SI Table 1  A sensitive array-based assay for identifying multiple TMPRSS2:ERG fusion gene variants 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. Chromosome rearrangements are a characteristic feature of cancer. More than 350 gene fusions, as a consequence of chromosome aberrations, have been identified (1) . While gene fusions are common in hematological malignancies, their presence in solid tumors is not as well studied due to several technical and analytic problems related to tumor heterogeneity (1) . Only very limited gene fusion events were discovered in solid tumors, mostly in sarcomas, until the recent discovery of TMPRSS2:ETS fusion genes in prostate cancer (2) . This finding has since changed the general view that gene fusions play only a minor role in the pathogenesis of epithelial tumors. Therefore, there is renewed interest in searching for fusion genes in solid tumors, due to their potential impact on basic research and clinical application as has been demonstrated in chronic myelogenous leukemia (CML) (3, 4) .