views of women with endometriosis? SUMMARY ANSWER: We have produced an international consensus statement on the classification of endometriosis through systematic appraisal of evidence and a consensus process that included representatives of national and international, medical and non-medical societies, patient organizations, and companies with an interest in endometriosis...
February 2017: Human Reproduction
https://www.readbyqxmd.com/read/27915271/changes-in-renal-gene-expression-associated-with-induced-ochratoxicosis-in-chickens-activation-and-deactivation-of-transcripts-after-varying-durations-of-exposure
#19
Cynthia P Zeferino, Kevin D Wells, Ana Silvia A M T Moura, George E Rottinghaus, David R Ledoux
Exposure to ochratoxin A (OTA) can lead to changes in global gene expression. This study investigated the individual expression of genes turned on and off in renal cells of chicks after different durations of exposure to dietary OTA. One hundred and eighty day-old male broiler chicks (Ross 308) were randomly assigned to a 3 × 3 factorial arrangement of treatments (3 levels of OTA: 0, 1 and 2 mg OTA/kg diet and 3 time periods: 7, 14 and 21 d). Birds were allocated to 36 pens (4 replicate pens of 5 birds each per treatment)...
June 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/27801969/high-performance-computation-of-landscape-genomic-models-including-local-indicators-of-spatial-association
#20
S Stucki, P Orozco-terWengel, B R Forester, S Duruz, L Colli, C Masembe, R Negrini, E Landguth, M R Jones, M W Bruford, P Taberlet, S Joost
With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics-i.e. the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present Samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental datasets...
November 1, 2016: Molecular Ecology Resources
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