Search results for "throughput"
showing 10 items of 483 documents
Real-time detection of BRAF V600E mutation from archival hairy cell leukemia FFPE tissue by nanopore sequencing
2018
The MinION is a miniaturized high-throughput next generation sequencing platform of novel conception. The use of nucleic acids derived from formalin-fixed paraffin-embedded samples is highly desirable, but their adoption for molecular assays is hurdled by the high degree of fragmentation and by the chemical-induced mutations stemming from the fixation protocols. In order to investigate the suitability of MinION sequencing on formalin-fixed paraffin-embedded samples, the presence and frequency of BRAF c.1799T > A mutation was investigated in two archival tissue specimens of Hairy cell leukemia and Hairy cell leukemia Variant. Despite the poor quality of the starting DNA, BRAF mutation was su…
Link adaptation with combined optimal frame size and rate selection in error-prone 802.11n networks
2008
In error-prone channel with low SNRs, the network throughput may drop significantly if the packet length becomes too large. On the other hand, too much protocol overhead will be introduced if the packet length is too small. In this paper, we study this tradeoff and propose an adaptive frame size algorithm for A-MPDU in 802.11n networks, which can maximize the throughput by selecting the optimized frame length under different channel conditions. When used together with rate selection, the network throughput can be further improved. Both analytical model and simulation results are presented, demonstrating that our algorithm outperforms the fixed length transmission scheme in 802.11n networks …
Does large NGS panel analysed using exome tumour sequencing improve the management of advanced non-small-cell lung cancers?
2020
Abstract Introduction Non-small-cell lung cancer (NSCLC) is one of the most common and deadly cancers. Several molecular drivers of oncogene addiction are now known to be strong predictive biomarkers for target therapies. Advances in large Next Generation Sequencing (LNGS) have improved the ability to detect potentially targetable mutations. However, the integration of LNGS into clinical management in an individualized manner remains challenging. Methods In this single-center observational study we included all patients with advanced NSCLC who underwent LNGS. Somatic and germline exome analysis was performed with a restriction on 323 cancer related genes. Variants were classified and Molecu…
Diet of the insectivorous bat 'Pipistrellus nathusii' during autumn migration and summer residence
2013
Migration is widespread among vertebrates, yet bat migration has received little attention and only in the recent decades has a better understanding of it been gained. Migration can cause significant changes in behaviour and physiology, due to increasing energy demands and aerodynamic constraints. Dietary shifts, for example, have been shown to occur in birds before onset of migration. For bats, it is not known if a change in diet occurs during migration, although breeding season–related dietary preference has been documented. It is known that a diet rich in fats and the accumulation of fat deposits do increase the flight range of migratory bats. Some bat species can be regarded as long-dis…
Statistical guidelines for quality control of next-generation sequencing techniques.
2021
Condition-specific statistical guidelines and accurate classification trees for quality control of functional genomics NGS files (RNA-seq, ChIP-seq and DNase-seq) have been generated using thousands of reference files from the ENCODE project and made available to the community.
RabbitQC: high-speed scalable quality control for sequencing data
2019
Abstract Motivation Modern sequencing technologies continue to revolutionize many areas of biology and medicine. Since the generated datasets are error-prone, downstream applications usually require quality control methods to pre-process FASTQ files. However, existing tools for this task are currently not able to fully exploit the capabilities of computing platforms leading to slow runtimes. Results We present RabbitQC, an extremely fast integrated quality control tool for FASTQ files, which can take full advantage of modern hardware. It includes a variety of operations and supports different sequencing technologies (Illumina, Oxford Nanopore and PacBio). RabbitQC achieves speedups between …
Measurement and Modeling of the Origins of Starvation in Congestion Controlled Mesh Networks
2008
Significant progress has been made in understanding the behavior of TCP and congestion-controlled traffic over multi- hop wireless networks. Despite these advances, however, no prior work identified severe throughput imbalances in the basic scenario of mesh networks, in which one-hop flows contend with two-hop flows for gateway access. In this paper, we demonstrate via real network measurements, test-bed experiments, and an analytical model that starvation exists in such a scenario, i.e., the one-hop flow receives most of the bandwidth while the two- hop flow starves. Our analytical model yields a solution consisting of a simple contention window policy that can be implemented via mechanism…
An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides
2018
Infection with human BK polyomavirus, a small double-stranded DNA virus, potentially results in severe complications in immunocompromised patients. Here, we describe the in vivo variability and evolution of the BK polyomavirus by deep sequencing. Our data reveal the highest genomic evolutionary rate described in double-stranded DNA viruses, i.e., 10−3–10−5 substitutions per nucleotide site per year. High mutation rates in viruses allow their escape from immune surveillance and adaptation to new hosts. By combining mutational landscapes across viral genomes with in silico prediction of viral peptides, we demonstrate the presence of significantly more coding substitutions within predicted cog…
Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates
2021
Due to the widespread of the COVID-19 pandemic, the SARS-CoV-2 genome is evolving in diverse human populations. Several studies already reported different strains and an increase in the mutation rate. Particularly, mutations in SARS-CoV-2 spike-glycoprotein are of great interest as it mediates infection in human and recently approved mRNA vaccines are designed to induce immune responses against it. We analyzed 1,036,030 SARS-CoV-2 genome assemblies and 30,806 NGS datasets from GISAID and European Nucleotide Archive (ENA) focusing on non-synonymous mutations in the spike protein. Only around 2.5% of the samples contained the wild-type spike protein with no variation from the reference. Among…
Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing
2016
ABSTRACT Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated 2 distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, …