1,721,597 research outputs found
Abstract 2707: Targeted RNA sequencing reveals thus far unknown diagnostically relevant fusion partners confirming its diagnostic potential
No full textAbstract
Introduction: The genomic landscape of hematological malignancies has been resolved mainly based on whole exome and whole genome sequencing, primarily targeting gene mutations. In addition to mutations, gene fusions have also been identified as therapeutic targets, impressively shown e.g. for BCR-ABL1 and ETV6-PDGFRB. Even though fluorescence in situ hybridization (FISH) is the current gold standard in fusion detection, it is by concept limited to the selected genes it is applied to. In contrast, targeted RNA sequencing is a valuable hypothesis-free approach to discover all possible fusion junctions in a single reaction.
Aim: Explore the value of targeted RNA sequencing in a routine diagnostic work up.
Patients and Methods: We sequenced 134 cases in parallel to our routine diagnostics workflow using chromosome banding analysis (CBA), FISH and real-time quantitative (RQ-PCR). Targeted RNA sequencing was performed on the NextSeq 500 using the TruSight RNA Fusion panel (Illumina, San Diego, CA) consisting of 7690 probes covering 507 genes known to be involved in gene fusions. Analysis was performed with the RNA-Seq Alignment App v1.2.0 (BaseSpace Sequence Hub) using Star for Alignment and Manta for gene fusion calling with default parameters (Illumina, San Diego, CA).
Results: In 127 of 134 (95%) cases the results of FISH, subsequently confirmed with RT-PCR were also picked up by RNA Seq. This included diagnostically highly relevant fusions like BCR-ABL1 (n=8), KMT2A rearrangements (n=7), PML-RARA (n=4), and ETV6 and NPM1 rearrangements. In addition to the confirmation of orthogonal results, we were able to identify novel rare gene fusions, which we subsequently confirmed by RQ-PCR. This included immediately targetable fusions like TNIP1-PDGFRB and ETV6-EFL1, ETV6-FOXO1, IRF2PB1-RARA, RARA-SAE1).
Conclusion: 1) In the vast majority of instances targeted RNA sequencing confirmed results obtained by FISH/RT-PCR and in addition discovered new rare gene fusions 2) Targetable genetic aberrations were identified, which were not identifiable by chromosome banding analysis but would now lead to more individualized treatment. 3) Thus, targeted RNA sequencing may be a valuable tool in routine diagnostics and for patients with rearrangements unresolved by standard techniques, also paving the way to precision medicine in a considerable number of patients.
Citation Format: Niroshan Nadarajah, Manja Meggendorfer, Torsten Haferlach, Wolfgang Kern, Claudia Haferlach. Targeted RNA sequencing reveals thus far unknown diagnostically relevant fusion partners confirming its diagnostic potential [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2707. doi:10.1158/1538-7445.AM2017-2707</jats:p
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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