Methods for detecting mutations using primer extension for detecting disease

• US 6,503,718 B2
• Filed: 01/10/2001
• Issued: 01/07/2003
• Est. Priority Date: 01/10/1999
• Status: Expired due to Fees

• Current Assignee: Esoterix Genetic Laboratories LLC (Laboratory Corporation Of America Holdings)
• Original Assignee: Exact Sciences Corporation
• Inventors: Shuber, Anthony P., Laken, Steven J., Pierceall, William
• Primary Examiner(s): Fredman, Jeffrey
• Assistant Examiner(s): Chunduru, Suryaprabha
• Application Number:
  US09/757,949
• Publication Number:
  US 20010018180A1
• Time in Patent Office: 727 Days
• Field of Search: 435/6, 435/91.2, 536/22.1, 536/24.33
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 1/703 Viruses associated with AIDS
• CPC Class Codes: C12Q 2533/101 Primer extension
• CPC Class Codes: C12Q 2535/101 Sanger sequencing method, i.e. oligonucleotide sequencing using primer elongation and dideoxynucleotides as chain terminators
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

Methods of the invention comprise assays for markers indicative of cancer, precancer, and other diseases or disorders. Assays of the invention are preformed on heterogeneous samples obtained from patients by non-invasive or minimally-invasive methods. Such assays may be employed alone or in combination with other disease screening techniques

Claims

1. A method for diagnosing colorectal cancer or precancer, the method comprising the steps of:

performing an assay to detect, in a stool sample from a patient, a nucleic acid mutation indicative of a colorectal lesion;

performing a sigmoidoscopy on said patient; and

diagnosing colorectal cancer or precancer in said patient if at least one of said assay step and said sigmoidoscopy step is positive,

wherein said nucleic acid mutation is a nucleic acid insertion or deletion, and

wherein said assay comprises the steps of;

(a) selecting a nucleic acid having a known wild-type sequence and having a target region comprising a repeat sequence having at most three different types of nucleotide bases selected from the group consisting of dGTP, dATP, dTTP, and dCTP;

(b) contacting a sample with an oligonucleotide primer that is complementary to a portion of said nucleic acid immediately upstream of said target region;

(c) extending said primer in the presence of nucleotide bases that are complementary to the nucleotide bases of the target region, thereby to form a primer extension product;

(d) extending the primer extension product in the presence of a labeled nucleotide complementary to a nucleotide base downstream from the target region in said nucleic acid, wherein said labeled nucleotide is not complementary to any of the nucleotide bases of the target region selected in step (a), thereby to produce a labeled extension product comprising a sequence that is complementary to the entire target region;

(e) terminating the primer extension product by incorporating a terminator nucleotide in said product that is complementary to a nucleotide downstream from the target region in a wild type nucleic acid, wherein said terminator nucleotide is not complementary to any of the nucleotides of the target region selected in step (a), said step of terminating the primer extension product being performed simultaneously with or immediately after step (d);

(f) detecting the labeled extension product; and

(g) comparing the size of the labeled extension product detected in step (f) to a standard, wherein a labeled extension product smaller than the standard is indicative of the presence of a deletion in the target region and a labeled extension product larger than the standard is indicative of the presence of an insertion in the target region.

2. The method of claim 1, wherein said assay is conducted prior to said sigmoidoscopy.

3. The method of claim 1, wherein said sigmoidoscopy is performed prior to said assay.

4. The method of claim 1, wherein said mutation is indicative of the presence of a colorectal lesion in the proximal colon.

5. The method of claim 1, wherein said sample includes a buffer comprising at least 100 mM EDTA.

8. The method of claim 1, wherein the labeled nucleotide and the terminator nucleotide are the same.

9. The method of claim 1, wherein more than one labeled nucleotide is incorporated into the extension product prior to incorporation of the terminator nucleotide.

10. The method of claim 1, wherein the nucleotide bases of step (c) are unlabeled.

11. The method of claim 1, wherein the labeling reaction of step (d) is performed in the presence of labeled nucleotide and unlabeled nucleotide of the same type.

12. The method of claim 10, wherein the ratio of labeled nucleotides to unlabeled nucleotides is 1:

1.6 (unlabeled;

labeled).

13. The method of claim 10, wherein more than one labeled nucleotide from step (d) is incorporated into the labeled extension product.

14. The method of claim 12, wherein only one of the incorporated nucleotides is labeled.

15. The method of claim 1, wherein said biological sample contains a heterogeneous mixture of mutant nucleic acid having a deletion in the target region and wild type nucleic acid with no deletion in the target region.

16. The method of claim 1, wherein a deletion in the target region is present in from about 1% to about 5% of the nucleic acid molecules containing the target region.

17. The method of claim 1, wherein the presence of a deletion in said target region is associated with the presence of a mutation at a separate genetic locus selected from the group consisting of APC, DCC, P53, and RAS.

18. The method of claim 1, wherein said target region is the poly-A tract at the BAT-26 locus.

19. The method of claim 1, wherein said target region is a microsatellite region.

6. A method for localizing a colorectal lesion in a patient, the method comprising the steps of:

performing an assay to detect, in a stool sample from a patient, a nucleic acid mutation indicative of said colorectal lesion;

performing a sigmoidoscopy on said patient;

diagnosing a proximal colonic lesion if said assay is positive for the mutation and said sigmoidoscopy is negative; and

diagnosing a distal colonic lesion if said sigmoidoscopy is positive and said assay is negative for the mutation,

wherein said nucleic acid mutation is a nucleic acid insertion or deletion, and

wherein said assay comprises the steps of;

(a) selecting a nucleic acid having a known wild-type sequence and having a target region comprising a repeat sequence having at most three different types of nucleotide bases selected from the group consisting of dGTP, dATP, dTTP, and dCTP;

(b) contacting a sample with an oligonucleotide primer that is complementary to a portion of said nucleic acid immediately upstream of said target region;

(c) extending said primer in the presence of nucleotide bases that are complementary to the nucleotide bases of the target region, thereby to form a primer extension product;

(d) extending the primer extension product in the presence of a labeled nucleotide complementary to a nucleotide base downstream from the target region in said nucleic acid, wherein said labeled nucleotide is not complementary to any of the nucleotide bases of the target region selected in step (a), thereby to produce a labeled extension product comprising a sequence that is complementary to the entire target region;

(e) terminating the primer extension product by incorporating a terminator nucleotide in said product that is complementary to a nucleotide downstream from the target region in a wild type nucleic acid, wherein said terminator nucleotide is not complementary to any of the nucleotides of the target region selected in step (a), said step of terminating the primer extension product being performed simultaneously with or immediately after step (d).

(f) detecting the labeled extension product; and

(g) comparing the size of the labeled extension product detected in step (f) to a standard, wherein a labeled extension product smaller than the standard is indicative of the presence of a deletion in the target region and a labeled extension product larger than the standard is indicative of the presence of an insertion in the target region.

7. A method for diagnosing hereditary non-polyposis colorectal cancer, the method comprising the steps of:

performing an assay to detect, in a stool sample from a patient, a nucleic acid mutation indicative of said hereditary non-polyposis colorectal cancer;

performing a colonoscopy on said patient; and

diagnosing hereditary non-polyposis colorectal cancer if said assay is positive and said colonoscopy reveals an adenoma,

wherein said nucleic acid mutation is a nucleic acid insertion or deletion, and

wherein said assay comprises the steps of;

(a) selecting a nucleic acid having a known wild-type sequence and having a target region comprising a repeat sequence having at most three different types of nucleotide bases selected from the group consisting of dGTP, dATP, dTTP, and dCTP;

(b) contacting a sample with an oligonucleotide primer that is complementary to a portion of said nucleic acid immediately upstream of said target region;

(c) extending said primer in the presence of nucleotide bases that are complementary to the nucleotide bases of the target region, thereby to form a primer extension product;

(d) extending the primer extension product in the presence of a labeled nucleotide complementary to a nucleotide base downstream from the target region in said nucleic acid, wherein said labeled nucleotide is not complementary to any of the nucleotide bases of the target region selected in step (a), thereby to produce a labeled extension product comprising a sequence that is complementary to the entire target region;

(e) terminating the primer extension product by incorporating a terminator nucleotide in said product that is complementary to a nucleotide downstream from the target region in a wild type nucleic acid, wherein said terminator nucleotide is not complementary to any of the nucleotides of the target region selected in step (a), said step of terminating the primer extension product being performed simultaneously with or immediately after step (d).

(f) detecting the labeled extension product; and

(g) comparing the size of the labeled extension product detected in step (f) to a standard, wherein a labeled extension product smaller than the standard is indicative of the presence of a deletion in the target region and a labeled extension product larger than the standard is indicative of the presence of an insertion in the target region.