Consulta: subjectFacets:"NGS"
Registros recuperados: 10
Data/hora: 17/06/2024 10:15:51

Impact of NGS in the medical sciences: genetic syndromes with an increased risk of developing cancer as an example of the use of new technologies
Provedor de dados: Genetics and Molecular Biology
Autores: Lapunzina,Pablo; López,Rocío Ortiz; Rodríguez-Laguna,Lara; García-Miguel,Purificación; Martínez,Augusto Rojas; Martínez-Glez,Víctor.
The increased speed and decreasing cost of sequencing, along with an understanding of the clinical relevance of emerging information for patient management, has led to an explosion of potential applications in healthcare. Currently, SNP arrays and Next-Generation Sequencing (NGS) technologies are relatively new techniques used to scan genomes for gains and losses, losses of heterozygosity (LOH), SNPs, and indel variants as well as to perform complete sequencing of a panel of candidate genes, the entire exome (whole exome sequencing) or even the whole genome. As a result, these new high-throughput technologies have facilitated progress in the understanding and diagnosis of genetic syndromes and cancers, two disorders traditionally considered to be separate...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: NGS; New technologies; Developmental syndrome; Cancer predisposition.
Ano: 2014
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572014000200010

CDH1 mutations in gastric cancer patients from northern Brazil identified by Next- Generation Sequencing (NGS)
Provedor de dados: Genetics and Molecular Biology
Autores: El-Husny,Antonette; Raiol-Moraes,Milene; Amador,Marcos; Ribeiro-dos-Santos,André M.; Montagnini,André; Barbosa,Silvanira; Silva,Artur; Assumpção,Paulo; Ishak,Geraldo; Santos,Sidney; Pinto,Pablo; Cruz,Aline; Ribeiro-dos-Santos,Ândrea.
Abstract Gastric cancer is considered to be the fifth highest incident tumor worldwide and the third leading cause of cancer deaths. Developing regions report a higher number of sporadic cases, but there are only a few local studies related to hereditary cases of gastric cancer in Brazil to confirm this fact. CDH1 germline mutations have been described both in familial and sporadic cases, but there is only one recent molecular description of individuals from Brazil. In this study we performed Next Generation Sequencing (NGS) to assess CDH1 germline mutations in individuals who match the clinical criteria for Hereditary Diffuse Gastric Cancer (HDGC), or who exhibit very early diagnosis of gastric cancer. Among five probands we detected CDH1 germline...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: CDH1; Germline mutations; HDGC; Gastric Cancer; NGS.
Ano: 2016
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572016000200189

Extinction and emergence of genomic haplotypes during the evolution of Avian coronavirus in chicken embryos
Provedor de dados: Genetics and Molecular Biology
Autores: Brandão,Paulo E.; Hora,Aline S.; Silva,Sheila O. S.; Taniwaki,Sueli A.; Berg,Mikael.
Abstract Avian coronavirus (AvCoV) is ubiquitously present on poultry as a multitude of virus lineages. Studies on AvCoV phenotypic traits are dependent on the isolation of field strains in chicken embryonated eggs, but the mutant spectrum on each isolate is not considered. This manuscript reports the previously unknown HTS (high throughput sequencing)-based complete genome haplotyping of AvCoV isolates after passages of two field strains in chicken embryonated eggs. For the first and third passages of strain 23/2013, virus loads were 6.699 log copies/ μL and 6 log copies/ μL and, for 38/2013, 5.699 log copies/μL and 2.699 log copies/μL of reaction, respectively. The first passage of strain 23/2013 contained no variant haplotype, while, for the third...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Avian coronavirus; Haplotype; Mutant spectrum; NGS; Evolution.
Ano: 2020
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572020000400202

Effect of vacuum and modified atmosphere packaging on the microbiological, chemical and sensory properties of tropical red drum ( Sciaenops ocellatus ) fillets stored at 4 °C
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Silbande, Adele; Adenet, Sandra; Chopin, Christine; Cornet, Josiane; Smith-ravin, Juliette; Rochefort, Katia; Leroi, Francoise.
Aims The effect of vacuum (VP – 4 °C) and CO2/N2–atmosphere (MAP – 4 °C) packaging on the quality of red drum fillets compared with whole gutted iced fish was investigated. Methods and results A metagenomic approach, bacterial enumeration and isolation, biochemical and sensory analyses were carried out. The organoleptic rejection of whole fish was observed at day 15 whereas VP and MAP fillets appeared unacceptable only after 29 days. At these dates, total mesophilic counts reached 107–108 CFU g− 1. According to Illumina MiSeq sequencing, Arthrobacter, Chryseobacterium, Brevibacterium, Staphylococcus and Kocuria were the main genera of the fresh red drum fillets. At the sensory rejection time, lactic acid bacteria (LAB), particularly Carnobacterium sp.,...
Tipo: Text
Palavras-chave: Seafood; Biogenic amine; VP; MAP; NGS; 16S rRNA gene.
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00407/51858/52468.pdf

GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Riviere, Guillaume; Klopp, Christophe; Ibouniyamine, Nabihoudine; Huvet, Arnaud; Boudry, Pierre; Favrel, Pascal.
Background: The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database. Description: We assembled 2204 million sequences obtained from 114 publicly...
Tipo: Text
Palavras-chave: Oyster; Transcriptome; Development; Stress; Tissues; NGS.
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00302/41321/40520.pdf

Quality assessment of ice-stored tropical yellowfin tuna (Thunnus albacares) and influence of vacuum and modified atmosphere packaging
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Dauchy Silbande, Adele; Adenet, Sandra; Smith-ravin, Juliette; Joffraud, Jean-jacques; Rochefort, Katia; Leroi, Francoise.
Metagenomic, microbial, chemical and sensory analyses of Thunnus albacares from Martinique and stored in ice (AIR – 0 °C), vacuum (VP – 4/8 °C) and modified atmosphere packaging (MAP – 4/8 °C) (70% CO2 – 30% O2) were carried out. The organoleptic rejection of AIR tuna was observed at day 13 when total bacterial counts equaled 106–107 CFU g−1. No extension of shelf-life was provided by VP and MAP. According to 16S rRNA gene sequence analyzed by Illumina MiSeq and PCR-TTGE, Rhodanobacter terrae was the main species of the freshly caught tuna. At the sensory rejection time, Brochothrix thermosphacta and Pseudomonas dominated the AIR products while B. thermosphacta alone or a mix of B. thermosphacta, Enterobacteriaceae and lactic acid bacteria (LAB) dominated...
Tipo: Text
Palavras-chave: Seafood; Fish; Microbiology; Sensory; NGS; 16S rRNA gene.
Ano: 2016
URL: https://archimer.ifremer.fr/doc/00344/45504/45056.pdf

Sobreexpresión de genes en la interacción de Spongospora subterranea (Wallr.) Lagerh. y dos cultivares de Solanum phureja Juz. et. Buk
Provedor de dados: Revista de Protección Vegetal
Autores: Rodríguez Fuerte,Verónica; Marín Montoya,Mauricio; Morales Osorio,Juan Gonzalo; Cotes Torres,José Miguel; Gutiérrez Sánchez,Pablo Andrés.
Con el fin de contribuir a un mejor conocimiento de los mecanismos que rigen la interacción entre Solanum phureja Juz. et. Buk. y Spongospora subterranea (Wallr.) Lagerh, agente causal de la sarna polvosa de la papa, se realizó en esta investigación el análisis del transcriptoma de dos cultivares: Criolla Colombia (susceptible) y Criolla Latina (tolerante), mediante pirosecuenciación 454. Los resultados indicaron diferencias entre los genes sobreexpresados en cada cultivar ante la infección con el patógeno. En el cultivar susceptible, la respuesta ocurre a partir de la activación transcripcional de genes asociados a la integridad de la pared celular, transducción de señales y genes involucrados en la respuesta a diferentes tipos de estrés. Los genes que...
Tipo: Journal article
Palavras-chave: NGS; PCR en tiempo real; Sarna polvosa; Transcriptoma.
Ano: 2014
URL: http://scielo.sld.cu/scielo.php?script=sci_arttext&pid=S1010-27522014000100003

ANÁLISIS FILOGENÉTICO Y VARIABILIDAD MOLECULAR DEL Potato virus X (PVX) EN CULTIVOS DE PAPA DE ANTIOQUIA
Provedor de dados: Acta Biológica Colombiana
Autores: GARCÍA RUÍZ,Daniela; GUTIÉRREZ SÁNCHEZ,Pablo; MARÍN MONTOYA,Mauricio.
En este estudio se determinaron las relaciones filogenéticas y los niveles de variación de aislamientos de PVX obtenidos en tejidos foliares de plantas de Solanum tuberosum subsp. andigena var. Diacol-Capiro y S. phureja var. Criolla Colombia en Antioquia, utilizando métodos de secuenciación de nueva generación (NGS) y de Sanger. Inicialmente, se detectó el PVX mediante DAS-ELISA (Agdia-PSA10000), confirmándose su presencia en ocho de las muestras por Inmunocaptura-RT-PCR en tiempo real (IC-RT-qPCR). Los resultados de las pruebas serológicas indicaron la infección de PVX en 14,7 % y 13,3 % de las muestras de Diacol-Capiro y Criolla Colombia, respectivamente. Su identidad fue confirmada por IC-RT-qPCR, con valores de ciclo umbral (Ct) de 15,04 a 27,59 y dos...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: DAS-ELISA; NGS; Potexvirus; RT-qPCR; Solanum spp; Variantes.
Ano: 2016
URL: http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S0120-548X2016000100011

CARACTERIZACIÓN MOLECULAR DEL Potato virus V (PVV) INFECTANDO Solanum phureja MEDIANTE SECUENCIACIÓN DE NUEVA GENERACIÓN
Provedor de dados: Acta Biológica Colombiana
Autores: ÁLVAREZ YEPES,Daniela; GUTIÉRREZ SÁNCHEZ,Pablo Andrés; MARÍN MONTOYA,Mauricio.
Las enfermedades virales son uno de los problemas más limitantes para la producción de papa en el mundo. Uno de los materiales de papa más susceptibles a los virus corresponde a Solanum phureja; sin embargo, en Colombia son pocos los estudios adelantados sobre los agentes causales que lo afectan. En este trabajo se realizó una caracterización molecular del Potato virus V (PVV) infectando plantas de S. phureja en Antioquia, utilizando métodos de secuenciación de nueva generación (NGS), pruebas de DAS-ELISA, RT-PCR en tiempo real (RT-qPCR) y RT-PCR convencional. Los resultados indican la ocurrencia de niveles muy variables de incidencia del virus entre lotes de cultivo (6,7 % a 86 %). El PVV tiene un genoma de 9828 nt que codifica para una poliproteína de...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: DAS-ELISA; NGS; Papa; Potyvirus; RT-qPCR.
Ano: 2016
URL: http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S0120-548X2016000300007

NEXT GENERATION SEQUENCING AND PROTEOMICS IN PLANT VIROLOGY: HOW IS COLOMBIA DOING?
Provedor de dados: Acta Biológica Colombiana
Autores: MADROÑERO,Leidy Johana; CORREDOR-ROZO,Zayda-Lorena; ESCOBAR-PÉREZ,Javier; VELANDIA-ROMERO,Myriam-Lucía.
ABSTRACT Crop production and trade are two of the most economically important activities in Colombia, and viral diseases cause a high negative impact to agricultural sector. Therefore, the detection, diagnosis, control, and management of viral diseases are crucial. Currently, Next-Generation Sequencing (NGS) and 'Omic' technologies constitute a right-hand tool for the discovery of novel viruses and for studying virus-plant interactions. This knowledge allows the development of new viral diagnostic methods and the discovery of key components of infectious processes, which could be used to generate plants resistant to viral infections. Globally, crop sciences are advancing in this direction. In this review, advancements in 'omic' technologies and their...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: NGS; Plant-virus interactions; Plant virology; Proteomics; Viral genomics.
Ano: 2019
URL: http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S0120-548X2019000300423