Relevant bibliographies by topics / Roche 454 sequencing

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Academic literature on the topic 'Roche 454 sequencing'

Author: Grafiati
Published: 2 June 2025
Last updated: 19 July 2025

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Journal articles on the topic "Roche 454 sequencing"

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Brayton, Bonnie, Mary Margaret Byron, Glen Chew, Trent Tamate, Timothy Quinn Crawford, and Jason Barbour. "Novel method for next generation sequencing of KIR by Roche 454 (P3383)." Journal of Immunology 190, no. 1_Supplement (2013): 135.19. http://dx.doi.org/10.4049/jimmunol.190.supp.135.19.

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Abstract Natural Killer cells are regulated by the polymorphic Killer Ig-like Receptor family. KIR genotype and expression has been associated with HIV-1 disease progression. We developed a high-throughput method to characterize both DNA genotype and RNA expression of KIR using a novel 454 sequencing method (Roche), for study of HIV and innate immunity. This method uses a 299bp and 395bp amplicon to distinguish and assign long - and short-tailed KIR. These amplicons, from motifs common to 3’ UTR of known KIR genes, amplify both KIR DNA and mRNA. We developed a custom bioinformatics pipeline to analyze 454 sequence reads and it compares each sequence (average 3000 reads per specimen) to a reference alignment of KIR genes via the BLAT algorithm. Using this method, we characterized KIR in a cohort of 700 treatment-naïve adults in early HIV-1 disease. Initial results indicate that our KIR DNA 454 sequencing data agree with KIR DNA genotyping results from mass spectrometry-based typing as well as sequence-specific oligonucleotide typing. KIR3DL1 expression on NK cells by flow cytometry shows 80% agreement with KIR mRNA expression from PBMCs by 454. The use of mRNA- and DNA-based next generation sequencing for human immune receptor genes, such as KIR, will accelerate genetic association and functional genetic studies of diseases of the immune system.
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Poulet, Axel, Maud Privat, Flora Ponelle, et al. "Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software." BioMed Research International 2016 (2016): 1–11. http://dx.doi.org/10.1155/2016/5623089.

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Screening forBRCAmutations in women with familial risk of breast or ovarian cancer is an ideal situation for high-throughput sequencing, providing large amounts of low cost data. However, 454, Roche, and Ion Torrent, Thermo Fisher, technologies produce homopolymer-associated indel errors, complicating their use in routine diagnostics. We developed software, named AGSA, which helps to detect false positive mutations in homopolymeric sequences. Seventy-two familial breast cancer cases were analysed in parallel by amplicon 454 pyrosequencing and Sanger dideoxy sequencing for genetic variations of theBRCAgenes. All 565 variants detected by dideoxy sequencing were also detected by pyrosequencing. Furthermore, pyrosequencing detected 42 variants that were missed with Sanger technique. Six amplicons contained homopolymer tracts in the coding sequence that were systematically misread by the software supplied by Roche. Read data plotted as histograms by AGSA software aided the analysis considerably and allowed validation of the majority of homopolymers. As an optimisation, additional 250 patients were analysed using microfluidic amplification of regions of interest (Access Array Fluidigm) of the BRCA genes, followed by 454 sequencing and AGSA analysis. AGSA complements a complete line of high-throughput diagnostic sequence analysis, reducing time and costs while increasing reliability, notably for homopolymer tracts.
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Klein, Hans-Ulrich, Christoph Bartenhagen, Alexander Kohlmann, et al. "R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data." Bioinformatics 27, no. 8 (2011): 1162–63. http://dx.doi.org/10.1093/bioinformatics/btr102.

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Tamaki, Hideyuki, Chris L. Wright, Xiangzhen Li, et al. "Analysis of 16S rRNA Amplicon Sequencing Options on the Roche/454 Next-Generation Titanium Sequencing Platform." PLoS ONE 6, no. 9 (2011): e25263. http://dx.doi.org/10.1371/journal.pone.0025263.

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Wang, Panpan, Shijun Xiao, Zhaofang Han, and Zhiyong Wang. "SNP discovery in large yellow croaker (Larimichthys crocea) using Roche 454 pyrosequencing sequencing platform." Conservation Genetics Resources 7, no. 4 (2015): 777–79. http://dx.doi.org/10.1007/s12686-015-0481-z.

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Watson, Simon J., Matthijs R. A. Welkers, Daniel P. Depledge, et al. "Viral population analysis and minority-variant detection using short read next-generation sequencing." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1614 (2013): 20120205. http://dx.doi.org/10.1098/rstb.2012.0205.

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RNA viruses within infected individuals exist as a population of evolutionary-related variants. Owing to evolutionary change affecting the constitution of this population, the frequency and/or occurrence of individual viral variants can show marked or subtle fluctuations. Since the development of massively parallel sequencing platforms, such viral populations can now be investigated to unprecedented resolution. A critical problem with such analyses is the presence of sequencing-related errors that obscure the identification of true biological variants present at low frequency. Here, we report the development and assessment of the Quality Assessment of Short Read (QUASR) Pipeline ( http://sourceforge.net/projects/quasr ) specific for virus genome short read analysis that minimizes sequencing errors from multiple deep-sequencing platforms, and enables post-mapping analysis of the minority variants within the viral population. QUASR significantly reduces the error-related noise in deep-sequencing datasets, resulting in increased mapping accuracy and reduction of erroneous mutations. Using QUASR, we have determined influenza virus genome dynamics in sequential samples from an in vitro evolution of 2009 pandemic H1N1 (A/H1N1/09) influenza from samples sequenced on both the Roche 454 GSFLX and Illumina GAIIx platforms. Importantly, concordance between the 454 and Illumina sequencing allowed unambiguous minority-variant detection and accurate determination of virus population turnover in vitro .
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Shikha, Bishnoi Lalhmangaihzuli Ghanshyam Sahu. "DNA Decoding." Science World a monthly e magazine 3, no. 7 (2023): 1476–79. https://doi.org/10.5281/zenodo.8170663.

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DNA decoding means determination of the order of arrangement of nucleotides in the DNA. The four nucleotides that makes up DNA are: Cytosine, Adenine, Guanine and Thymine. The different generations of DNA sequencing are: first generation that consists of Sanger sequencing method and Maxam-Gilbert sequencing method; second generation consisting Roche 454, Illumina Solexa and ABI-SOLiD techniques; third generation consists of Helicos, PacBio and Ion Torrent and fourth generation consists of Nanopore sequencers. The first-generation sequencing methods have limitation that it could sequence a small number of DNA sequence in one go and that the cost per base is very high. Therefore, development of the high throughput new generations of sequencing was required to sequence the genome of individuals or organisms for diagnosis and treatment in short period of time with low cost.
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Liu, Lin, Yinhu Li, Siliang Li, et al. "Comparison of Next-Generation Sequencing Systems." Journal of Biomedicine and Biotechnology 2012 (2012): 1–11. http://dx.doi.org/10.1155/2012/251364.

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With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world’s biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.
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Song, Ju Yeon, Haeyoung Jeong, Dong Su Yu, et al. "Draft Genome Sequence of Streptomyces clavuligerus NRRL 3585, a Producer of Diverse Secondary Metabolites." Journal of Bacteriology 192, no. 23 (2010): 6317–18. http://dx.doi.org/10.1128/jb.00859-10.

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ABSTRACT Streptomyces clavuligerus is an important industrial strain that produces a number of antibiotics, including clavulanic acid and cephamycin C. A high-quality draft genome sequence of the S. clavuligerus NRRL 3585 strain was produced by employing a hybrid approach that involved Sanger sequencing, Roche/454 pyrosequencing, optical mapping, and partial finishing. Its genome, comprising four linear replicons, one chromosome, and four plasmids, carries numerous sets of genes involved in the biosynthesis of secondary metabolites, including a variety of antibiotics.
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Buntzman, Adam, Benjamin Vincent, Shaun Steele, Jesse Walsh, Thomas Kepler, and Jeffrey Frelinger. "Large Scale T cell receptor repertoire sequencing of murine CD8+ T cells. (144.5)." Journal of Immunology 184, no. 1_Supplement (2010): 144.5. http://dx.doi.org/10.4049/jimmunol.184.supp.144.5.

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Abstract Theoretically, mice can produce 1015 possible αβ T cell receptors (TCRs), with over 106 TCR clonotypes present at a given time. Data driven estimates based on a rigorous analysis of this massive complex repertoire have not been done due to the cost of obtaining a large set of TCR sequences. The advent of next generation DNA sequencing platforms (Illumina, SOLiD, 454) has brought TCR sequence analysis into the realm of possibility. Matching the platform with the TCR template’s unique characteristics is essential. Each T cell rearranges its genome to generate a unique TCR (VDJ recombination), with nongermline bases enzymatically produced at the junctions. Attempts to “assemble” TCR sequences from short reads (35bp, Illumina) that do not span the recombination junctions have introduced an assembly conundrum. However, the 454 pyrosequencing platform’s 250bp sequence reads generate full TCR clonotypes with no need for overlap assembly. Herein, we provide the first large scale C57Bl/6 mouse TCR β repertoire on a long read platform (Roche 454). To illustrate our methods strength, we have generated hundreds of thousands of TCRs from multiple B6 mice. To estimate the procedures error rates we have sequenced TCRs from a recombinase deficient TCR transgenic mouse (P14). This technique enables organism level analysis of T cell lineage specification, selection, and regulation during development and in disease states (infectious, autoimmune, graft and vaccine responses).
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Dissertations / Theses on the topic "Roche 454 sequencing"

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Guedes, Fernanda Alves de Freitas. "Pirossequenciamento do transcriptoma de folha de Lippia alba por meio da plataforma 454 GS FLX (Roche)." Universidade Federal de Juiz de Fora (UFJF), 2011. https://repositorio.ufjf.br/jspui/handle/ufjf/2496.

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Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-09-15T12:46:42Z No. of bitstreams: 1 fernandaalvesdefreitasguedes.pdf: 2011976 bytes, checksum: 6684b1525d9f87a2f6e72eadaa42fc34 (MD5)<br>Approved for entry into archive by Diamantino Mayra (mayra.diamantino@ufjf.edu.br) on 2016-09-26T20:18:53Z (GMT) No. of bitstreams: 1 fernandaalvesdefreitasguedes.pdf: 2011976 bytes, checksum: 6684b1525d9f87a2f6e72eadaa42fc34 (MD5)<br>Made available in DSpace on 2016-09-26T20:18:53Z (GMT). No. of bitstreams: 1 fernandaalvesdefreitasguedes.pdf: 2011976 bytes, checksum: 6684b1525d9f87a2f6e72eadaa42fc34 (MD5) Previous issue date: 2011-02-28<br>CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior<br>Lippia alba, também conhecida popularmente como erva cidreira, é uma espécie amplamente distribuída pelas Américas podendo ser encontrada por praticamente todo o Brasil. Muito usada pela medicina popular para o tratamento de problemas gastrointestinais e respiratórios, a folha desta espécie produz um óleo essencial rico em terpenos, principalmente mono e sesquiterpenos. Estes compostos não são apenas de interesse farmacológico, como também industrial. A composição deste óleo pode variar em função de fatores abióticos e também de variações genotípicas. Diante da complexidade da síntese destes compostos a proposta deste trabalho foi uma ampla caracterização do transcriptoma de folha de Lippia alba, além da identificação de prováveis enzimas envolvidas na síntese de terpenos. Para isso, foi feito um sequenciamento deste transcriptoma usando a plataforma 454 (Roche) seguido de uma montagem de novo. Esta plataforma tem sido cada vez mais utilizada para o sequenciamento de transcriptomas numa abordagem conhecida como RNA-Seq. O sequenciamento de biblioteca preparada a partir de RNA total em 1/8 de placa gerou 104.631 leituras com comprimento médio de 184,48bp num total de 19.302.161 bases. Foram feitas montagens das leituras usando 2 diferentes assemblers a fim de compará-las. Com o Newbler 2.5 foi possível montar 2.686 contigs com comprimento médio de 349bp, enquanto o SeqMan2.2 gerou 13.448 contigs com média de 284bp. Em seguida, foi feita a anotação funcional com o Blast2GO para os contigs obtidos nas duas montagens, tendo sido anotados 51,49% e 30,88%, respectivamente, dos contigs do Newbler e do SeqMan. Por fim, a análise das sequências anotadas revelou algumas enzimas potencialmente envolvidas com a síntese de terpenos. Os resultados obtidos neste estudo pioneiro sobre a espécie comprovam que as tecnologias NGS podem ser uma ferramenta bastante eficiente para o sequenciamento de transcriptomas e servirão como referência para o preparo mais específico de novas bibliotecas. Futuros sequenciamentos devem contribuir para uma melhor cobertura do transcriptoma permitindo a descoberta inclusive de transcritos raros.<br>Lippia alba, popularly known as erva cidreira, is widely distributed throughout the Americas and can be found through almost whole Brazil. This species is largely used in folk medicine to treat gastrointestinal and respiratory problems, especially leaves, which produce an essential oil rich in terpenes, mainly mono-and sesquiterpenes. These compounds are not only of pharmacological interest, as well as industrial. Composition of essencial oil can vary depending on the developmental stage, the plant part and other abiotic factors. However, genotypic variations also contribute to oil composition variation. Given the complexity of terpenes synthesis, including diversity of enzymes involved in these metabolic pathways, the purpose of this work was a L. alba leaf transcriptome characterization, in addition to identifying some enzymes probably involved in terpene synthesis. For that, it was made a transcriptome sequencing using 454 platform (Roche) followed by a de novo assembly. This platform, along with other NGS technologies, has been increasingly used for transcriptome sequencing in an approach known as RNA-Seq. Sequencing of a library prepared from total RNA in 1/8 plate generated 104,631 reads with average length of 184.48 bp and a total of 19,302,161 bases. Read assemblies were made using two different assemblers in order to compare them. While Newbler 2.5, proprietary software platform, assembled 2686 contigs with average length of 349bp, SeqMan2.2 generated 13,448 contigs with an average of 284bp. Then, functional annotation was performed with Blast2GO for all contigs from both assemblies; 51.49% and 30.88% of contigs, respectively, from Newbler and SeqMan were annotated. Finally, analysis of annotated sequences revealed some enzymes potentially involved in terpene synthesis. Results obtained from this pioneering study on the species show that NGS technology can be a very efficient tool for transcriptome sequencing and they will serve as reference for preparation of other more specific libraries. New sequencings should contribute to a better coverage of this transcriptome, allowing discovery of even rare transcripts.
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Pinder, Shaun. "Detecting Changes in the Gut Microbiome following Human Biotherapy via Pyrosequencing of the 16S rRNA Gene." Thesis, 2013. http://hdl.handle.net/10214/6578.

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Human biotherapy (HBT) or fecal transplants have been shown to be an effective treatment for patients with recurrent Clostridium difficile infection (CDI). This study examines the microbial populations present in CDI patients pre- and post-HBT by extracting bacterial DNA from stool samples and performing pyrosequencing of the 16S rRNA gene. We then compared these microbial populations to those of the donors. We examined 19 pairs of patient samples, of which 14 were clinically cured of CDI, and 5 patients were failures. The successful treatment of CDI was associated with an increase in diversity and richness of the patient's fecal microbiome. The majority of those cured showed an increase in the proportion of Firmicutes and decrease in the proportion of Proteobacteria, although varying antibiotic exposure and innate variability between patients was observed.<br>MSc thesis<br>NSERC, CIHR, St. Joseph's Healthcare Hamilton
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Book chapters on the topic "Roche 454 sequencing"

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Soares, Ana Raquel, Patrícia M. Pereira, and Manuel A. S. Santos. "Next-Generation Sequencing of miRNAs with Roche 454 GS-FLX Technology: Steps for a Successful Application." In Methods in Molecular Biology. Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-427-8_13.

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Slatter, Tania, and Alison Fitches. "DNA sequencing." In Tools and Techniques in Biomolecular Science. Oxford University Press, 2013. http://dx.doi.org/10.1093/hesc/9780199695560.003.0004.

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This chapter looks at DNA sequencing, a technique used to determine the precise order of the nucleotide bases-adenine, guanine, cytosine, and thymine-in a DNA fragment. The chapter explains the first-generation sequencing methods: the chemical method introduced by Maxam and Gilbert in 1977, the Sanger dideoxy-chain-termination sequencing method, and the chain-termination cycle sequencing method. It also tackles the uses of next-generation sequencing methods which use newer technologies. The chapter gives an overview of the next-generation sequencing procedure and explains the template preparation. It describes the various sequencing platforms, namely, the Roche 454, Illumina system, and SOLiD system. The chapter also lists some bioinformatic tools for the analysis of next-generation sequencing data. Lastly, it discusses the limitations of next-generation sequencing.
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Conference papers on the topic "Roche 454 sequencing"

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Misra, Sanchit, Ramanathan Narayanan, Wei-keng Liao, Alok Choudhary, and Simon Lin. "pFANGS: Parallel high speed sequence mapping for Next Generation 454-roche Sequencing reads." In Distributed Processing, Workshops and Phd Forum (IPDPSW 2010). IEEE, 2010. http://dx.doi.org/10.1109/ipdpsw.2010.5470894.

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Uhrhammer, Nancy A., Yannick Bidet, Laurence Lafarge, and Yves-Jean Bignon. "Abstract 3988: Mutation screening of the BRCA genes using Roche-454 pyrosequencing: comparison with fluorescent dideoxy sequencing." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-3988.

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Soverini, Simona, Caterina De Benedittis, Alessandra Gnani, et al. "Abstract 1884: Resistance to second-line tyrosine kinase inhibitor treatment in imatinib-resistant Philadelphia-positive leukemia patients can be anticipated by ultra-deep sequencing of the BCR-ABL kinase domain using Roche 454 technology." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-1884.

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