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Nucleic Acids Research Advance Access published online on September 15, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn585
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

A sensitive array-based assay for identifying multiple TMPRSS2:ERG fusion gene variants

Qing Lu1, Esperanza Nunez2, Chunrun Lin2, Kimberly Christensen3, Tracy Downs1,4, Dennis A. Carson1,5, Jessica Wang-Rodriguez1,3 and Yu-Tsueng Liu1,5,*

1Moores Cancer Center, 2Howard Hughes Medical Institute, 3Department of Pathology, 4Department of Surgery and 5Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA

*To whom correspondence should be addressed. Tel: +1 858 534 9972; Fax: +1 858 534 5399; Email: ytliu{at}ucsd.edu

Correspondence may also be addressed to Jessica Wang-Rodriguez. Tel: +1 858 642 3511; Fax: +1 858 642 3918; Email: jwrodriguez{at}ucsd.edu

Received May 7, 2007. Revised August 25, 2008. Accepted August 26, 2008.

Studies of gene fusions in solid tumors are not as extensive as in hematological malignancies due to several technical and analytical problems associated with tumor heterogeneity. Nevertheless, there is a growing interest in the role of fusion genes in common epithelial tumors after the discovery of recurrent TMPRSS2:ETS fusions in prostate cancer. Among all of the reported fusion partners in the ETS gene family, TMPRSS2:ERG is the most prevalent one. Here, we present a simple and sensitive microarray-based assay that is able to simultaneously determine multiple fusion variants with a single RT–PCR in impure RNA specimens. The assay detected TMPRSS2:ERG fusion transcripts with a detection sensitivity of <10 cells in the presence of more than 3000 times excess normal RNA, and in primary prostate tumors having no >1% of cancer cells. The ability to detect multiple transcript variants in a single assay is critically dependent on both the primer and probe designs. The assay should facilitate clinical and basic studies for fusion gene screening in clinical specimens, as it can be readily adapted to include multiple gene loci.


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