Assessment of Fusion Gene Status in Sarcomas Using a Custom Made Fusion Gene Microarray
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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1168805", "https://ndownloader.figshare.com/files/1168806"], "description"=>"<div><p>Sarcomas are relatively rare malignancies and include a large number of histological subgroups. Based on morphology alone, the differential diagnoses of sarcoma subtypes can be challenging, but the identification of specific fusion genes aids correct diagnostication. The presence of individual fusion products are routinely investigated in Pathology labs. However, the methods used are time-consuming and based on prior knowledge about the expected fusion gene and often the most likely break-point. In this study, 16 sarcoma samples, representing seven different sarcoma subtypes with known fusion gene status from a diagnostic setting, were investigated using a fusion gene microarray. The microarray was designed to detect all possible exon-exon breakpoints between all known fusion genes in a single analysis. An automated scoring of the microarray data from the 38 known sarcoma-related fusion genes identified the correct fusion gene among the top-three hits in 11 of the samples. The analytical sensitivity may be further optimised, but we conclude that a sarcoma-fusion gene microarray is suitable as a time-saving screening tool to identify the majority of the correct fusion genes.</p></div>", "links"=>[], "tags"=>["Computational biology", "microarrays", "genetics", "Cancer genetics", "Diagnostic medicine", "pathology", "General pathology", "biomarkers", "epidemiology", "Biomarker epidemiology", "oncology", "Cancer detection and diagnosis", "Cancer screening", "Cancers and neoplasms", "Bone and soft tissue sarcomas", "fusion", "sarcomas"], "article_id"=>771736, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Marthe Løvf", "Gard O. S. Thomassen", "Fredrik Mertens", "Nuno Cerveira", "Manuel R. Teixeira", "Ragnhild A. Lothe", "Rolf I. Skotheim"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0070649.s001", "https://dx.doi.org/10.1371/journal.pone.0070649.s002"], "stats"=>{"downloads"=>4, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Assessment_of_Fusion_Gene_Status_in_Sarcomas_Using_a_Custom_Made_Fusion_Gene_Microarray_/771736", "title"=>"Assessment of Fusion Gene Status in Sarcomas Using a Custom Made Fusion Gene Microarray", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-08-13 03:35:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1168803"], "description"=>"1<p>All 38 investigated fusion genes are ranked based on the likelihood of being the correct fusion gene in the particular sample. Lower numbers indicate higher likelihood.</p>2<p>Information about RT-PCR protocols for fusion gene detection. In house: protocol not previously published. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070649#s2\" target=\"_blank\">Materials and Methods</a> for more details. NK: Normal karyotype.</p>", "links"=>[], "tags"=>["Computational biology", "microarrays", "genetics", "Cancer genetics", "Diagnostic medicine", "pathology", "General pathology", "biomarkers", "epidemiology", "Biomarker epidemiology", "oncology", "Cancer detection and diagnosis", "Cancer screening", "Cancers and neoplasms", "Bone and soft tissue sarcomas", "investigated"], "article_id"=>771734, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Marthe Løvf", "Gard O. S. Thomassen", "Fredrik Mertens", "Nuno Cerveira", "Manuel R. Teixeira", "Ragnhild A. Lothe", "Rolf I. Skotheim"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070649.t001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Samples_investigated_in_the_study_/771734", "title"=>"Samples investigated in the study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-13 03:35:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1168801"], "description"=>"<p>A. <i>EWSR1</i>-<i>NR4A3</i> in the 168/97 sample. B. <i>SS18</i>-<i>SSX1</i> in the 9972 sample. I) Intensity heat map of chimeric oligos. Each square represents one possible exon-exon boundary between the two gene partners. One square is highly expressed (A: 13-3, B: 10-6) and reflects the presence of chimeric RNA covering the corresponding exon-exon boundary. This fusion breakpoint corresponds with a shift in relative expression measured by intragenic oligos covering both the upstream (II) and downstream (III) fusion gene partners. Blue and red colours represent the two possible chimeric transcripts generated from the fusion gene.</p>", "links"=>[], "tags"=>["Computational biology", "microarrays", "genetics", "Cancer genetics", "Diagnostic medicine", "pathology", "General pathology", "biomarkers", "epidemiology", "Biomarker epidemiology", "oncology", "Cancer detection and diagnosis", "Cancer screening", "Cancers and neoplasms", "Bone and soft tissue sarcomas", "ranked", "fusion", "genes", "sarcoma"], "article_id"=>771732, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Marthe Løvf", "Gard O. S. Thomassen", "Fredrik Mertens", "Nuno Cerveira", "Manuel R. Teixeira", "Ragnhild A. Lothe", "Rolf I. Skotheim"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070649.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_ranked_fusion_genes_in_two_sarcoma_samples_/771732", "title"=>"Top ranked fusion genes in two sarcoma samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-13 03:35:57"}

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Relative Metric

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