Methods of screening for supracolonic neoplasms based on stool samples containing a nucleic acid marker indicative of a neoplasm

• US 7,981,612 B2
• Filed: 03/05/2008
• Issued: 07/19/2011
• Est. Priority Date: 12/07/1999
• Status: Expired due to Fees

• Current Assignee: Exact Sciences Development Company LLC (Exact Sciences Corporation), Mayo Foundation For Medical Education And Research (Mayo Clinic)
• Original Assignee: Exact Sciences Corporation, Mayo Foundation For Medical Education And Research (Mayo Clinic)
• Inventors: Alquist, David A., Shuber, Anthony P.
• Primary Examiner(s): Horlick; Kenneth R.
• Application Number:
  US12/042,988
• Publication Number:
  US 20080254547A1
• Time in Patent Office: 1,231 Days
• Field of Search: 435/6, 435/91.2
• US Class Current: 435/6.14
• CPC Class Codes: C07K 14/47 from mammals
• CPC Class Codes: C07K 14/4746 p53
• CPC Class Codes: C07K 14/82 Translation products from oncogenes
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The invention provides methods and materials for detecting supracolonic aerodigestive premalignant and malignant neoplasms. Specifically, the invention provides methods and materials for determining whether a stool sample from a mammal contains a neoplasm-specific marker from a neoplasm located in the supracolonic aerodigestive tissue of a mammal.

Claims

1. A method for detecting a supracolonic aerodigestive neoplasm in a mammal, said method comprising:

detecting the presence of long DNA greater than 250 base pairs in length in a stool sample obtained from a mammal, wherein an amount of long DNA greater than 250 base pairs is indicative of a supracolonic aerodigestive neoplasm, wherein an amount of long DNA greater than 250 base pairs is an amount greater than expected to be present in a stool sample obtained from a mammal who does not have cancer, and wherein the sequence or identity of the long DNA is not in itself indicative of supracolonic aerodigestive neoplasm; and

performing at least one additional cancer screening technique to detect a location of the supracolonic aerodigestive neoplasm present in the mammal.

2. The method of claim 1, wherein said supracolonic aerodigestive neoplasm comprises a premalignant neoplasm.

3. The method of claim 1, wherein said supracolonic aerodigestive neoplasm comprises a malignant neoplasm.

4. The method of claim 1, wherein said supracolonic aerodigestive neoplasm is selected from the group consisting of lung, naso-oro-pharyngeal, esophageal, stomach, liver, bile duct, gall bladder, small intestine, and pancreas neoplasms.

5. The method of claim 1, wherein said mammal is a human.

6. The method of claim 1, wherein said long DNA comprises DNA greater than 300 base pairs in length.

7. The method of claim 1, wherein said long DNA comprises DNA greater than 400 base pairs in length.

8. The method of claim 1, wherein said long DNA comprises DNA greater than 500 base pairs in length.

9. The method of claim 1, wherein said long DNA comprises DNA greater than 1000 base pairs in length.

10. The method of claim 1, wherein said method further comprises detecting at least one additional neoplasm-specific marker indicative of a neoplasm in said stool sample.

11. The method of claim 10, wherein said at least one additional neoplasm-specific marker is selected from the group consisting of nucleic acid markers, polypeptide markers, and cell markers.

12. The method of claim 10, wherein said at least one additional neoplasm-specific marker is a neoplasm-specific nucleic acid marker.

13. The method of claim 12, wherein said neoplasm-specific nucleic acid marker is selected from the group consisting of nucleic acid having a point mutation and a nucleic acid that reflects microsatellite instability.

14. The method of claim 1, wherein said long DNA comprises DNA greater than 800 base pairs in length.

15. The method of claim 1, wherein said long DNA comprises DNA greater than 1500 base pairs in length.

16. The method of claim 1, wherein said long DNA comprises DNA greater than 1.8 Kb in length.

17. The method of claim 1, wherein said long DNA comprises DNA greater than 2500 base pairs in length.