Complete mitochondrial genome sequences as a diagnostic tool for the health sciences

• US 20050026167A1
• Filed: 12/11/2003
• Published: 02/03/2005
• Est. Priority Date: 06/11/2001
• Status: Abandoned Application

• Current Assignee: Genesis Genomics Inc
• Original Assignee: Genesis Genomics Inc
• Inventors: Birch-Machin, Mark, Th'ng, John, Ngom, Alioune, Dakubo, Gabriel D., Parr, Ryan, Thayer, Robert
• Application Number:
  US10/732,374
• Publication Number:
  US 20050026167A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• 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 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

Abstract

The examination of mutations in the mitochondrial genome is used as a diagnostic system for diseases such as prostate cancer, and non melanoma skin cancer. Characteristic mutations and rearrangements including, point mutations (transitions, transversions), deletions, inversions, duplications, recombinations, insertions or combinations thereof in the mitochondrial genome are used as early indicators of prostate cancer, and non melanoma skin cancer. Moreover, the 4977 bp, or “common deletion” as well as other associated mutations and/or deletions are used as a measure of aging.

Claims

1. A method of detecting mutations associated with a disease, a disorder or aging in a subject having mtDNA, comprising:

a. providing a biological sample from the subject;

b. extracting DNA from the biological sample;

c. detecting the presence of mutations in the mtDNA; and

d. determining whether the mutations are associated with normal interpopulation or intrapopulation variations, or whether the mutations are associated with the disease, the disorder or aging.

2. The method of claim 1 further comprising at least one of

a. determining total mutation load in the mtDNA of the biological sample;

and

b. determining the identity of the mutation in the mtDNA of the biological sample.

3. The method of claim 1 wherein the biological sample is chosen from normal tissue, non-involved tissue, benign tissue, atypical tissue, histologically abnormal tissue and diseased tissue of the subject.

4. The method of claim 1 where the step of determining whether the mutations are associated with normal interpopulation or intrapopulation variations, or whether the mutations are associated with the disease, the disorder or aging comprises at least one of:

(a) comparing the mtDNA of the biological sample to a database, the database containing data of interpopulation and intrapopulation variations, and mutations associated with the disease, the disorder or aging; and

(b) determining total mutation load of the biological sample.

5. Use of the method of claim 1 for a diagnosis, wherein the diagnosis is chosen from predisposition to a disease or a disorder, early detection of a disease or a disorder, genesis of a disease or a disorder, presence of a disease or a disorder, and progression of a disease or a disorder.

6. The method of claim 1 wherein the step of detecting the presence of mutations is chosen from:

a. sequencing the mtDNA;

b. amplifying mtDNA by PCR;

c. Southern, Northern, Western and South-Western blot hybridizations;

d. denaturing HPLC;

e. hybridization to microarrays, gene chips or biochips;

f. molecular marker analysis; and

g. a combination of any of a) through f).

7. The method of claim 6 wherein the mitochondrial DNA which is sequenced comprises the entire mitochondrial genome.

8. The method of claim 1 wherein the disease is non-melanoma skin cancer.

9. The method of claim 1 wherein the disease is prostate cancer.

10. The method of claim 1 where the mutation is heteroplasmic at any level.

11. The method of claim 4 wherein the database contains at least a statistically significant number of mitochondrial DNA sequences, the mitochondrial DNA sequences having been obtained from a maternal line, a non-maternal line, or both.

12. A kit for diagnosing a disease comprising a disposable chip, microarray, means for holding the disposable chip, means for extraction of mitochondrial DNA and means for access to a database of mitochondrial DNA sequences.

14. The kit of any of claims 12 or 13 wherein the disease is non-melanoma skin cancer.

15. The kit of any of claims 12 or 13 wherein the disease is prostate cancer.

13. A kit for determining predisposition to a disease or early detection of a disease comprising a disposable chip, microarray, means for holding the disposable chip, means for extraction of mitochondrial DNA and means for access to a database of mitochondrial DNA sequences.

16. An array comprising a plurality of nucleic acid members, and a solid substrate, wherein each nucleic acid member is indicative of the presence of a disease, a disorder or aging, or used to determine a prohibiting index by quantifying the proportion of base pair deletions and mutations associated with a disease, a disorder or aging, and is chosen from mitochondrial DNA, RNA transcribed from mitochondrial DNA, and cDNA, wherein each nucleic acid member has a unique position on said array and is stably associated with the solid substrate.

18. The array of any of claims 16 or 17 wherein each member is indicative of prostate cancer.

19. The array of any of claims 16 or 17 wherein each member is indicative of non-melanoma skin cancer.

20. The array of any of claims 16 or 17 wherein each member is associated with aging.

17. An array comprising a plurality of nucleic acid members, and a solid substrate, wherein each nucleic acid member is indicative of the predisposition to a disease, a disorder or aging, or used to determine a prohibiting index by quantifying the proportion of base pair deletions and mutations associated with a disease, a disorder or aging, and is chosen from mitochondrial DNA, RNA transcribed from mitochondrial DNA, and cDNA, wherein each nucleic acid member has a unique position on said array and is stably associated with the solid substrate.

21. A method of detecting heteroplasmy in a subject containing mtDNA comprising:

a. providing a biological sample from the subject;

b. extracting DNA from the biological sample; and

c. performing denaturing HPLC on the sample.

22. A database containing a plurality of human mitochondrial DNA sequences, the mitochondrial DNA sequences are chosen from normal control sequences associated with non-disease states, sequences associated with interpopulation variations, sequences associated with intrapopulation variations, sequences associated with pre-neoplasia, sequences associated with neoplasia, sequences associated with progression towards malignancy, sequences associated with malignancy, sequences associated with the presence of disease and sequences indicative of the predisposition to disease.

25. The method of claim 23 wherein the step of detecting the presence of mutations in the mitochondrial DNA comprises at least one of:

(a) comparing the mtDNA of the biological sample to the database of claim 22;

(b) comparing the mtDNA of the biological sample to a sample of mtDNA from non-involved tissue or non-involved bodily fluid from the subject;

(c) comparing the mtDNA of the biological sample to a sample of mtDNA from a maternal relative of the subject;

(d) determining total mutation load of the biological sample; and

(e) identifying the mutations.

30. The method of claim 29 wherein the step of detecting the presence of mutations in the mitochondrial DNA comprises at least one of:

(a) comparing the mtDNA of the biological sample to the database of claim 22;

(b) comparing the mtDNA of the biological sample to a sample of mtDNA from non-involved tissue or non-involved bodily fluid from the subject;

(c) comparing the mtDNA of the biological sample to a sample of mtDNA from a maternal relative of the subject;

(d) determining total mutation load of the biological sample; and

(e) identifying the mutations.

23. A method of monitoring a person for the presence of pre-neoplasia, neoplasia or progression of neoplasia toward potential malignancy, in a biological sample from a subject, comprising:

(a) providing a biological sample from the subject;

(b) extracting DNA from the biological sample;

(c) detecting the presence of mutations in the mtDNA;

(d) determining whether the mutations are associated with normal interpopulation or intrapopulation variations, or whether the mutations are associated with pre-neoplasia, neoplasia or progression of neoplasia toward potential malignancy; and

(e) repeating steps (a) to (d).

24. The method of claim 23 wherein the biological sample is from a tissue that is chosen from benign tissue, normal tissue, atypical tissue and histologically abnormal tissue.

26. The method of claim 23 wherein the pre-neoplasia, neoplasia or progression of neoplasia is prostate cancer.

27. The method of monitoring the progression of neoplasia of claim 23 further comprising monitoring the person at successive time periods for an increase in mutations or an increase in mutated mitochondrial genomes.

28. An oligonucleotide probe chosen from SEQ ID NO. 19 to 101.

29. A method of determining whether pre-neoplasia, neoplasia, or malignancy in a biological sample from a subject is latent or aggressive in its growth pattern, comprising:

(a) providing a biological sample from the subject;

(b) extracting DNA from the biological sample;

(c) detecting the presence of mutations in the mtDNA;

(d) determining whether the mutations are associated with normal interpopulation or intrapopulation variations, or whether the mutations are associated with pre-neoplasia, neoplasia or progression of neoplasia toward potential malignancy; and

(e) repeating steps (a) through (d).