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


RESULTS
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 TCF3:PBX1, ETV6:RUNX1, and TMPRSS2:ERG) from all six positive controls consisting of leukemia cell lines and prostate cancer biopsies.


CONCLUSIONS
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.
Skotheim
Rolf I
RI
Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway. rolf.i.skotheim@rr-research.no
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
D000465:Algorithms; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics; D045744:Cell Line, Tumor; D050676:Core Binding Factor Alpha 2 Subunit / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D000075062:Pre-B-Cell Leukemia Transcription Factor 1; D011471:Prostatic Neoplasms / Q000235:genetics; D011518:Proto-Oncogene Proteins / Q000235:genetics; D050783:Proto-Oncogene Proteins c-ets / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D012697:Serine Endopeptidases / Q000235:genetics; D015534:Trans-Activators / Q000235:genetics; D000071230:Transcriptional Regulator ERG; D000097764:ETS Translocation Variant 6 Protein
D051792:Basic Helix-Loop-Helix Proteins; D050676:Core Binding Factor Alpha 2 Subunit; D004268:DNA-Binding Proteins; D015514:Oncogene Proteins, Fusion; D000075062:Pre-B-Cell Leukemia Transcription Factor 1; D011518:Proto-Oncogene Proteins; D050783:Proto-Oncogene Proteins c-ets; D012097:Repressor Proteins; D012697:Serine Endopeptidases; D015534:Trans-Activators; D000071230:Transcriptional Regulator ERG; D000097764:ETS Translocation Variant 6 Protein; C072312:ERG protein, human; C493728:RUNX1 protein, human; C407909:TCF3 protein, human; C083400:PBX1 protein, human; C421305:TMPRSS2 protein, human