3.4kb MITOCHONDRIAL DNA DELETION FOR USE IN THE DETECTION OF CANCER
The present invention broadly claims a method for detecting cancer in an individual. The method comprises detecting a deletion in the nucleic acid sequence between residues 10743 and 12125 in mitochondrial DNA. The method comprises obtaining a biological sample from the individual; extracting the mitochondrial DNA (mtDNA) from the sample; quantifying the amount of mtDNA in the sample having a deletion in the nucleic acid sequence between residues 10743 and 14125 of the mtDNA genome; and comparing the amount of mtDNA in the sample having the deletion to at least one known reference sample.
1 . A method of detecting a cancer in an individual comprising;
a) obtaining a biological sample from the individual;
b) extracting mitochondrial DNA, mtDNA, from the sample;
c) quantifying the amount of mtDNA in the sample having a deletion in the nucleic acid sequence spanning approximately residues 10744 and 14124 of the mtDNA genome;
d) comparing the amount of mtDNA in the sample having the deletion to at least one known reference value.
2 . The method of claim 1 wherein the deletion has a nucleic acid sequence corresponding to the sequence identified in SEQ ID NO: 1.
3 . The method of claim 1 wherein the at least one known reference value is the amount of the deletion in a reference sample of mtDNA from known non-cancerous tissue or body fluid.
4 . The method of claim 1 wherein the at least one known reference value is the amount of the deletion in a reference sample of mtDNA from known cancerous tissue or body fluid.
5 . The method of claim 1 wherein the step of quantifying is conducted using real-time PCR.
6 . The method of claim 5 wherein the quantifying of the deletion includes first amplifying a target region of mtDNA that is indicative of the deletion, and quantifying the amount of the amplified target region.
7 . The method of claim 5 wherein a PCR primer having a sequence corresponding to SEQ ID NO: 2 is used as part of a pair of amplification primers for amplifying the target region.
8 . The method of claim 1 wherein the cancer is prostate cancer.
9 . The method of claim 1 wherein the cancer is breast cancer.
10 . The method of claim 1 wherein the biological sample is a body tissue or body fluid.
11 . The method of claim 10 wherein the biological sample is selected from the group consisting of breast tissue, prostate tissue, prostate massage fluid, and urine.
12 . The method of claim 6 wherein the reference value is a cycle threshold.
13 . The method according to claim 6 wherein the amplifying of the target region is conducted using a pair of amplification primers, one of the pair of amplification primers overlapping a splice joining regions on opposite ends of the deletion.
14 . A method of detecting a cancer in an individual comprising;
a) obtaining a biological sample from the individual;
b) extracting mitochondrial DNA, mtDNA, from the sample;
c) quantifying the amount of mtDNA in the sample having a deletion in the nucleic acid sequence spanning approximately residues 10744 and 14124 of the mtDNA genome;
d) comparing the amount of mtDNA in the sample having the deletion to the amount of the deletion in a reference sample of mtDNA from known non-cancerous tissue or body fluid;
wherein an elevated amount of the deletion in the biological sample compared to the reference sample is indicative of cancer.
15 . The method of claim 14 wherein the deletion has a nucleic acid sequence corresponding to the sequence identified in SEQ ID NO: 1.
16 . The method of claim 14 further comprising the step of comparing the amount of mtDNA in the sample having the deletion to the amount of the deletion in a reference sample of mtDNA from known cancerous tissue or body fluid.
17 . The method of claim 14 wherein the quantifying of the deletion includes amplifying a target region of mtDNA that is indicative of the deletion, and quantifying the amount of the amplified target region.
18 . The method of claim 17 wherein a PCR primer having a sequence corresponding to SEQ ID NO: 2 is used as part of a pair of amplification primers for amplifying the target region.
19 . The method of claim 17 wherein the step of quantifying is conducted using real-time PCR.
20 . The method of claim 14 wherein the cancer is prostate cancer.
21 . The method of claim 14 wherein the cancer is breast cancer.
22 . The method of claim 14 wherein the biological sample is a body tissue or body fluid.
23 . The method of claim 22 wherein the biological sample is selected from the group consisting of breast tissue, prostate tissue, prostate massage fluid, and urine.
24 . The method according to 17 wherein the amplifying of the target region is conducted using a pair of amplification primers, one of the pair of amplification primers overlapping a splice joining regions on opposite ends of the deletion.
25 . A method of detecting a cancer in an individual comprising;
a) obtaining a biological sample from the individual;
b) extracting mitochondrial DNA, mtDNA, from the sample;
c) quantifying the amount of mtDNA in the sample having a deletion in the nucleic acid sequence spanning approximately residues 10744 and 14124 of the mtDNA genome;
d) comparing the amount of mtDNA in the sample having the deletion to the amount of the deletion in a reference sample of mtDNA from known cancerous tissue or body fluid;
wherein a similar level of the deletion in the biological sample compared to the reference sample is indicative of cancer.
26 . The method of claim 25 wherein the deletion has a nucleic acid sequence corresponding to the sequence identified in SEQ ID NO: 1.
27 . The method of claim 25 further comprising the step of comparing the amount of mtDNA in the sample having the deletion to the amount of the deletion in a reference sample of mtDNA from known non-cancerous tissue or body fluid;
28 . The method of claim 25 wherein the quantifying of the deletion includes amplifying a target region of mtDNA that is indicative of the deletion, and quantifying the amount of the amplified target region.
29 . The method of claim 28 wherein a PCR primer having a sequence corresponding to SEQ ID NO: 2 is used as part of a pair of amplification primers for amplifying the target region.
30 . The method of claim 28 wherein the step of quantifying is conducted using real-time PCR.
31 . The method of claim 25 wherein the cancer is prostate cancer.
32 . The method of claim 25 wherein the cancer is breast cancer.
33 . The method of claim 25 wherein the biological sample is a body tissue or body fluid.
34 . The method of claim 33 wherein the biological sample is selected from the group consisting of breast tissue, prostate tissue, prostate massage fluid, and urine.
35 . The method according to claim 28 wherein the amplifying of the target region is conducted using a pair of amplification primers, one of the pair of amplification primers overlapping a splice joining regions on opposite ends of the deletion.
36 . A method of monitoring an individual for the development of a cancer comprising:
a) obtaining a biological sample;
b) extracting mtDNA from the sample;
c) quantifying the amount of mtDNA in the sample having a deletion in the nucleic acid sequence spanning approximately residues 10744 and 14124 of the mtDNA genome;
d) repeating steps a) to c) over a duration of time;
e) wherein an increasing level of the deletion over the duration of time is indicative of cancer.
37 . The method of claim 36 wherein the deletion has a nucleic acid sequence corresponding to the sequence identified in SEQ ID NO: 1.
38 . The method of claim 36 further comprising at least one step selected from the group consisting of: (a) comparing the amount of mtDNA in the sample having the deletion to the amount of the deletion in a reference sample of mtDNA from known non-cancerous tissue or body fluid; and (b) comparing the amount of mtDNA in the sample having the deletion to the amount of the deletion in a reference sample of mtDNA from known cancerous tissue or body fluid.
39 . The method of claim 36 wherein the quantifying of the deletion includes amplifying a target region of mtDNA that is indicative of the deletion, and quantifying the amount of the amplified target region.
40 . The method of claim 39 wherein the step of quantifying is conducted using real-time PCR.
41 . The method of claim 39 wherein a PCR primer having a sequence corresponding to SEQ ID NO: 2 is used as part of a pair of amplification primers for amplifying the target region.
42 . The method of claim 36 wherein the cancer is prostate cancer.
43 . The method of claim 36 wherein the cancer is breast cancer.
44 . The method of claim 36 wherein the biological sample is a body tissue or body fluid.
45 . The method of claim 44 wherein the biological sample is selected from the group consisting of breast tissue, prostate tissue, prostate massage fluid, and urine.
46 . A method of detecting a cancer in an individual comprising;
a) obtaining a biological sample from the individual;
b) extracting mitochondrial DNA, mtDNA, from the sample;
c) quantifying the amount of mtDNA in the sample having a sequence corresponding to the sequence identified in SEQ ID NO: 1;
d) comparing the amount of mtDNA in the sample corresponding to SEQ ID NO: 1 to at least one known reference value.
47 . The method of claim 46 wherein the at least one known reference value is the amount of the sequence corresponding to SEQ ID NO: 1 in a reference sample of mtDNA from known non-cancerous tissue or body fluid.
48 . The method of claim 46 wherein the at least one known reference value is the amount of the sequence corresponding to SEQ ID NO: 1 in a reference sample of mtDNA from known cancerous tissue or body fluid.
49 . The method of claim 46 wherein the step of quantifying is conducted using real-time PCR.
50 . The method of claim 49 wherein the quantifying of the deletion includes first amplifying a target region of mtDNA that is indicative of the deletion, and quantifying the amount of the amplified target region.
51 . The method of claim 46 wherein one of a pair of PCR primers used in the amplifying of the target region overlaps a rejoining site of the sequence corresponding to SEQ ID NO: 1, after the sequence has re-circularized.
52 . The method of claim 49 wherein a PCR primer having a sequence corresponding to SEQ ID NO: 9 is used as part of a pair of amplification primers for amplifying the target region.
53 . The method of claim 46 wherein the cancer is prostate cancer.
54 . The method of claim 46 wherein the cancer is breast cancer.
55 . The method of claim 46 wherein the biological sample is a body tissue or body fluid.
56 . The method of claim 55 wherein the biological sample is selected from the group consisting of breast tissue, prostate tissue, prostate massage fluid, and urine.
57 . The method of claim 49 wherein the reference value is a cycle threshold.