1. A method for detecting a MIPOL1-ETV1 genetic rearrangement and one or more markers associated with prostate cancer in a biological sample, the method comprising:a) contacting a biological sample with:
i) a probe directly labeled with a detectable label and comprising a sequence that is complementary to a junction at which an ETV1 gene is inserted into a MIPOL1 gene; or
ii) a first probe directly labeled with a detectable label and comprising a sequence complementary to a MIPOL1 gene and a second probe directly labeled with a detectable label and comprising a sequence complementary to an ETV1 gene; or
iii) a first amplification oligonucleotide comprising a sequence complementary to a MIPOL1 gene, a second amplification oligonucleotide comprising a sequence complementary to an ETV1 gene, and a probe directly labeled with a detectable label and comprising a sequence complementary to the product produced from the first and second primers; and
b) detecting in the biological sample expression of a marker selected from the set of markers consisting of AMACR/P504S, PCA3, PCGEM1, prostein/P501S, P503S, P504S, P509S, P510S, prostase/P703P, P710P, prostate specific antigen (PSA), prostatic acid phosphatase (PAP), prostate binding protein (PBP), ABCC5(MDR5), ADAMTS1, AMACR, ANNEXINA11, ANNEXINA1, ANNEXINA4, APP, ARHB, ASNS, ATF2, C1S, C4BPA, C7, CATHEPSINB, CATHEPSINH, CAVEOLIN2, CCND2, CFLAR, CLUSTERIN, COL15A1, COL1A2, COL3A1, c-terminal binding protein, CTBP1, CTBP2, CYSTATINC, E2EPF, EDNRB, EGR1, EPHA1, ETS2, EZH2, FASN, FAT, FHL1, FIBRONECTIN1, FKBP5, FLS353, FOLH1, FOSB, FZD7, GELSOLIN, GP73, GSTM1, GSTM3, GSTM5, GSTP1, HEPSIN, HEVIN, IGFBP3, IGFBP5, IL1R1, IL1R2, ITGA1, ITGB4, ITM2C, JUN, KERATIN5, LIMK1, LUMICAN, MADH4, MAP3K10, MAPK6, MCAM, MEIS1, MEIS2, MMECD10, MOESIN, MPDZ, MTA1, MYBL2, MYLK, NBL1, NCK1, NRAS, PCM1, pim-1, PLA2G2A, PP1CB, PPP2CB, PRKCL2, PSG9, RAB2, RAB5A, RAP2, RIG, S100A11, SCYA2, SEPP1, SGK, SKI, SLUG, TACC1, TASTIN, TBXA2F, TBXA2R, TFCP2, THROMBOSPONDIN1, TIMP2, TNFS10, TNFSF10, TOP2A, TRAF4, TRAP1, UBCH10, VAV2, VIMENTIN, VINCULIN, and YWHAB.