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Next generation sequencing

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https://www.readbyqxmd.com/read/28655203/kronos-a-workflow-assembler-for-genome-analytics-and-informatics
#1
M Jafar Taghiyar, Jamie Rosner, Diljot Grewal, Bruno M Grande, Radhouane Aniba, Jasleen Grewal, Paul C Boutros, Ryan D Morin, Ali Bashashati, Sohrab P Shah
Background: The field of next generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into 'best practices' for automated analysis of NGS datasets) still requires significant programming investment and expertise. Results: We present Kronos , a software platform for facilitating the development and execution of modular, auditable and distributable bioinformatics workflows...
June 26, 2017: GigaScience
https://www.readbyqxmd.com/read/28654985/transcriptomic-profiling-of-posterior-polymorphous-corneal-dystrophy
#2
Doug D Chung, Ricardo F Frausto, Benjamin R Lin, Evelyn M Hanser, Zack Cohen, Anthony J Aldave
Purpose: To investigate the molecular basis of posterior polymorphous corneal dystrophy (PPCD) by examining the PPCD transcriptome and the effect of decreased ZEB1 expression on corneal endothelial cell (CEnC) gene expression. Methods: Next-generation RNA sequencing (RNA-seq) analyses of corneal endothelium from two PPCD-affected individuals (one with PPCD3 and one of unknown genetic cause) compared with two age-matched controls, and primary human CEnC (pHCEnC) transfected with siRNA-mediated ZEB1 knockdown...
June 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28654689/a-high-density-intraspecific-snp-linkage-map-of-pigeonpea-cajanas-cajan-l-millsp
#3
Sheetal Arora, Ajay Kumar Mahato, Sangeeta Singh, Paritra Mandal, Shefali Bhutani, Sutapa Dutta, Giriraj Kumawat, Bikram Pratap Singh, A K Chaudhary, Rekha Yadav, K Gaikwad, Amitha Mithra Sevanthi, Subhojit Datta, Ranjeet S Raje, Tilak R Sharma, Nagendra Kumar Singh
Pigeonpea (Cajanus cajan (L.) Millsp.) is a major food legume cultivated in semi-arid tropical regions including the Indian subcontinent, Africa, and Southeast Asia. It is an important source of protein, minerals, and vitamins for nearly 20% of the world population. Due to high carbon sequestration and drought tolerance, pigeonpea is an important crop for the development of climate resilient agriculture and nutritional security. However, pigeonpea productivity has remained low for decades because of limited genetic and genomic resources, and sparse utilization of landraces and wild pigeonpea germplasm...
2017: PloS One
https://www.readbyqxmd.com/read/28654459/hodgkin-lymphoma-in-a-patient-with-ifap-syndrome-a-case-report-and-review-of-literature
#4
Nader Shakibazad, Mahdi Shahriari, Soroor Inaloo
The IFAP syndrome is a rare X-linked recessive inheritance disorder with defect of the MBTPS2 gene defined by the triad of follicular ichthyosis, alopecia, and photophobia. A total of 40 cases has been reported, but no correlation with Hodgkin lymphoma has been reported yet. A 3.5-year-old boy was diagnosed with IFAP syndrome confirmed by Next Generation Sequencing. He was on regular follow-up when he developed prolonged fever and lymphadenopathy. His lymph node biopsy showed Hodgkin lymphoma with mixed cellularity subtype...
June 26, 2017: Journal of Pediatric Hematology/oncology
https://www.readbyqxmd.com/read/28654195/dynamics-of-the-oral-microbiota-as-a-tool-to-estimate-time-since-death
#5
Joe Adserias Garriga, Narciso M Quijada, Marta Hernandez, David Rodríguez Lázaro, Dawnie Steadman, Jesús Garcia-Gil
Oral cavity harbors one of the most diverse microbiomes in the human body. It has been shown to be the second most complex in the body after the gastro- intestinal tract. Upon death, the indigenous microorganisms lead the decomposition of the carcass. Therefore, oral cavity and gastro-intestinal tract microbiomes, play a key role in human decomposition. The aim of the present study is to monitor the microbiome of decaying bodies on a daily basis and to identify signature bacterial taxa, that can improve postmortem interval estimation...
June 27, 2017: Molecular Oral Microbiology
https://www.readbyqxmd.com/read/28654067/bidirectional-retroviral-integration-site-pcr-methodology-and-quantitative-data-analysis-workflow
#6
Gajendra W Suryawanshi, Song Xu, Yiming Xie, Tom Chou, Namshin Kim, Irvin S Y Chen, Sanggu Kim
Integration Site (IS) assays are a critical component of the study of retroviral integration sites and their biological significance. In recent retroviral gene therapy studies, IS assays, in combination with next-generation sequencing, have been used as a cell-tracking tool to characterize clonal stem cell populations sharing the same IS. For the accurate comparison of repopulating stem cell clones within and across different samples, the detection sensitivity, data reproducibility, and high-throughput capacity of the assay are among the most important assay qualities...
June 14, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28654059/comprehensive-dna-methylation-analysis-using-a-methyl-cpg-binding-domain-capture-based-method-in-chronic-lymphocytic-leukemia-patients
#7
Santhilal Subhash, Meena Kanduri
The role of long noncoding RNAs (lncRNAs) in cancer is coming to the forefront due to growing interest in understanding their mechanistic functions during cancer development and progression. Despite this, the global epigenetic regulation of lncRNAs and repetitive sequences in cancer has not been well investigated, particularly in chronic lymphocytic leukemia (CLL). This study focuses on a unique approach: the immunoprecipitation-based capture of double-stranded, methylated DNA fragments using methyl-binding domain (MBD) proteins, followed by next-generation sequencing (MBD-seq)...
June 16, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28654052/flow-sorting-and-exome-sequencing-of-the-reed-sternberg-cells-of-classical-hodgkin-lymphoma
#8
Jonathan B Reichel, Jason McCormick, Jonathan R Fromm, Olivier Elemento, Ethel Cesarman, Mikhail Roshal
The Hodgkin Reed-Sternberg cells of classical Hodgkin lymphoma are sparsely distributed within a background of inflammatory lymphocytes and typically comprise less than 1% of the tumor mass. Material derived from bulk tumor contains tumor content at a concentration insufficient for characterization. Therefore, fluorescence activated cell sorting using eight antibodies, as well as side- and forward-scatter, is described here as a method of rapidly separating and concentrating with high purity thousands of HRS cells from the tumor for subsequent study...
June 10, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28653203/ras-screening-in-colorectal-cancer-a-comprehensive-analysis-of-the-results-from-the-uk-neqas-colorectal-cancer-external-quality-assurance-schemes-2009-2016
#9
Susan D Richman, Jennifer Fairley, Rachel Butler, Zandra C Deans
Evidence strongly indicates that extended RAS testing should be undertaken in mCRC patients, prior to prescribing anti-EGFR therapies. With more laboratories implementing testing, the requirement for External Quality Assurance schemes increases, thus ensuring high standards of molecular analysis. Data was analysed from 15 United Kingdom National External Quality Assessment Service (UK NEQAS) for Molecular Genetics Colorectal cancer external quality assurance (EQA) schemes, delivered between 2009 and 2016. Laboratories were provided annually with nine colorectal tumour samples for genotyping...
June 26, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28653176/amino-acid-synthesis-deficiencies
#10
REVIEW
T J de Koning
In recent years the number of disorders known to affect amino acid synthesis has grown rapidly. Nor is it just the number of disorders that has increased: the associated clinical phenotypes have also expanded spectacularly, primarily due to the advances of next generation sequencing diagnostics. In contrast to the "classical" inborn errors of metabolism in catabolic pathways, in which elevated levels of metabolites are easily detected in body fluids, synthesis defects present with low values of metabolites or, confusingly, even completely normal levels of amino acids...
June 26, 2017: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/28653026/mono-di-and-tri-ssrs-data-extraction-storage-from-1403-virus-genomes-with-next-generation-retrieval-mechanism
#11
K V S S R Murthy, K V V Satyanarayana
Now a day׳s SSRs occupy the dominant role in different areas of bio-informatics like new virus identification, DNA finger printing, paternity & maternity identification, disease identification, future disease expectations and possibilities etc., Due to their wide applications in various fields and their significance, SSRs have been the area of interest for many researchers. In the SSRs extraction, retrieval algorithms are used; if retrieval algorithms quality is improved then automatically SSRs extraction system will achieve the most relevant results...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28652783/prioritizing-single-nucleotide-polymorphisms-and-variants-associated-with-clinical-mastitis
#12
Prashanth Suravajhala, Alfredo Benso
Next-generation sequencing technology has provided resources to easily explore and identify candidate single-nucleotide polymorphisms (SNPs) and variants. However, there remains a challenge in identifying and inferring the causal SNPs from sequence data. A problem with different methods that predict the effect of mutations is that they produce false positives. In this hypothesis, we provide an overview of methods known for identifying causal variants and discuss the challenges, fallacies, and prospects in discerning candidate SNPs...
2017: Advances and Applications in Bioinformatics and Chemistry: AABC
https://www.readbyqxmd.com/read/28651553/ig-and-tr-single-chain-fragment-variable-scfv-sequence-analysis-a-new-advanced-functionality-of-imgt-v-quest-and-imgt-highv-quest
#13
Véronique Giudicelli, Patrice Duroux, Sofia Kossida, Marie-Paule Lefranc
BACKGROUND: IMGT®, the international ImMunoGeneTics information system® ( http://www.imgt.org ), was created in 1989 in Montpellier, France (CNRS and Montpellier University) to manage the huge and complex diversity of the antigen receptors, and is at the origin of immunoinformatics, a science at the interface between immunogenetics and bioinformatics. Immunoglobulins (IG) or antibodies and T cell receptors (TR) are managed and described in the IMGT® databases and tools at the level of receptor, chain and domain...
June 26, 2017: BMC Immunology
https://www.readbyqxmd.com/read/28651543/profiling-of-drought-responsive-microrna-and-mrna-in-tomato-using-high-throughput-sequencing
#14
Minmin Liu, Huiyang Yu, Gangjun Zhao, Qiufeng Huang, Yongen Lu, Bo Ouyang
BACKGROUND: Abiotic stresses cause severe loss of crop production. Among them, drought is one of the most frequent environmental stresses, which limits crop growth, development and productivity. Plant drought tolerance is fine-tuned by a complex gene regulatory network. Understanding the molecular regulation of this polygenic trait is crucial for the eventual success to improve plant yield and quality. Recent studies have demonstrated that microRNAs play critical roles in plant drought tolerance...
June 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28651381/meta-barcoding-in-combination-with-palynological-inference-is-a-potent-diagnostic-marker-for-honey-floral-composition
#15
Rama Chandra Laha, Surajit De Mandal, Lalhmanghai Ralte, Laldinfeli Ralte, Nachimuthu Senthil Kumar, Guruswami Gurusubramanian, Ramalingam Satishkumar, Raja Mugasimangalam, Nagesh Aswathnarayana Kuravadi
Identification of floral samples present in honey is important in order to determine the medicinal value, enhance the production of honey as well as to conserve the honey bees. Traditional approaches for studying pollen samples are based on microscopic observation which is laborious, time intensive and requires specialized palynological knowledge. Present study compares two composite honey metagenome collected from 20 samples in Mizoram, Northeast India using three gene loci- rbcL, matK and ITS2 that was sequenced using a next-generation sequencing (NGS) platform (Illumina Miseq)...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28650976/effect-of-praziquantel-on-the-differential-expression-of-mouse-hepatic-genes-and-parasite-atp-binding-cassette-transporter-gene-family-members-during-schistosoma-mansoni-infection
#16
Melissa C Sanchez, Katina V Krasnec, Amalia S Parra, Christian von Cabanlong, Geoffrey N Gobert, Boris Umylny, Pauline M Cupit, Charles Cunningham
Schistosomiasis is a chronic parasitic disease caused by sexually dimorphic blood flukes of the genus Schistosoma. Praziquantel (PZQ) is the only drug widely available to treat the disease but does not kill juvenile parasites. Here we report the use of next generation sequencing to study the transcriptional effect of PZQ on murine hepatic inflammatory, immune and fibrotic responses to Schistosoma mansoni worms and eggs. An initial T helper cell 1 (Th1) response is induced against schistosomes in mice treated with drug vehicle (Vh) around the time egg laying begins, followed by a T helper cell 2 (Th2) response and the induction of genes whose action leads to granuloma formation and fibrosis...
June 26, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28650483/disease-model-discovery-from-3-328-gene-knockouts-by-the-international-mouse-phenotyping-consortium
#17
Terrence F Meehan, Nathalie Conte, David B West, Julius O Jacobsen, Jeremy Mason, Jonathan Warren, Chao-Kung Chen, Ilinca Tudose, Mike Relac, Peter Matthews, Natasha Karp, Luis Santos, Tanja Fiegel, Natalie Ring, Henrik Westerberg, Simon Greenaway, Duncan Sneddon, Hugh Morgan, Gemma F Codner, Michelle E Stewart, James Brown, Neil Horner, Melissa Haendel, Nicole Washington, Christopher J Mungall, Corey L Reynolds, Juan Gallegos, Valerie Gailus-Durner, Tania Sorg, Guillaume Pavlovic, Lynette R Bower, Mark Moore, Iva Morse, Xiang Gao, Glauco P Tocchini-Valentini, Yuichi Obata, Soo Young Cho, Je Kyung Seong, John Seavitt, Arthur L Beaudet, Mary E Dickinson, Yann Herault, Wolfgang Wurst, Martin Hrabe de Angelis, K C Kent Lloyd, Ann M Flenniken, Lauryl M J Nutter, Susan Newbigging, Colin McKerlie, Monica J Justice, Stephen A Murray, Karen L Svenson, Robert E Braun, Jacqueline K White, Allan Bradley, Paul Flicek, Sara Wells, William C Skarnes, David J Adams, Helen Parkinson, Ann-Marie Mallon, Steve D M Brown, Damian Smedley
Although next-generation sequencing has revolutionized the ability to associate variants with human diseases, diagnostic rates and development of new therapies are still limited by a lack of knowledge of the functions and pathobiological mechanisms of most genes. To address this challenge, the International Mouse Phenotyping Consortium is creating a genome- and phenome-wide catalog of gene function by characterizing new knockout-mouse strains across diverse biological systems through a broad set of standardized phenotyping tests...
June 26, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28650476/cry2h-seq-a-massively-multiplexed-assay-for-deep-coverage-interactome-mapping
#18
Shelly A Trigg, Renee M Garza, Andrew MacWilliams, Joseph R Nery, Anna Bartlett, Rosa Castanon, Adeline Goubil, Joseph Feeney, Ronan O'Malley, Shao-Shan C Huang, Zhuzhu Z Zhang, Mary Galli, Joseph R Ecker
Broad-scale protein-protein interaction mapping is a major challenge given the cost, time, and sensitivity constraints of existing technologies. Here, we present a massively multiplexed yeast two-hybrid method, CrY2H-seq, which uses a Cre recombinase interaction reporter to intracellularly fuse the coding sequences of two interacting proteins and next-generation DNA sequencing to identify these interactions en masse. We applied CrY2H-seq to investigate sparsely annotated Arabidopsis thaliana transcription factors interactions...
June 26, 2017: Nature Methods
https://www.readbyqxmd.com/read/28650266/disease-suppressive-soils-new-insights-from-the-soil-microbiome
#19
Daniel Schlatter, Linda L Kinkel, Linda S Thomashow, David M Weller, Timothy Carl Paulitz
Soils suppressive to soilborne pathogens have been identified world-wide for almost 60 years and attributed mainly to suppressive or antagonistic microorganisms. Rather than identifying, testing and applying potential biocontrol agents in an inundative fashion, research into suppressive soils has attempted to understand how indigenous microbiomes can reduce disease, even in the presence of the pathogen, susceptible host, and favorable environment. Recent advances in next-generation sequencing of microbiomes have provided new tools to reexamine and further characterize the nature of these soils...
June 26, 2017: Phytopathology
https://www.readbyqxmd.com/read/28649842/lipo-oligomer-nanoformulations-for-targeted-intracellular-protein-delivery
#20
Peng Zhang, Benjamin Steinborn, Ulrich Lächelt, Stefan Zahler, Ernst Wagner
Here, we report novel lipo-oligoaminoamide nanoformulations for targeted intracellular protein delivery. Formulations are generated by first bioreversibly conjugating a sequence-defined amphiphilic lipo-oligomer 728 to the cargo protein via disulfide bonds, followed by formulation of the formed 728-SS-protein conjugate with different helper lipids in various compositions. The triblock oligoaminoamide 728 contains cysteines for reversible covalent protein conjugation and crosslink-stabilization of formed nanoparticles, polyethylene glycol (PEG) for shielding and providing a hydrophilic domain, eight cationizable succinoyl tetraethylene pentamine (Stp) repeats for endosomal buffering and escape into the cytosol, and a tetra-oleic acid block for hydrophobic stabilization...
June 26, 2017: Biomacromolecules
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