A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis
<p>Abstract</p> <p>Background</p> <p>The ability to detect neoplasia-specific fusion genes is important not only in cancer research, but also increasingly in clinical settings to ensure that correct diagnosis is made and the optimal treatment is chosen. However, the ava...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2009-01-01
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| Series: | Molecular Cancer |
| Online Access: | http://www.molecular-cancer.com/content/8/1/5 |
| _version_ | 1811318348802162688 |
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| author | Ribeiro Franclim R Micci Francesca Lind Guro E Eken Marthe Thomassen Gard OS Skotheim Rolf I Cerveira Nuno Teixeira Manuel R Heim Sverre Rognes Torbjørn Lothe Ragnhild A |
| author_facet | Ribeiro Franclim R Micci Francesca Lind Guro E Eken Marthe Thomassen Gard OS Skotheim Rolf I Cerveira Nuno Teixeira Manuel R Heim Sverre Rognes Torbjørn Lothe Ragnhild A |
| author_sort | Ribeiro Franclim R |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The ability to detect neoplasia-specific fusion genes is important not only in cancer research, but also increasingly in clinical settings to ensure that correct diagnosis is made and the optimal treatment is chosen. However, the available methodologies to detect such fusions all have their distinct short-comings.</p> <p>Results</p> <p>We describe a novel oligonucleotide microarray strategy whereby one can screen for all known oncogenic fusion transcripts in a single experiment. To accomplish this, we combine measurements of chimeric transcript junctions with exon-wise measurements of individual fusion partners. To demonstrate the usefulness of the approach, we designed a DNA microarray containing 68,861 oligonucleotide probes that includes oligos covering all combinations of chimeric exon-exon junctions from 275 pairs of fusion genes, as well as sets of oligos internal to all the exons of the fusion partners. Using this array, proof of principle was demonstrated by detection of known fusion genes (such as <it>TCF3:PBX1</it>, <it>ETV6:RUNX1</it>, and <it>TMPRSS2:ERG</it>) from all six positive controls consisting of leukemia cell lines and prostate cancer biopsies.</p> <p>Conclusion</p> <p>This new method bears promise of an important complement to currently used diagnostic and research tools for the detection of fusion genes in neoplastic diseases.</p> |
| first_indexed | 2024-04-13T12:23:58Z |
| format | Article |
| id | doaj.art-2255c8eb6b1d481e8be5f3da28eae83b |
| institution | Directory Open Access Journal |
| issn | 1476-4598 |
| language | English |
| last_indexed | 2024-04-13T12:23:58Z |
| publishDate | 2009-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Molecular Cancer |
| spelling | doaj.art-2255c8eb6b1d481e8be5f3da28eae83b2022-12-22T02:47:04ZengBMCMolecular Cancer1476-45982009-01-0181510.1186/1476-4598-8-5A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysisRibeiro Franclim RMicci FrancescaLind Guro EEken MartheThomassen Gard OSSkotheim Rolf ICerveira NunoTeixeira Manuel RHeim SverreRognes TorbjørnLothe Ragnhild A<p>Abstract</p> <p>Background</p> <p>The ability to detect neoplasia-specific fusion genes is important not only in cancer research, but also increasingly in clinical settings to ensure that correct diagnosis is made and the optimal treatment is chosen. However, the available methodologies to detect such fusions all have their distinct short-comings.</p> <p>Results</p> <p>We describe a novel oligonucleotide microarray strategy whereby one can screen for all known oncogenic fusion transcripts in a single experiment. To accomplish this, we combine measurements of chimeric transcript junctions with exon-wise measurements of individual fusion partners. To demonstrate the usefulness of the approach, we designed a DNA microarray containing 68,861 oligonucleotide probes that includes oligos covering all combinations of chimeric exon-exon junctions from 275 pairs of fusion genes, as well as sets of oligos internal to all the exons of the fusion partners. Using this array, proof of principle was demonstrated by detection of known fusion genes (such as <it>TCF3:PBX1</it>, <it>ETV6:RUNX1</it>, and <it>TMPRSS2:ERG</it>) from all six positive controls consisting of leukemia cell lines and prostate cancer biopsies.</p> <p>Conclusion</p> <p>This new method bears promise of an important complement to currently used diagnostic and research tools for the detection of fusion genes in neoplastic diseases.</p>http://www.molecular-cancer.com/content/8/1/5 |
| spellingShingle | Ribeiro Franclim R Micci Francesca Lind Guro E Eken Marthe Thomassen Gard OS Skotheim Rolf I Cerveira Nuno Teixeira Manuel R Heim Sverre Rognes Torbjørn Lothe Ragnhild A A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis Molecular Cancer |
| title | A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis |
| title_full | A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis |
| title_fullStr | A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis |
| title_full_unstemmed | A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis |
| title_short | A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis |
| title_sort | universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis |
| url | http://www.molecular-cancer.com/content/8/1/5 |
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