3.4kb MITOCHONDRIAL DNA DELETION FOR USE IN THE DETECTION OF CANCER

Abstract

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.