MIPOL1-ETV1 gene rearrangements
First Claim
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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;
orii) 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;
oriii) 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.
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Abstract
Compositions and methods associated with recurrent MIPOL1-ETV1 genetic rearrangements that are useful for cancer diagnosis and therapy are disclosed.
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Citations
22 Claims
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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:
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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;
orii) 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;
oriii) 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. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
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13. A kit for detecting a MIPOL1-ETV1 genetic rearrangement and one or more markers associated with prostate cancer in a biological sample, the kit comprising:
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a) a first component selected from the group consisting of; 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; 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; and 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) a second component comprising a probe directly labeled with a detectable label and for detecting 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. - View Dependent Claims (14, 15, 16)
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17. An assay composition comprising a sample from a subject and:
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a) a first component selected from the group consisting of; i) a junction 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; 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; and 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 an amplicon probe directly labeled with a detectable label and comprising a sequence complementary to the amplicon produced from the first and second primers; and b) a second component comprising a probe directly labeled with a detectable label and for detecting 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 WTHAB. - View Dependent Claims (18, 19, 20, 21, 22)
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Specification