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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Pilot-study for a novel universal tool for detection of oncogenic fusion transcripts

ABSTRACT: A novel oligonucleotide microarray design is described whereby one can screen for all known oncogenic fusion transcripts by one microarray hybridization. Measurements of chimeric transcript junctions are combined with exon-wise measurements of individual fusion partners. Keywords: Nimblegen custom-design The pilot data included a design with 68,861 oligonucleotide probes 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. Proof of principle was demonstrated by detection of known fusion genes (such as TCF3:PBX1, ETV6:RUNX1, and TMPRSS2:ERG) from six positive controls consisting of leukemia cell lines and prostate cancer biopsies.

ORGANISM(S): Homo sapiens

SUBMITTER: Guro Lind

PROVIDER: E-GEOD-14435 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis.

Skotheim Rolf I RI Thomassen Gard O S GO Eken Marthe M Lind Guro E GE Micci Francesca F Ribeiro Franclim R FR Cerveira Nuno N Teixeira Manuel R MR Heim Sverre S Rognes Torbjørn T Lothe Ragnhild A RA

Molecular cancer 20090119

<h4>Background</h4>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.<h4>Results</h4>We describe a novel oligonucleotide microarray strategy whereby one can screen for all known oncogenic fusion transcripts in a single experiment. To a ...[more]

PMID: 19152679

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Pilot-study for a novel universal tool for detection of oncogenic fusion transcripts

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2009-01-19 | GSE14435 | GEO

Antibody detection of translocations (ADOT) in Ewing Sarcoma

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Project description:We have utilized a version 2.0 of our Fusion gene microarray (version 1.0 described by PMID: 19152679 and GEO, GPL8078) to screen cancer cell lines for known fusion genes We assembled a comprehensive database of published fusion genes, including those which have been reported only in individual studies and samples, and fusion genes resulting from deep sequencing of cancer genomes and transcriptomes. From the total set of 548 fusion genes, we designed 197,846 unique oligonucleotides, targeting both chimeric transcript junctions as well as sequences internal to each of the fusion gene partners. We investigated the presence of fusion genes in a series of 67 cell lines originating from 15 different cancer types. Data from ten leukaemia cell lines with known fusion gene status were used to evaluate and calibrate an automated scoring algorithm. In five out of ten cell lines the correct fusion gene was the top most scoring hit, and one came second, all six passing a cut-off of 50 percent of theoretical maximum-score. Two additional fusion genes, BCAS4-BCAS3 from the MCF-7 breast cancer cell line and CCDC6-RET from the TPC-1 thyroid cancer cell line were validated as true positive fusion transcripts from the remaining 57 cell lines. A total of 67 cell lines from various cancer types were analysed for presence of known fusion genes

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A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium

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