Search results for "Next Generation Sequencing"

Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies

2019

New analytics of post-transcriptional RNA modifications have paved the way for a tremendous upswing of the biological and biomedical research in this field. This especially applies to methods that included RNA-Seq techniques, and which typically result in what is termed global scale modification mapping. In this process, positions inside a cell`s transcriptome are receiving a status of potential modification sites (so called modification calling), typically based on a score of some kind that issues from the particular method applied. The resulting data are thought to represent information that goes beyond what is contained in typical transcriptome data, and hence the field has taken to use …

FROM EPIGENETICS TO ANTI-DOPING APPLICATION: A NEW TOOL OF DETECTION

2017

Eukaryotic genomes transcribe up to 90% of the genomic DNA but only 1–2% of these transcripts encode for proteins, whereas the vast majority are transcribed as non-coding RNAs (ncRNAs). They are divided into short ncRNA, particularly microRNA (miRNA) and small interference RNA (siRNA), and long ncRNAs. Noteworthy, they are unexpectedly stable since they are protected from degradation through different mechanisms: package in exosomes/microvesicles structures, in apoptotic bodies, in HDL lipoprotein, or by RNA binding proteins. For several years already, biomarkers have been used to detect biological disease; in the last years, a requirement appeared to find some of them to unearth the signs …

Tumor Heterogeneity, Single-Cell Sequencing, and Drug Resistance

2016

Tumor heterogeneity has been compared with Darwinian evolution and survival of the fittest. The evolutionary ecosystem of tumors consisting of heterogeneous tumor cell populations represents a considerable challenge to tumor therapy, since all genetically and phenotypically different subpopulations have to be efficiently killed by therapy. Otherwise, even small surviving subpopulations may cause repopulation and refractory tumors. Single-cell sequencing allows for a better understanding of the genomic principles of tumor heterogeneity and represents the basis for more successful tumor treatments. The isolation and sequencing of single tumor cells still represents a considerable technical ch…

Do shifts in life strategies explain microbial community responses to increasing nitrogen in tundra soil?

2016

Subarctic tundra soils store large quantities of the global organic carbon (C) pool as the decomposition of plant litter and soil organic matter is limited by low temperatures and limiting nutrients. Mechanisms that drive organic matter decomposition are still poorly understood due to our limited knowledge of microbial communities and their responses to changing conditions. In subarctic tundra large grazers, in particular reindeer, exert a strong effect on vegetation and nutrient availability causing drastic nutrient pulses in the soils located along the migratory routes. Here we studied the effect of increased nitrogen (N) availability on microbial community structure and activities by lab…

Bacterial community response to changes in a tri-trophic cascade during a whole-lake fish manipulation

2015

Microbial communities play a key role in biogeochemical processes by degrading organic material and recycling nutrients, but can also be important food sources for upper trophic levels. Trophic cascades might modify microbial communities either directly via grazing or indirectly by inducing changes in other biotic or in abiotic factors (e.g., nutrients). We studied the effects of a tri-trophic cascade on microbial communities during a whole-lake manipulation in which European perch (Perca fluviatilis) were added to a naturally fishless lake divided experimentally into two basins. We measured environmental parameters (oxygen, temperature, and nutrients) and zooplankton biomass and studied th…

Customised next-generation sequencing multigene panel to screen a large cohort of individuals with chromatin-related disorder

2020

BackgroundThe regulation of the chromatin state by epigenetic mechanisms plays a central role in gene expression, cell function, and maintenance of cell identity. Hereditary disorders of chromatin regulation are a group of conditions caused by abnormalities of the various components of the epigenetic machinery, namely writers, erasers, readers, and chromatin remodelers. Although neurological dysfunction is almost ubiquitous in these disorders, the constellation of additional features characterizing many of these genes and the emerging clinical overlap among them indicate the existence of a community of syndromes. The introduction of high-throughput next generation sequencing (NGS) methods f…

Identification Of P.Leu167Del Apoe Gene Mutation By Next Generation Sequencing In A Large Hypercholesterolemic Family

2019

Evaluación del valor diagnóstico y pronóstico de las alteraciones moleculares en la leucemia mieloide aguda de novo mediante el empleo de técnicas de…

2020

La leucemia mieloide aguda (LMA) es una enfermedad muy heterogénea desde el punto de vista biológico con numerosas alteraciones moleculares implicadas en su patogenia. El análisis simultáneo de estas alteraciones génicas es imprescindible para conocer los mecanismos de leucemogénesis y evaluar sus implicaciones clínicas de manera individualizada en cada paciente. Las técnicas de next generation sequencing (NGS) han demostrado ser una herramienta eficaz para el análisis integrado de la complejidad de las neoplasias mieloides, por ello, el objetivo de este estudio es realizar una validación técnica y clínica de un panel de NGS dirigida a genes o regiones recurrentemente mutados en la enfermed…

Medication for Acromegaly Reduces Expression of MUC16, MACC1 and GRHL2 in Pituitary Neuroendocrine Tumour Tissue

2021

Acromegaly is a disease mainly caused by pituitary neuroendocrine tumor (PitNET) overproducing growth hormone. First-line medication for this condition is the use of somatostatin analogs (SSAs), that decrease tumor mass and induce antiproliferative effects on PitNET cells. Dopamine agonists (DAs) can also be used if SSA treatment is not effective. This study aimed to determine differences in transcriptome signatures induced by SSA/DA therapy in PitNET tissue. We selected tumor tissue from twelve patients with somatotropinomas, with half of the patients receiving SSA/DA treatment before surgery and the other half treatment naive. Transcriptome sequencing was then carried out to identify diff…

No evidence of EMAST in whole genome sequencing data from 248 colorectal cancers.

2021

Microsatellite instability (MSI) is caused by defective DNA mismatch repair (MMR), and manifests as accumulation of small insertions and deletions (indels) in short tandem repeats of the genome. Another form of repeat instability, elevated microsatellite alterations at selected tetranucleotide repeats (EMAST), has been suggested to occur in 50% to 60% of colorectal cancer (CRC), of which approximately one quarter are accounted for by MSI. Unlike for MSI, the criteria for defining EMAST is not consensual. EMAST CRCs have been suggested to form a distinct subset of CRCs that has been linked to a higher tumor stage, chronic inflammation, and poor prognosis. EMAST CRCs not exhibiting MSI have b…