MOLECULAR STAGING OF STAGE II AND III COLON CANCER AND PROGNOSIS

• US 20090192045A1
• Filed: 01/19/2009
• Published: 07/30/2009
• Est. Priority Date: 01/22/2008
• Status: Abandoned Application

• Current Assignee: Veridex LLC (Johnson & Johnson)
• Original Assignee: Veridex LLC (Johnson & Johnson)
• Inventors: Zhang, Yi, Wang, Yixin, Jiang, Yuqiu
• Application Number:
  US12/355,906
• Publication Number:
  US 20090192045A1
• Time in Patent Office: Days
• US Class Current: 506/7
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

Kits and articles include reagents for conducting a seven gene assay to stage colon cancer as Stage II or Stage III colon cancer.

Claims

1. A method of staging colorectal cancer status comprising identifying differential modulation in a combination of genes consisting essentially of Seq ID NO1, Seq ID NO 3, Seq ID NO 5, Seq ID NO 7, Seq ID NO9, Seq ID NO11, and Seq ID NO 13.

2. The method of claim 1 wherein Stage II and Stage III colorectal cancer are distinguished.

3. The method of claim 2 wherein the comparison of expression patterns is conducted with pattern recognition methods.

4. The method of claim 3 wherein the pattern recognition methods include the use of a Cox proportional hazards analysis.

5. The method of claim 1 conducted on primary tumor sample.

6. The method of claim 1 wherein if the gene expression pattern of a sample is that of the patter of the Cox proportional hazard analysis indicating Stage II then the colorectal cancer is Stage II colorectal cancer and if it is not then it is Stage III colorectal cancer.

7. A kit for staging colorectal cancer patient comprising materials for detecting isolated nucleic acid sequences, their compliments, or portions thereof of a combination of genes that includes Seq ID NO1, Seq ID NO 3, Seq ID NO 5, Seq ID NO 7, Seq ID NO9, Seq ID NO11, and Seq ID NO 13.

8. The kit of claim 7 wherein the only combination of genes is Seq ID NO1, Seq ID NO 3, Seq ID NO 5, Seq ID NO 7, Seq ID NO9, Seq ID NO11, and Seq ID NO 13 and housekeeping or control genes.

9. The kit of claim 8 further comprising reagents for conducting a microarray analysis.

10. The kit of claim 9 further comprising a medium through which said nucleic acid sequences, their compliments, or portions thereof are assayed.

11. Articles for assessing colorectal cancer status comprising materials for identifying nucleic acid sequences, their complements, or portions thereof of a combination of genes that includes Seq ID NO 1, Seq ID NO 3, Seq ID NO 5, Seq ID NO 7, Seq ID NO9, Seq ID NO11, and Seq ID NO 13.

12. The article of claim 11 wherein the only combination of genes is Seq ID NO1, Seq ID NO 3, Seq ID NO 5, Seq ID NO 7, Seq ID NO9, Seq ID NO11, and Seq ID NO 13 and housekeeping or control genes.

13. The article of claim 12 further comprising reagents for conducting a microarray analysis.

14. The article of claim 13 further comprising a medium through which said nucleic acid sequences, their compliments, or portions thereof are assayed.

15. The article of claim 11 comprising reagents for conducting a PCR reaction wherein said reagents include probes and primers for detecting genes consisting essentially of Seq ID NO1, Seq ID NO 3, Seq ID NO 5, Seq ID NO 7, Seq ID NO9, Seq ID NO11, and Seq ID NO 13 and housekeeping or control genes.

16. The article of claim 15 further comprising instructions for analyzing the results of the use of the kit to stage colorectal cancer.

17. The article of claim 16 wherein the instructions are computer instructions.

18. The article of claim 17 wherein the computer instructions are contained on a magnetic or optical medium.