MIPOL1-ETV1 gene rearrangements

• US 9,719,143 B2
• Filed: 03/30/2016
• Issued: 08/01/2017
• Est. Priority Date: 07/06/2007
• Status: Active Grant

• Current Assignee: Board of Regents of the University of Michigan (University of Michigan)
• Original Assignee: Board of Regents of the University of Michigan (University of Michigan)
• Inventors: Chinnaiyan, Arul M., Tomlins, Scott, Dhanasekaran, Saravana Mohan
• Primary Examiner(s): HORLICK, KENNETH R
• Application Number:
  US15/084,721
• Publication Number:
  US 20160208343A1
• Time in Patent Office: 489 Days
• Field of Search: 435 612, 435 912
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

Compositions and methods associated with recurrent MIPOL1-ETV1 genetic rearrangements that are useful for cancer diagnosis and therapy are disclosed.

Claims

1. A composition comprising:

(a) a first amplification oligonucleotide that comprises a sequence that hybridizes specifically to an ETV1 gene;

(b) a second amplification oligonucleotide that comprises a sequence that hybridizes specifically to a MIPOL1 gene; and

(c) a directly labeled probe comprising a sequence that is capable of hybridizing to a nucleic acid comprising a MIPOL1-ETV1 genetic rearrangement.

2. The composition of claim 1 further comprising an amplicon produced in an amplification reaction using the first and second amplification oligonucleotides.

3. The composition of claim 2 wherein the directly labeled probe is hybridized to the amplicon.

4. The composition of claim 2 wherein the amplification reaction is a polymerase chain reaction (PCR), a reverse transcription polymerase chain reaction (RT-PCR), a transcription-mediated amplification (TMA), a ligase chain reaction (LCR), a strand displacement amplification (SDA), or a nucleic acid sequence based amplification (NASBA).

5. The composition of claim 1 wherein the directly labeled probe hybridizes specifically to a sequence located between the sequence hybridized to by the first amplification oligonucleotide and the sequence hybridized to by the second amplification oligonucleotide.

6. The composition of claim 1 wherein the nucleic acid comprising a MIPOL1-ETV1 genetic rearrangement has a length of 200 or fewer nucleotides.

7. The composition of claim 1 wherein the first amplification oligonucleotide, the second amplification oligonucleotide, and/or the probe comprise a modified nucleotide or a nucleotide analog.

8. The composition of claim 2 wherein the amplicon is produced from a sample selected from the group consisting of tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions, and prostate cells.

9. The composition of claim 1 wherein the directly labeled probe is affixed to a solid support.

10. A kit comprising:

(a) a first amplification oligonucleotide that comprises a sequence that hybridizes specifically to an ETV1 gene;

(b) a second amplification oligonucleotide that comprises a sequence that hybridizes specifically to a MIPOL1 gene; and

(c) a directly labeled probe comprising a sequence that hybridizes to a nucleic acid comprising a MIPOL1-ETV1 genetic rearrangement.

11. The kit of claim 10 further comprising a control nucleic acid.

12. A method for detecting a MIPOL1-ETV1 genetic rearrangement in a biological sample, the method comprising:

(a) producing an amplicon from a biological sample using;

(i) a first amplification oligonucleotide that comprises a sequence that hybridizes specifically to an ETV1 gene; and

(ii) a second amplification oligonucleotide that comprises a sequence that hybridizes specifically to a MIPOL1 gene; and

(b) hybridizing a directly labeled probe comprising a sequence that hybridizes to a nucleic acid comprising a MIPOL1-ETV1 genetic rearrangement to the amplicon.

13. The method of claim 12 further comprising acquiring the biological sample.

14. The method of claim 12 further comprising identifying an individual from whom the biological sample was derived as having or at risk of having prostate cancer when hybridization of said probe to said amplicon is detected.

15. The method of claim 12 wherein producing the amplicon comprises use of an amplification method selected from the group consisting of;

polymerase chain reaction (PCR), reverse transcription polymerase chain reaction (RT-PCR), transcription-mediated amplification (TMA), ligase chain reaction (LCR), strand displacement amplification (SDA), and nucleic acid sequence based amplification (NASBA).

16. The method of claim 12, wherein the biological sample is selected from the group consisting of tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions, and prostate cells.