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| Naji, M. |
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| Motta, Antonella |
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| Aletan, Dirar |
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| Mohamed, Tarek |
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| Ertürk, Emre |
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| Taccardi, Nicola |
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| Kononenko, Denys |
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| Petrov, R. H. | Madrid |
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| Alshaaer, Mazen | Brussels |
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| Bih, L. |
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| Casati, R. |
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| Muller, Hermance |
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| Kočí, Jan | Prague |
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| Šuljagić, Marija |
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| Kalteremidou, Kalliopi-Artemi | Brussels |
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| Azam, Siraj |
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| Ospanova, Alyiya |
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| Blanpain, Bart |
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| Ali, M. A. |
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| Popa, V. |
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| Rančić, M. |
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| Ollier, Nadège |
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| Azevedo, Nuno Monteiro |
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| Landes, Michael |
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| Rignanese, Gian-Marco |
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Horak, Peter
University of Southampton
in Cooperation with on an Cooperation-Score of 37%
Topics
Publications (23/23 displayed)
- 2021Abstract 449: A standard operating procedure for the curation of gene fusions
- 2021Gas-induced differential refractive index enhanced guidance in hollow-core optical fiberscitations
- 2020Four-port integrated waveguide coupler exploiting bi-directional propagation of two single-mode waveguides
- 2018Wavelength conversion and supercontinuum generation in silicon optical fiberscitations
- 2018Novel fiber design for wideband conversion and amplification in multimode fiberscitations
- 2016Phase matched parametric amplification via four-wave mixing in optical microfiberscitations
- 2016Nanopores within 3D-structured gold film for sensing applications
- 2016All-fiber fourth and fifth harmonic generation from a single sourcecitations
- 2015Tunable optical buffer based on III-V MEMS design
- 2014Fabrication of multiple parallel suspended-core optical fibers by sheet-stackingcitations
- 2013Laser-induced forward transfer on compliant receiverscitations
- 2012Laser-induced crystalline optical waveguide in glass fiber formatcitations
- 2011Manipulating the structure of ion Coulomb crystals with light
- 20111.06 µm picosecond pulsed, normal dispersion pumping for generating efficient broadband infrared supercontinuum in meter-length single-mode tellurite holey fiber with high Raman gain coefficientcitations
- 2010Dispersion controlled highly nonlinear fibers for all optical processing at telecoms wavelengthscitations
- 2010Near-zero dispersion, highly nonlinear lead-silicate W-type fiber for applications at 1.55µmcitations
- 2010Efficient near-infrared supercontinuum generation in tellurite holey fiber pumped 320nm within the normal dispersion regime
- 2009Optical fiber nanowires and microwires: fabrication and applicationscitations
- 2009Dispersion-shifted all-solid high index-contrast microstructured optical fiber for nonlinear applications at 1.55µmcitations
- 2009Four-wave mixing-based wavelength conversion in a short-length of a solid 1D microstructured fibre
- 2008Single-mode tellurite glass holey fiber with extremely large mode area for infrared nonlinear applicationscitations
- 2007RGB generation by four-wave mixing in small-core holey fibers
- 2007Mid-IR supercontinuum generation from non-silica microstructured optical fiberscitations
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document
Abstract 449: A standard operating procedure for the curation of gene fusions
Abstract
<jats:title>Abstract</jats:title><jats:p>Despite the well-established role of recurrent gene fusions as oncogenic drivers, current practices for characterizing and interpreting gene fusion events in clinical testing and in biomedical literature are inconsistent. From the conceptual definition of gene fusions to the salient elements that characterize these alterations, a lack of community-driven standards for the curation of gene fusions has resulted in a disparate landscape of fusion representations and supporting tools. Consequently, the evidence-based clinical evaluation of gene fusions requires extensive expert review for accurate interpretation of observed gene fusions with respect to putative evidence from biomedical literature. Furthermore, the lack of these standards inhibits the interoperability of tools, resources, and pipelines - impeding data sharing and downstream utility.To address these challenges, a cross-consortia initiative between the Variant Interpretation for Cancer Consortium and ClinGen was formed to develop a standard operating procedure (SOP) for the curation of gene fusions. The SOP is under development by an international and diverse set of experts in the representation, detection, and clinical interpretation of gene fusions. Participating stakeholders across academic, government, and industry sectors showcased challenges and solutions, and participated in community surveys and discussions to define and develop the SOP for this diverse class of alterations.An initial result of this effort was the precise molecular definition of genomic events and features constituting gene fusions. We distinguish these from similar but distinct classes of structural alterations through clinically-relevant examples. Next, we discuss our findings on community practices around the description and evaluation of gene fusions. We provide our recommendations for characterization and representation of gene fusions from these practices, and compare these recommendations to existing variant representation standards and formats (e.g. HGVS variant nomenclature). We also discuss the concurrent application of formats for standardized human- and machine-readable representations of gene fusion events.We conclude with discussion of the salient elements to enable rapid, scalable, and consistent evaluation of fusions curated from the biomedical literature. Recommendations are provided for the standardized capture of these elements to enable both intuitive and precise characterization of this diverse class of alterations in clinical reporting and literature. In summary, we provide a clinical-practice driven framework and nomenclature for gene fusions, including recommendations for human readability, computational precision, and data integrity within the SOP. This work is a substantial advancement towards standardized communication, investigation, and sharing of gene fusion data across clinical and research domains and specialties.</jats:p><jats:p>Citation Format: Alex H. Wagner, Ioannis S. Vlachos, Dmitriy Sonkin, Panieh Terraf, Chimene Kesserwan, Andrea Sboner, Thomas Coard, Christian Reich, Deborah I. Ritter, Peter Horak, Ying S. Zou, Anna Tanska, Aaron M. Berlin, Anna Lu, Daniel Cameron, Heather E. Williams, Wan-Hsin Lin, Gokce Toruner, Arpad Danos, Jason Saliba, Huiling Xu, Xinjie Xu, Georgina Ryland, Michele Ceccarelli, Liying Zhang, Sarah Rapisardo, Catherine Rehder, Xuelu Liu, Aparna Pallavajjala, Nicole Park, Laveniya Satgunaseelan, Kristy Lee, Jie Liu, Obi Griffith, Robert R. Freimuth, Albrecht Stenzinger, Linda B. Baughn, Michael Baudis, Jennifer Lee, Marilyn Li, Angshumoy Roy, Gordana Raca. A standard operating procedure for the curation of gene fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 449.</jats:p>