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NGS sequencing

Hilaire C Lam, Julie S Nijmeh, Elizabeth P Henske
In just the past five years, dramatic changes have occurred in the clinical management of Tuberous Sclerosis Complex (TSC). Detailed knowledge about the role of the TSC proteins in regulating the activity of the mammalian Target of Rapamycin Complex 1 (mTORC1) underlies this paradigm-shifting progress. Advances continue to be made in understanding the genetic pathogenesis of the different tumours that occur in TSC, including pivotal discoveries using next-generation sequencing (NGS). For example, the pathogenesis of angiofibromas is now known to involve UV-induced mutations, and the pathogenesis of multifocal renal cell carcinoma (RCC) in TSC is now known to result from distinct second-hit mutations...
October 18, 2016: Journal of Pathology
Yun Long, Yinxin Zhang, Yanping Gong, Ruixue Sun, Longxiang Su, Xin Lin, Ao Shen, Jiali Zhou, Zhuoma Caiji, Xinying Wang, Dongfang Li, Honglong Wu, Hongdong Tan
BACKGROUND AND AIMS: Bacteremia is a common serious manifestation of disease in the intensive care unit (ICU), which requires quick and accurate determinations of pathogens to select the appropriate antibiotic treatment. To overcome the shortcomings of traditional bacterial culture (BC), we have adapted next-generation sequencing (NGS) technology to identify pathogens from cell-free plasma DNA. METHODS: In this study, 78 plasma samples from ICU patients were analyzed by both NGS and BC methods and verified by PCR amplification/Sanger sequencing and ten plasma samples from healthy volunteers were analyzed by NGS as negative controls to define or calibrate the threshold of the NGS methodology...
July 2016: Archives of Medical Research
Jingzi Zhong, Tiantian Xu, Gang Chen, Haixia Liao, Jiapeng Zhang, Dan Lan
Introduction Duchenne and Becker muscular dystrophies (DMD and BMD) are X-linked myopathies caused by mutations of the dystrophin gene. Methods Multiplex ligation-dependent probe amplification (MLPA) combined with next-generation sequencing (NGS) of the exons of the dystrophin gene were performed in 92 suspected DMD/BMD patients. Patients with negative results were subjected to additional muscle diseases panel tests. Results DNA rearrangements were detected in 65(70.65%) patients using MLPA. The deletions primarily clustered at exons 45-55, followed by exons 2-19...
October 17, 2016: Muscle & Nerve
Joshua J Meeks, Benedito A Carneiro, Sachin G Pai, Daniel T Oberlin, Alfred Rademaker, Kyle Fedorchak, Sohail Balasubramanian, Julia Elvin, Nike Beaubier, Francis J Giles
The genetic mechanisms associated with progression of high-risk non-muscle-invasive bladder cancer (HR-NMIBC) have not been described. We conducted selective next-generation sequencing (NGS) of HR-NMIBC and compared the genomic profiles of cancers that responded to intravesical therapy and those that progressed to muscle-invasive or advanced disease. DNA was extracted from paraffin-embedded sections from 25 HR-NMIBCs (22 with T1HG; 3 with TaHG with or without carcinoma in situ). Ten patients with HR-NMIBC developed progression (pT2+ or N+) ("progressors")...
October 14, 2016: Oncotarget
Daniel H Hovelson, Scott A Tomlins
Molecular biomarkers play little role in the current treatment of metastatic castration-resistant prostate cancer (CRPC). The advent of next-generation sequencing (NGS) has enabled the comprehensive molecular characterization of the genomic and transcriptomic landscape of both untreated primary prostate cancer and CRPC. Recent studies demonstrating the feasibility of interinstitution studies obtaining and NGS profiling of metastatic biopsies, targeted NGS approaches applicable to routine formalin-fixed, paraffin-embedded specimens, and NGS approaches applicable to circulating DNA and circulating tumor cells portend near-term adoption of NGS approaches in the management and treatment of CRPC...
September 2016: Cancer Journal
Apurva Jain, Milind Javle
Biliary tract cancers (BTCs) are relatively uncommon orphan tumors that have an aggressive disease course and a poor clinical outcome. Surgery is the only curative treatment, but most patients present with advanced disease and therefore have a limited survival. Gemcitabine and cisplatin based chemotherapy has been the only widely accepted standard systemic therapy regimen in these patients but these tumors can be chemoresistant, further complicating their management. In recent times, there has been considerable research in the genetics of BTC and with the advent of new, advanced technologies like next-generation sequencing (NGS) we are achieving a greater understanding of its disease biology...
October 2016: Journal of Gastrointestinal Oncology
Akiko Mori, Masatsugu Toyota, Masayoshi Shimada, Mika Mekata, Tetsuya Kurata, Masao Tasaka, Miyo T Morita
Forward genetics is a powerful approach used to link genotypes and phenotypes, and mutant screening/analysis has provided deep insights into many aspects of plant physiology. Gravitropism is a tropistic response in plants, in which hypocotyls and stems sense the direction of gravity and grow upward. Previous studies of gravitropic mutants have suggested that shoot endodermal cells in Arabidopsis stems and hypocotyls are capable of sensing gravity (i.e., statocytes). In the present study, we report a new screening system using hypergravity conditions to isolate enhancers of gravitropism mutants, and we also describe a rapid and efficient genome mapping method, using next-generation sequencing (NGS) and single nucleotide polymorphism (SNP)-based markers...
2016: Frontiers in Plant Science
Siobhan Eustace Ryan, Fergus Ryan, Veronica O'Dwyer, Derek Neylan
PURPOSE: Approximately 95% of patients who are diagnosed with Leber's hereditary optic neuropathy (LHON) have one of three mitochondrial point mutations responsible for the disease, G3460A, G11778A, and T14484C. The purpose of this study was to develop a novel multiplex real-time amplification-refractory mutation system (ARMS) PCR combined with high-resolution melt curves to identify the individual mutations involved. The study aimed to provide a more robust, cost- and time-effective mutation detection strategy than that offered with currently available methods...
2016: Molecular Vision
Vojtech Bystry, Tomas Reigl, Adam Krejci, Martin Demko, Barbora Hanakova, Andrea Grioni, Henrik Knecht, Max Schlitt, Peter Dreger, Leopold Sellner, Dietrich Herrmann, Marine Pingeon, Myriam Boudjoghra, Jos Rijntjes, Christiane Pott, Anton W Langerak, Patricia J T A Groenen, Frederic Davi, Monika Brüggemann, Nikos Darzentas
MOTIVATION: The study of immunoglobulins and T cell receptors using next-generation sequencing has finally allowed exploring immune repertoires and responses in their immense variability and complexity. Unsurprisingly, their analysis and interpretation is a highly convoluted task. RESULTS: We thus implemented ARResT/Interrogate, a web-based, interactive application. It can organize and filter large amounts of immunogenetic data by numerous criteria, calculate several relevant statistics, and present results in the form of multiple interconnected visualizations...
October 13, 2016: Bioinformatics
Jang-Il Sohn, Jin-Wu Nam
As the advent of next-generation sequencing (NGS) technology, various de novo assembly algorithms based on the de Bruijn graph have been developed to construct chromosome-level sequences. However, numerous technical or computational challenges in de novo assembly still remain, although many bright ideas and heuristics have been suggested to tackle the challenges in both experimental and computational settings. In this review, we categorize de novo assemblers on the basis of the type of de Bruijn graphs (Hamiltonian and Eulerian) and discuss the challenges of de novo assembly for short NGS reads regarding computational complexity and assembly ambiguity...
October 14, 2016: Briefings in Bioinformatics
Sukriye Celikkol-Aydin, Christine C Gaylarde, Tim Lee, Robert E Melchers, Devin L Witt, Iwona B Beech
16S rRNA gene profiling using a pipeline involving the Greengenes database revealed that bacterial populations in innermost (proximal to the steel surface) and outer regions of biofilms on carbon steel exposed 3 m below the surface at an offshore site in the Gulf of Guinea differed from one another and from seawater. There was a preponderance of gammaproteobacterial sequences, representing organisms known for hydrocarbon degradation. Total DNA from the innermost layer was 1500 times that recovered from the outermost...
October 6, 2016: Marine Environmental Research
Gera D Te Raa, Arnon P Kater
Despite the availability of novel targeted agents, TP53 defects remain the most important adverse prognostic factor in chronic lymphocytic leukemia (CLL). Detection of deletion of TP53 locus (17p deletion) by fluorescent in situ hybridization (FISH) has become standard and performed prior to every line of treatment as the incidence dramatically increases as relapses occur. As monoallelic mutations of TP53 equally affect outcome, novel methods are being developed to improve detection of TP53 defects and include next-generation sequencing (NGS) and functional assays...
March 2016: Best Practice & Research. Clinical Haematology
Emili Montserrat, Tycho Bauman, Julio Delgado
Medicine has been 'personalized' (i.e. centred in persons) since its foundation. Recently, however, the term 'personalized medicine' (or, better, 'precision medicine') has been introduced to define 'a form of medicine that uses information about a person's genes, proteins, and environment to prevent, diagnose, and treat disease'. This concept has gained momentum thanks to next-generation-sequencing (NGS) techniques that allow identification of molecular characteristics unique to the patient and to the tumour...
March 2016: Best Practice & Research. Clinical Haematology
Michelangelo Fiorentino, Elisa Gruppioni, Francesco Massari, Francesca Giunchi, Annalisa Altimari, Chiara Ciccarese, Davide Bimbatti, Aldo Scarpa, Roberto Iacovelli, Camillo Porta, Sarhadi Virinder, Giampaolo Tortora, Walter Artibani, Riccardo Schiavina, Andrea Ardizzoni, Matteo Brunelli, Sakari Knuutila, Guido Martignoni
Renal cell cancer (RCC) is characterized by histological and molecular heterogeneity that may account for variable response to targeted therapies. We evaluated retrospectively with a next generation sequencing (NGS) approach using a pre-designed cancer panel the mutation burden of 32 lesions from 22 metastatic RCC patients treated with at least one tyrosine kinase or mTOR inhibitor. We identified mutations in the VHL, PTEN, JAK3, MET, ERBB4, APC, CDKN2A, FGFR3, EGFR, RB1, TP53 genes. Somatic alterations were correlated with response to therapy...
October 10, 2016: Oncotarget
María Abáigar, Cristina Robledo, Rocío Benito, Fernando Ramos, María Díez-Campelo, Lourdes Hermosín, Javier Sánchez-Del-Real, Jose M Alonso, Rebeca Cuello, Marta Megido, Juan N Rodríguez, Guillermo Martín-Núñez, Carlos Aguilar, Manuel Vargas, Ana A Martín, Juan L García, Alexander Kohlmann, M Consuelo Del Cañizo, Jesús M Hernández-Rivas
To explore novel genetic abnormalities occurring in myelodysplastic syndromes (MDS) through an integrative study combining array-based comparative genomic hybridization (aCGH) and next-generation sequencing (NGS) in a series of MDS and MDS/myeloproliferative neoplasms (MPN) patients. 301 patients diagnosed with MDS (n = 240) or MDS/MPN (n = 61) were studied at the time of diagnosis. A genome-wide analysis of DNA copy number abnormalities was performed. In addition, a mutational analysis of DNMT3A, TET2, RUNX1, TP53 and BCOR genes was performed by NGS in selected cases...
2016: PloS One
Santiago Avila-Ríos, Claudia García-Morales, Margarita Matías-Florentino, Daniela Tapia-Trejo, Bismarck F Hernández-Álvarez, Sumaya E Moreira-López, Carlos J Quant-Durán, Guillermo Porras-Cortés, Gustavo Reyes-Terán
BACKGROUND: Increasing HIV pre-treatment drug resistance (PDR) levels have been observed in regions with increasing antiretroviral treatment (ART) coverage. However, data is lacking for several low/middle-income countries. We present the first PDR survey in Nicaragua since ART introduction in the country in 2003. METHODS: HIV-infected, ART-naïve Nicaraguan individuals were enrolled at Roberto Calderón Hospital, the largest national HIV referral center, from 2011 to 2015...
2016: PloS One
Kinga M Bujakowska, Rosario Fernandez-Godino, Emily Place, Mark Consugar, Daniel Navarro-Gomez, Joseph White, Emma C Bedoukian, Xiaosong Zhu, Hongbo M Xie, Xiaowu Gai, Bart P Leroy, Eric A Pierce
PURPOSE: Despite substantial progress in sequencing, current strategies can genetically solve only approximately 55-60% of inherited retinal degeneration (IRD) cases. This can be partially attributed to elusive mutations in the known IRD genes, which are not easily identified by the targeted next-generation sequencing (NGS) or Sanger sequencing approaches. We hypothesized that copy-number variations (CNVs) are a major contributor to the elusive genetic causality of IRDs. METHODS: Twenty-eight cases previously unsolved with a targeted NGS were investigated with whole-genome single-nucleotide polymorphism (SNP) and comparative genomic hybridization (CGH) arrays...
October 13, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Jose Maria Bastida Bermeja, Jose Ramon González-Porras, Cristina Jiménez, Rocio Benito, Gonzalo R Ordoñez, Maria Teresa Álvarez-Román, M Elena Fontecha, Kamila Janusz, David Castillo, Rosa María Fisac, Luis Javier García-Frade, Carlos Aguilar, María Paz Martínez, Nuria Bermejo, Sonia Herrero, Ana Balanzategui, Jose Manuel Martin-Antorán, Rafael Ramos, Maria Jose Cebeiro, Emilia Pardal, Carmen Aguilera, Belen Pérez-Gutierrez, Manuel Prieto, Susana Riesco, Maria Carmen Mendoza, Ana Benito, Ana Hortal Benito-Sendin, Víctor Jiménez-Yuste, Jesus Maria Hernández-Rivas, Ramon García-Sanz, Marcos González-Díaz, Maria Eugenia Sarasquete
Currently, molecular diagnosis of haemophilia A and B (HA and HB) highlights the excess risk-inhibitor development associated with specific mutations, and enables carrier testing of female relatives and prenatal or preimplantation genetic diagnosis. Molecular testing for HA also helps distinguish it from von Willebrand disease (VWD). Next-generation sequencing (NGS) allows simultaneous investigation of several complete genes, even though they may span very extensive regions. This study aimed to evaluate the usefulness of a molecular algorithm employing an NGS approach for sequencing the complete F8, F9 and VWF genes...
October 13, 2016: Thrombosis and Haemostasis
María-Eugenia DeCastro, Esther Rodríguez-Belmonte, María-Isabel González-Siso
Microbial populations living in environments with temperatures above 50°C (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. Since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. The integrated study of the whole-community DNA from an environment, known as metagenomics, coupled with the development of next generation sequencing (NGS) technologies, has allowed the generation of large amounts of data from thermophiles...
2016: Frontiers in Microbiology
Seungkyu Choi, Jai Hyang Go, Eun Kyung Kim, Hojung Lee, Won Mi Lee, Chun-Sung Cho, Kyudong Han
Extranodal natural killer (NK)/T-cell lymphoma, nasal type (NKTCL), is a malignant disorder of cytotoxic lymphocytes of NK or T cells. It is an aggressive neoplasm with a very poor prognosis. Although extranodal NKTCL reportedly has a strong association with Epstein-Barr virus, the molecular pathogenesis of NKTCL has been unexplored. The recent technological advancements in next-generation sequencing (NGS) have made DNA sequencing cost- and time-effective, with more reliable results. Using the Ion Proton Comprehensive Cancer Panel, we sequenced 409 cancer-related genes to identify somatic mutations in five NKTCL tissue samples...
September 2016: Genomics & Informatics
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