Methods for detecting nucleic acids indicative of cancer

• US 6,964,846 B1
• Filed: 04/07/2000
• Issued: 11/15/2005
• Est. Priority Date: 04/09/1999
• Status: Expired due to Fees

• Current Assignee: Exact Sciences Corporation
• Original Assignee: Exact Sciences Corporation
• Inventors: Shuber, Anthony P.
• Primary Examiner(s): SWITZER, JULIET CAROLINE
• Application Number:
  US09/545,162
• Time in Patent Office: 2,048 Days
• Field of Search: 435/6, 435/91.2, 536/23.1
• US Class Current: 435/6.14
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: G01N 33/57419 of colon
• CPC Class Codes: G01N 33/57473 involving carcinoembryonic antigen, i.e. CEA

Abstract

The invention provides methods for screening tissue or body fluid samples for nucleic acid indicia of cancer or precancer.

Method are provided for screening a patient for cancer or precancer by detecting the presence of nucleic acid fragments that are longer than nucleic acid fragments expected to be present in a sample obtained from a healthy individual. In one embodiment, a positive screen for cancer or precancer is identified when a patient tissue or body fluid sample comprising exfoliated cells or cellular debris contains an amount of nucleic acid of a length greater than about 200 base pairs that exceeds a predetermined amount.

Claims

1. A method for screening a patient for a colorectal cancer or a colorectal precancer, the method comprising the steps of:

detecting in a patient stool sample comprising exfoliated cells or cellular debris a first amount of a long nucleic acid of a length greater than 200 base pairs in length;

wherein said long nucleic acid is present in both normal and cancerous or precancerous cells;

comparing the first amount of long nucleic acid in said patient stool sample to a second amount of said long nucleic acid present in a stool sample from patient free of colorectal cancer or precancer;

determining whether said first amount of long nucleic acid exceeds the second amount of long nucleic acid in said sample from a patient free of colorectal cancer or precancer; and

;

identifying a positive screen for an indicator of a colorectal cancer or precancer if said amount of long nucleic acid in said patient stool sample does exceed said second amount of long nucleic acid in said sample from a patient free of colorectal cancer or precancer.

3. The method of claim 1 or claim 2, wherein said detecting or determining comprises conducting an amplification reaction designed to amplify only nucleic acids fragments that are greater than 200 base pair in length.

4. The method of claim 1 or claim 2, further comprising the step of enriching said sample for human DNA.

5. The method of claim 1 or claim 2, further comprising the step of isolating human DNA from said sample.

2. The method for screening a patient for a colorectal cancer or a colorectal precancer, the method comprising the steps of:

determining in patient stool sample comprising exfoliated cells or cellular debris a first amount of long nucleic acid of a length greater then 200 base pairs;

determining in said stool sample a second amount of nucleic acid of a length less than said long nucleic acid;

determining a ratio between said first amount and said amount; and

identifying a positive screen for an indicator of a colorectal cancer or precancer if said ratio exceeds a

threshold ratio for patient who do not have a colorectal cancer or a precancer.