Transcriptomics

Dataset Information

3

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: Manuel R Teixeira  Francesca Micci  Nuno Cerveira  Ragnhild A Lothe  Guro E Lind  Sverre Heim  Marthe Eken  Franclim R Ribeiro  Gard Olav Thomassen  Torbjørn Rognes  Gard O Thomassen  Rolf I Skotheim 

PROVIDER: E-GEOD-14435 | ArrayExpress | 2010-05-06

SECONDARY ACCESSION(S): GSE14435PRJNA111769

REPOSITORIES: GEO, ArrayExpress

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Publications

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


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.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 measurem  ...[more]

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