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  • 1
    Online Resource
    Online Resource
    Type of Medium: Online Resource
    Pages: 1 Online-Ressource (S. 1-14)
    ISSN: 1088-9051
    URL: Volltext  (kostenfrei)
    Language: Undetermined
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  • 2
    Book
    Book
    Wildau : Beyerlein
    Associated volumes
    Type of Medium: Book
    Language: German
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  • 3
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    Publication Date: 2021-06-15
    Description: Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole genome, whole exome, and targeted exon sequencing). Global mismatch rates and C·G 〉 T·A substitutions were comparable between matched FF/FFPE samples, and discordant rates were low (〈0.26%) in all samples. Finally, low-pass whole genome sequencing produces similar pattern of copy number alterations between FF/FFPE pairs. The results from our studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes.
    Keywords: ddc:616
    Language: English
    Type: article , doc-type:article
    Format: application/pdf
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  • 4
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    Publication Date: 2021-06-15
    Description: The use of a priori knowledge in the alignment of targeted sequencing data is investigated using computational experiments. Adapting a Needleman–Wunsch algorithm to incorporate the genomic position information from the targeted capture, we demonstrate that alignment can be done to just the target region of interest. When in addition use is made of direct string comparison, an improvement of up to a factor of 8 in alignment speed compared to the fastest conventional aligner (Bowtie) is obtained. This results in a total alignment time in targeted sequencing of around 7 min for aligning approximately 56 million captured reads. For conventional aligners such as Bowtie, BWA or MAQ, alignment to just the target region is not feasible as experiments show that this leads to an additional 88% SNP calls, the vast majority of which are false positives (∼92%).
    Keywords: ddc:570
    Language: English
    Type: article , doc-type:article
    Format: application/pdf
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  • 5
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    Publication Date: 2021-06-15
    Description: Structural variations (SVs) in genomic DNA can have profound effects on the evolution of living organisms, on phenotypic variations and on disease processes. A critical step in discovering the full extent of structural variations is the development of tools to characterize these variations accurately in next generation sequencing data. Toward this goal, we developed a software pipeline named digit that implements a novel measure of mapping ambiguity to discover interchromosomal SVs from mate-pair and pair-end sequencing data. The workflow robustly handles the high numbers of artifacts present in mate-pair sequencing and reduces the false positive rate while maintaining sensitivity. In the simulated data set, our workflow recovered 96% of simulated SVs. It generates a self-updating library of common translocations and allows for the investigation of patient- or group-specific events, making it suitable for discovering and cataloging chromosomal translocations associated with specific groups, traits, diseases or population structures.
    Keywords: ddc:576
    Language: English
    Type: article , doc-type:article
    Format: application/pdf
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  • 6
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    Unknown
    Publication Date: 2021-06-15
    Description: Current genomic studies are limited by the availability of fresh tissue samples. Here, we show that Illumina RNA sequencing of formalin-fixed diagnostic tumor samples produces gene expression that is strongly correlated with matched frozen tumor samples (r 〉 0.89). In addition, sequence variations identified from FFPE RNA show 99.67% concordance with that from exome sequencing of matched frozen tumor samples. Because FFPE is a routine diagnostic sample preparation, the feasibility results reported here will facilitate the setup of large-scale research and clinical studies in medical genomics that are currently limited by the availability of fresh frozen samples.
    Keywords: ddc:570
    Language: English
    Type: article , doc-type:article
    Format: application/pdf
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  • 7
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    Publication Date: 2021-06-15
    Description: mRNA-seq is a paradigm-shifting technology because of its superior sensitivity and dynamic range and its potential to capture transcriptomes in an agnostic fashion, i.e., independently of existing genome annotations. Implementation of the agnostic approach, however, has not yet been fully achieved. In particular, agnostic mapping of pre-mRNA splice sites has not been demonstrated. The present study pursued dual goals: (1) to advance mRNA-seq bioinformatics toward unbiased transcriptome capture and (2) to demonstrate its potential for discovery in neuroscience by applying the approach to an in vivo model of neurological disease. We have performed mRNA-seq on the L4 dorsal root ganglion (DRG) of rats with chronic neuropathic pain induced by spinal nerve ligation (SNL) of the neighboring (L5) spinal nerve. We found that 12.4% of known genes were induced and 7% were suppressed in the dysfunctional (but anatomically intact) L4 DRG 2 wk after SNL. These alterations persisted chronically (2 mo). Using a read cluster classifier with strong test characteristics (ROC area 97%), we discovered 10,464 novel exons. A new algorithm for agnostic mapping of pre-mRNA splice junctions (SJs) achieved a precision of 97%. Integration of information from all mRNA-seq read classes including SJs led to genome reannotations specifically relevant for the species used (rat), the anatomical site studied (DRG), and the neurological disease considered (pain); for example, a 64-exon coreceptor for the nociceptive transmitter substance P was identified, and 21.9% of newly discovered exons were shown to be dysregulated. Thus, mRNA-seq with agnostic analysis methods appears to provide a highly productive approach for in vivo transcriptomics in the nervous system.
    Keywords: ddc:570
    Language: English
    Type: article , doc-type:article
    Format: application/pdf
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  • 8
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    Unknown
    Publication Date: 2021-06-15
    Description: Phytoplasma-associated diseases are reported for more than 1,000 plant species worldwide. Only a few genome sequences are available in contrast to the economical importance of these bacterial pathogens. A new strategy was used to retrieve phytoplasma strain-specific genome data. Multiple displacement amplification was performed on DNA obtained from 〈3 g of plant tissue from tobacco and parsley samples infected with ‘stolbur' strains. Random hexamers and Phi29 polymerase were evaluated with and without supplementation by group-assigned oligonucleotides providing templates for Illumina's sequencing approach. Metagenomic drafts derived from individual and pooled strain-specific de novo assemblies were analyzed. Supplementation of the Phi29 reaction with the group-assigned oligonucleotides resulted in an about 2-fold enrichment of the percentage of phytoplasma-assigned reads and thereby improved assembly results. The obtained genomic drafts represent the largest datasets available from ‘stolbur' phytoplasmas. Sequences of the two strains (558 kb, 448 proteins and 516 kb, 346 proteins, respectively) were annotated allowing the identification of prominent membrane proteins and reconstruction of core pathways. Analysis of a putative truncated sucrose phosphorylase provides hints on sugar degradation. Furthermore, it is shown that drafts obtained from repetitive-rich genomes allow only limited analysis on multicopy regions and genome completeness.
    Keywords: ddc:660
    Language: English
    Type: article , doc-type:article
    Format: application/pdf
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  • 9
    Book
    Book
    Hawaii : IEEE [Hawaii]
    Keywords: Biologie allgemein
    Abstract: The alpha-subunit of the rapid delayed rectifier Ikr has been identified to be composed of multiple function domains. However, much less is known about the electrophysiological consequences of the interaction properties in the assembled channel protein. In this paper, we present a detailed conformational kinetic model through characterizing allosteric interactions between the voltage sensing domain and the cytoplasmic activation gate. The correlation of kinetic properties to action potential (AP) dynamics was investigated at different basic cycle lengths. We found that in response to driving forces ranging from -40 mV to 60 mV, two open states were populated. A significant elevation of Ikr at the early AP was attributable to an available reserve and the open-state accumulation, leading to shortening of AP duration at rapid rates. In contrast, the development of a dominant late peak Ikr with a steep slope morphology observed at slow rates arose from the allosteric coupled activation pathway. The existence of available reserve suggests Ikr has a repolarization reserve which facilitates its rate adaptation.
    Type of Medium: Book
    Publication type: Anthology article
    Access type: Metadata only Access
    Peer-reviewed: yes
    ISBN: 978-1-4244-3706-1
    Language: English
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  • 10
    Book
    Book
    Amsterdam : Elsevier
    Keywords: Biologie allgemein ; Outcome measures ; Neurotoxicity
    Abstract: The predisposition of patients to develop polyneuropathy in response to toxic exposure may have a genetic basis. The previous study Alliance N08C1 found an association of the Charcot-Marie-Tooth disease (CMT) gene ARHGEF10 with paclitaxel chemotherapy induced peripheral neuropathy (CIPN) related to the three non-synonymous, recurrent single nucleotide variants (SNV), whereby rs9657362 had the strongest effect, and rs2294039 and rs17683288 contributed only weakly. In the present report, Alliance N08CA was chosen to attempt to replicate the above finding. N08CA was chosen because it is the methodologically most similar study (to N08C1) performed in the CIPN field to date. N08CA enrolled patients receiving the neurotoxic chemotherapy agent paclitaxel. Polyneuropathy was assessed by serial repeat administration of the previously validated patient reported outcome instrument CIPN20. A study-wide, Rasch type model was used to perform extreme phenotyping in n = 138 eligible patients from which "cases" and "controls" were selected for genetic analysis of SNV performed by TagMan PCR. A significant association of ARHGEF10 with CIPN was found under the pre-specified primary endpoint, with a significance level of p = 0.024. As in the original study, the strongest association of a single SNV was seen for rs9657362 (odds ratio = 3.56, p = 0.018). To further compare results across the new and the previous study, a statistical "classifier" was tested, which achieved a ROC area under the curve of 0.60 for N08CA and 0.66 for N08C1, demonstrating good agreement Retesting of the primary endpoint of N08C1 in the replication study N08CA validated the association of ARHGEF10 with CIPN. (C) 2015 Elsevier B.V. All rights reserved.
    Type of Medium: Book
    Publication type: Journal article
    Access type: Metadata only Access
    Peer-reviewed: yes
    ISSN: 0374-8642
    Language: English
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