PROGNOSTIC MARKERS FOR CLASSIFYING COLORECTAL CARCINOMA ON THE BASIS OF EXPRESSION PROFILES OF BIOLOGICAL SAMPLES

• US 20090269775A1
• Filed: 11/01/2007
• Published: 10/29/2009
• Est. Priority Date: 11/02/2006
• Status: Abandoned Application

• Current Assignee: Signature Diagnostics AG (Roche Holding AG)
• Original Assignee: Signature Diagnostics AG (Roche Holding AG)
• Inventors: Clevert, Djork-Arne, Adams, Hans-Peter, Hinzmann, Bernd, Mayr, Tobias
• Application Number:
  US12/519,216
• Publication Number:
  US 20090269775A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2600/158 Expression markers

Abstract

The invention relates to the use of gene expression profiles for predicting the probability of recurrence or metastases to develop in remote organs of patients from which a primary colon carcinoma has been removed.

Claims

1. A method for predicting the probability of recurrence of a colorectal carcinoma or of metastases in remote organs of a patient with colon cancer, comprising determining a gene expression profile of 30 marker genes (as depicted in SEQ ID NOs:

1 to

     30) or of a selection thereof.

2. The method according to claim 1, in which the expression profile of the maker gene is compared to a reference pattern which is indicative for the recurrence of the colon carcinoma of a patient.

3. The method according to claim 2, wherein the comparison of the expression profile is performed with a method for pattern recognition.

4. The method according to claim 3, wherein the pattern recognition method consist of a double nested bootstrap approach in combination with a Decision-Tree-Analysis for determining the individual relevance of the genes.

5. The method according to claim 3, wherein the pattern recognition method consist of a double nested bootstrap approach in combination with a Radom-Forest-Analysis for determining the individual relevance of the genes.

6. The method according to claim 1, wherein a primary colon carcinoma is analyzed.

7. The method according to claim 1, in which a primary colon carcinoma of stage UICC-I or UICC-II is analyzed.

8. The method according to claim 1, in which the expression profile of marker genes as defined in the SEQ ID NOs:

1 to 9 or of any combination of at least two of said genes is determined.

16. The method according to claim 1, wherein the measured difference in expression is statically significant.

17. The method according to claim 1, wherein the determination of the expression profile comprises the determination of at least one marker gene which has at least 90% identity to one of the marker genes depicted in SEQ ID NO:

1 to 30.

18. The method according to claim 1, wherein the expression profile of the marker gene is obtained from a tumor sample of a patient.

19. The method according to claim 18, wherein the expression profile of the marker gene is determined through measuring the quantity of mRNA from the marker gene.

27. The method according to claim 18, wherein the quantity of the mRNA of marker genes is determined using gene chip technology, (RT-) PCR, Northern Hybridization, Dot-Blot, or in situ hybridization.

9. (canceled)

10. (canceled)

11. (canceled)

12. (canceled)

13. (canceled)

14. (canceled)

15. (canceled)

20. A prognostic portfolio consisting of the genes with the nucleic acid sequences of SEQ ID NO 1 to SEQ ID NO 30, their reverse complementary sequences or parts of these sequences or combinations thereof, which are suitable for detecting the differential expression of the sequences contained in the portfolio.

21. A cDNA- or oligonucleotide-microarray which comprises sequences according to claim 20.

22. A kit for determining the probability of recurrence of metastases in remote organs of a patient with colon cancer that contains means for detection of nucleic acid sequences according to claim 20.

23. A kit for determining the probability of the recurrence or of metastases in remote organs of a patient with colon cancer which comprises a cDNA or oligonucleotide-microarray which comprises sequences according to claim 20 as a material for detecting a nucleic acid sequence according to claim 20.

24. A kit according to claim 22 that determines the gene expression of the gene with the SEQ ID NOs 1 to 9.

26. A kit according to claim 22 that determines the gene expression of the gene with the SEQ ID NOs 1 to 5.

25. (canceled)

28. (canceled)

29. A kit for determining the status of a colorectal carcinoma, the kit comprising materials that permit the detection of nucleic acids comprising SEQ ID NOs 1-30 in a sample from said colorectal carcinoma.