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https://www.readbyqxmd.com/read/28912962/gene-panel-sequencing-in-brazilian-patients-with-retinitis-pigmentosa
#1
Kárita Antunes Costa, Mariana Vallim Salles, Chris Whitebirch, John Chiang, Juliana Maria Ferraz Sallum
BACKGROUND: Retinal dystrophies constitute a group of diseases characterized by clinical variability and pronounced genetic heterogeneity. Retinitis pigmentosa is the most common subtype of hereditary retinal dystrophy and is characterized by a progressive loss of peripheral field vision (Tunnel Vision), eventual loss of central vision, and progressive night blindness. The characteristics of the fundus changes include bone-spicule formations, attenuated blood vessels, reduced and/or abnormal electroretinograms, changes in structure imaged by optical coherence tomography, and subjective changes in visual function...
2017: International Journal of Retina and Vitreous
https://www.readbyqxmd.com/read/28838068/rat-genome-and-model-resources
#2
Mary Shimoyama, Jennifer R Smith, Elizabeth Bryda, Takashi Kuramoto, Laura Saba, Melinda Dwinell
Rats remain a major model for studying disease mechanisms and discovery, validation, and testing of new compounds to improve human health. The rat's value continues to grow as indicated by the more than 1.4 million publications (second to human) at PubMed documenting important discoveries using this model. Advanced sequencing technologies, genome modification techniques, and the development of embryonic stem cell protocols ensure the rat remains an important mammalian model for disease studies. The 2004 release of the reference genome has been followed by the production of complete genomes for more than two dozen individual strains utilizing NextGen sequencing technologies; their analyses have identified over 80 million variants...
July 1, 2017: ILAR Journal
https://www.readbyqxmd.com/read/28759038/high-depth-high-accuracy-microsatellite-genotyping-enables-precision-lung-cancer-risk-classification
#3
K R Velmurugan, R T Varghese, N C Fonville, H R Garner
There remains a large discrepancy between the known genetic contributions to cancer and that which can be explained by genomic variants, both inherited and somatic. Recently, understudied repetitive DNA regions called microsatellites have been identified as genetic risk markers for a number of diseases including various cancers (breast, ovarian and brain). In this study, we demonstrate an integrated process for identifying and further evaluating microsatellite-based risk markers for lung cancer using data from the cancer genome atlas and the 1000 genomes project...
July 31, 2017: Oncogene
https://www.readbyqxmd.com/read/28701812/next-generation-data-systems-and-knowledge-products-to-support-agricultural-producers-and-science-based-policy-decision-making
#4
Susan M Capalbo, John M Antle, Clark Seavert
Research on next generation agricultural systems models shows that the most important current limitation is data, both for on-farm decision support and for research investment and policy decision making. One of the greatest data challenges is to obtain reliable data on farm management decision making, both for current conditions and under scenarios of changed bio-physical and socio-economic conditions. This paper presents a framework for the use of farm-level and landscape-scale models and data to provide analysis that could be used in NextGen knowledge products, such as mobile applications or personal computer data analysis and visualization software...
July 2017: Agricultural Systems
https://www.readbyqxmd.com/read/28701811/next-generation-agricultural-system-data-models-and-knowledge-products-introduction
#5
John M Antle, James W Jones, Cynthia E Rosenzweig
Agricultural system models have become important tools to provide predictive and assessment capability to a growing array of decision-makers in the private and public sectors. Despite ongoing research and model improvements, many of the agricultural models today are direct descendants of research investments initially made 30-40 years ago, and many of the major advances in data, information and communication technology (ICT) of the past decade have not been fully exploited. The purpose of this Special Issue of Agricultural Systems is to lay the foundation for the next generation of agricultural systems data, models and knowledge products...
July 2017: Agricultural Systems
https://www.readbyqxmd.com/read/28701810/next-generation-agricultural-system-models-and-knowledge-products-synthesis-and-strategy
#6
EDITORIAL
John M Antle, James W Jones, Cynthia Rosenzweig
The purpose of this Special Issue of Agricultural Systems is to lay the foundation for the next generation of agricultural systems data, models and knowledge products. In the Introduction to this Special Issue, we described a vision for accelerating the rate of agricultural innovation and meeting the growing global need for food and fiber. In this concluding article of the NextGen Special Issue we synthesize insights and formulate a strategy to advance data, models, and knowledge products that are consistent with this vision...
July 2017: Agricultural Systems
https://www.readbyqxmd.com/read/28655556/comparison-of-two-bioinformatics-tools-used-to-characterize-the-microbial-diversity-and-predictive-functional-attributes-of-microbial-mats-from-lake-obersee-antarctica
#7
Hyunmin Koo, Joseph A Hakim, Casey D Morrow, Peter G Eipers, Alfonso Davila, Dale T Andersen, Asim K Bej
In this study, using NextGen sequencing of the collective 16S rRNA genes obtained from two sets of samples collected from Lake Obersee, Antarctica, we compared and contrasted two bioinformatics tools, PICRUSt and Tax4Fun. We then developed an R script to assess the taxonomic and predictive functional profiles of the microbial communities within the samples. Taxa such as Pseudoxanthomonas, Planctomycetaceae, Cyanobacteria Subsection III, Nitrosomonadaceae, Leptothrix, and Rhodobacter were exclusively identified by Tax4Fun that uses SILVA database; whereas PICRUSt that uses Greengenes database uniquely identified Pirellulaceae, Gemmatimonadetes A1-B1, Pseudanabaena, Salinibacterium and Sinobacteraceae...
June 24, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28617221/identification-of-cancer-specific-motifs-in-mimotope-profiles-of-serum-antibody-repertoire
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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...
April 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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