Next-generation sequencing analysis
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Sequencing errors are key confounding factors for detecting low-frequency genetic variants that are important for cancer molecular diagnosis, treatment, and surveillance using deep next-generation sequencing (NGS). However, there is a lack of comprehensive understanding of errors introduced at various steps of a conventional NGS workflow, such as sample handling, library preparation, PCR enrichment, and sequencing. In this study, we use current NGS technology to systematically investigate these questions.
15p vigalileogalilei 27-02-2022 14 2 Download
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To investigate a possible transmission of blaCMY-2 along the food production chain, we conducted a nextgeneration sequencing (NGS)-based analysis of 164 CMY-2-producing E. coli isolates from humans, livestock animals and foodstuff from Germany.
17p vitzuyu2711 29-09-2021 10 1 Download
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The last 10 years have seen the rise of countless functional genomics studies based on NextGeneration Sequencing (NGS). In the vast majority of cases, whatever the species, whatever the experiment, the two first steps of data analysis consist of a quality control of the raw reads followed by a mapping of those reads to a reference genome/transcriptome.
11p visilicon2711 20-08-2021 6 1 Download
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Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu) are good fish species for aquaculture. The tambacu, individuals originating from the induced hybridization of the female tambaqui with the male pacu, present rapid growth and robustness, characteristics which have made the tambacu a good choice for Brazilian fish farms.
17p vilichoo2711 23-06-2021 10 1 Download
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Common buckwheat (2n = 2x = 16) is an outcrossing pseudocereal whose seeds contain abundant nutrients and potential antioxidants. As these beneficial compounds are damaged by preharvest sprouting (PHS) and PHS is likely to increase with global warming, it is important to find efficient ways to develop new PHS-tolerant lines.
13p vijichea2711 28-05-2021 7 1 Download
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Cancer immunotherapy has demonstrated significant clinical activity in different cancers. T cells represent a crucial component of the adaptive immune system and are thought to mediate anti-tumoral immunity. Antigenspecific recognition by T cells is via the T cell receptor (TCR) which is unique for each T cell.
14p vioklahoma2711 19-11-2020 12 0 Download
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The rapid development of next-generation sequencing (NGS) technology has continuously been refreshing the throughput of sequencing data. However, due to the lack of a smart tool that is both fast and accurate, the analysis task for NGS data, especially those with low-coverage, remains challenging.
14p viconnecticut2711 28-10-2020 13 1 Download
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The use of whole genome sequence has increased recently with rapid progression of nextgeneration sequencing (NGS) technologies. However, storing raw sequence reads to perform large-scale genome analysis pose hardware challenges.
10p vicoachella2711 27-10-2020 7 0 Download
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Next-generation sequencing is revolutionising diagnosis and treatment of rare diseases, however its application to understanding common disease aetiology is limited. Rare disease applications binarily attribute genetic change(s) at a single locus to a specific phenotype.
15p vijisoo2711 27-10-2020 14 1 Download
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Processing and analysis of DNA sequences obtained from nextgeneration sequencing (NGS) face some difficulties in terms of the correct prediction of DNA sequencing outcomes without the implementation of bioinformatics approaches.
13p vicolorado2711 22-10-2020 13 0 Download
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With the development of sequencing technologies, there may be some disputes on sequencing analysis. The aim of this study was to investigate different allele frequency thresholds of mutations in targeted genes on prognostic analyses using a panel of cancer associated gene exons (CAGE) in oral squamous cell carcinoma (OSCC).
10p vimanila2711 29-06-2020 5 1 Download
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RNA sequencing (RNA-seq)-based whole transcriptome analysis (WTA) using ever-evolving nextgeneration sequencing technologies has become a primary tool for coding and/or noncoding transcriptome profiling. As WTA requires RNA-seq data for both coding and noncoding RNAs, one key step for obtaining high-quality RNA-seq data is to remove ribosomal RNAs, which can be accomplished by using various commercial kits. Nonetheless, an ideal rRNA removal method should be efficient, user-friendly and cost-effective so it can be adapted for homemade RNA-seq library construction.
12p partimesinhvien 08-05-2020 15 0 Download