Apparatus and method for drug screening

• US 6,849,403 B1
• Filed: 11/28/2000
• Issued: 02/01/2005
• Est. Priority Date: 09/08/1999
• 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.
• Primary Examiner(s): Fredman, Jeffrey
• Assistant Examiner(s): CHUNDURU, SURYAPRABHA
• Application Number:
  US09/724,274
• Time in Patent Office: 1,526 Days
• Field of Search: 435/6, 435/91.2, 536/24.33, 424/9.351
• US Class Current: 435/6.14
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The present invention provides kits and methods for screening drugs and drug candidates for activity by determining the presence or absence of high integrity nucleic acid in a sample.

Claims

1. A method for screening drug activity, the method comprising the steps of:

(a) determining a baseline level of high integrity nucleic acid associated with a nucleic acid locus in a first sample obtained from a patient having a disease or at least one indicium of a disease, wherein the high integrity nucleic acid is derived from a genome of the patient and the disease comprises at least one of cancer, pre-cancer, a disease associated with apoptosis, and a disease associated with programmed cell death;

(b) treating the patient with a drug candidate; and

(c) determining whether the high integrity nucleic acid associated with the nucleic acid locus in a second sample obtained from the patient is reduced.

2. The method of claim 1 wherein the determining steps comprise amplifying a target nucleic acid to determine the presence of high integrity nucleic acid in the samples.

3. The method of claim 2 wherein the target nucleic acid is amplified with one forward primer and at least two reverse primers.

4. The method of claim 2 wherein the target nucleic acid is amplified with at least two pairs of forward and reverse primers.

5. The method of claim 1 wherein the determining steps comprise capturing the high integrity nucleic acid.

6. The method of claim 5 wherein the high integrity nucleic acid is captured on a support-based complementary nucleic acid probe.

7. The method of claim 1 wherein a positive screen is determined by the presence of a lower amount of high integrity nucleic acid in the second sample relative to an amount of high integrity nucleic acid in the first sample.

8. The method of claim 1 wherein the samples are selected from the group consisting of stool, sputum, pus, blood serum, blood plasma, urine, saliva, colostrum, bile, and pancreatic juice.

9. The method of claim 7 wherein a positive screen indicates activity of the drug candidate.

10. The method of claim 7 wherein a positive screen indicates induction of programmed cell death.

11. The method of claim 7 wherein a positive screen indicates induction of apoptotic activity.

12. The method of claim 1 wherein the drug candidate comprises a nucleic acid.

13. The method of claim 1 wherein the drug candidate comprises a peptide.

14. The method of claim 1 wherein the drug candidate comprises a chemical compound.

15. The method of claim 1 wherein the drug candidate comprises a candidate for an anti-cancer drug.

16. The method of claim 1 wherein activity of a drug candidate is predictive of alleviation of disease symptoms by the drug candidate.

17. The method of claim 1 wherein at least one of the samples is contained in a buffer comprising at least 150 mM EDTA.

24. The method of claim 1 wherein the nucleic acid locus is selected from the group consisting of a coding region of a gene, a portion of a coding region of a gene, a noncoding region of a gene, a portion of a noncoding region of a gene, a regulatory element of a gene, a portion of a regulatory element of a gene, an RNA, and a fragment of genomic DNA.

25. The method of claim 1 wherein the patient is a human.

18. A method for screening drug activity, the method comprising the steps of:

(a) determining a baseline level of high integrity nucleic acid associated with a nucleic acid locus in a sample from a subject having a disease or at least one indicium of a disease, wherein the high integrity nucleic acid is derived from a genome of the subject and the disease comprises at least one of cancer, pre-cancer, a disease associated with apoptosis, and a disease associated with programmed cell death;

(b) treating the sample with a drug candidate; and

(c) determining whether high integrity nucleic acid associated with the nucleic acid locus in the sample is reduced.

19. The method of claim 18 wherein the step of treating is performed ex vivo.

20. The method of claim 18 wherein the subject comprises an animal model of a disease.

21. The method of claim 18 wherein the sample is contained in a buffer comprising at least 150 mM EDTA.

26. The method of claim 18 wherein the subject is an animal model of a disease.

22. A method for screening drug activity, the method comprising the steps of:

(a) determining a baseline level of high integrity nucleic acid associated with a n nucleic acid locus in a sample from an animal model of a disease or an animal model that displays at least one indicium of a disease, wherein the high integrity nucleic acid is derived from a genome of the animal model and the disease comprises at least one of cancer, pre-cancer, a disease associated with apoptosis, and a disease associated with programmed cell death;

(b) treating the animal model with a drug candidate; and

(c) determining whether the high integrity nucleic acid associated with the nucleic acid locus in a second sample obtained from the animal model is reduced.

23. The method of claim 22 wherein the sample is contained in a buffer comprising at least 150 mM EDTA.