3.4 kb 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.

What we claim is: 
     
         1 . A method of detecting a cancer in an individual comprising;
 a) obtaining a biological sample from the individual;   b) 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;   c) comparing the amount of mtDNA in the sample having the deletion to the amount of the deletion in a reference sample of mtDNA wherein the reference sample is from a known non-cancerous tissue or body fluid or from a known cancerous tissue or body fluid;   wherein if the reference sample is from a known non-cancerous tissue or body fluid, then an elevated level of the deletion in the biological sample compared to the non-cancerous reference sample is indicative of cancer and if the reference sample is from a known cancerous tissue or body fluid sample then an equivalent or elevated level of the deletion in the biological sample compared to the cancerous reference sample is indicative of cancer.   
     
     
         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 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. 
     
     
         4 . The method of  claim 3  wherein a 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. 
     
     
         5 . The method of  claim 1  wherein the step of quantifying is conducted using real-time PCR. 
     
     
         6 . The method of  claim 1  wherein the cancer is prostate cancer. 
     
     
         7 . The method of  claim 1  wherein the cancer is breast cancer. 
     
     
         8 . The method of  claim 1  wherein the biological sample is a body tissue or body fluid. 
     
     
         9 . The method of  claim 8  wherein the biological sample is breast tissue, prostate tissue, prostate massage fluid, or urine. 
     
     
         10 . The method according to  claim 3  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. 
     
     
         11 . A method of monitoring an individual for the development of a cancer comprising;
 a) obtaining a biological sample;   b) 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;   c) repeating steps a) to b) over a duration of time; and   d) wherein an increasing level of the deletion over the duration of time is indicative of cancer.   
     
     
         12 . The method of  claim 11  wherein the deletion has a nucleic acid sequence corresponding to the sequence identified in SEQ ID NO: 1. 
     
     
         13 . The method of  claim 11  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. 
     
     
         14 . The method of  claim 11  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. 
     
     
         15 . The method of  claim 11  wherein the step of quantifying is conducted using real-time PCR. 
     
     
         16 . The method of  claim 14  wherein a 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. 
     
     
         17 . The method of  claim 11  wherein the cancer is prostate cancer. 
     
     
         18 . The method of  claim 11  wherein the cancer is breast cancer. 
     
     
         19 . The method of  claim 11  wherein the biological sample is a body tissue or body fluid. 
     
     
         20 . The method of  claim 19  wherein the biological sample is breast tissue, prostate tissue, prostate massage fluid, or urine. 
     
     
         21 . A method of detecting a cancer in an individual comprising;
 a) obtaining a biological sample from the individual;   b) quantifying the amount of mtDNA in the sample having a sequence corresponding to the sequence identified in SEQ ID NO: 1;   c) comparing the amount of mtDNA in the sample corresponding to SEQ ID NO: 1 to at least one known reference value, wherein the at least one known reference value is the amount of mtDNA corresponding to SEQ ID NO: 1 in a reference sample of mtDNA from known non-cancerous tissue or body fluid or a reference sample of mtDNA from known cancerous tissue or body fluid, and   wherein if the reference value is from a reference sample of mtDNA from known non-cancerous tissue or body fluid then an elevated amount of the mtDNA corresponding to SEQ ID NO: 1 in the biological sample compared to the non-cancerous reference sample is indicative of cancer and wherein if the reference value is from a reference sample of mtDNA from known cancerous tissue or body fluid then an equivalent or elevated amount of the mtDNA corresponding to SEQ ID NO: 1 in the biological sample compared to the cancerous reference sample is indicative of cancer.   
     
     
         22 . The method of  claim 21  wherein the step of quantifying is conducted using real-time PCR. 
     
     
         23 . The method of  claim 21  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. 
     
     
         24 . The method of  claim 21  wherein one of a pair of 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. 
     
     
         25 . The method of  claim 23  wherein a 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. 
     
     
         26 . The method of  claim 21  wherein the cancer is prostate cancer. 
     
     
         27 . The method of  claim 21  wherein the cancer is breast cancer. 
     
     
         28 . The method of  claim 21  wherein the biological sample is a body tissue or body fluid. 
     
     
         29 . The method of  claim 28  wherein the biological sample breast tissue, prostate tissue, prostate massage fluid, or urine. 
     
     
         30 . The method of  claim 22  wherein the reference value is a cycle threshold. 
     
     
         31 . A method of detecting a deletion spanning approximately nucleotides 10744 to 14124 of the human mtDNA genome, wherein said deletion is associated with prostate cancer, in a subject having mtDNA, comprising:
 a) providing a biological sample from the subject;   b) detecting the presence of the deletion in the mtDNA, wherein presence of the deletion in the mtDNA indicates prostate cancer, a predisposition to prostate cancer or the progression of prostate cancer.   
     
     
         32 . The method of  claim 31 , wherein the step of detecting the presence of the deletion in the mtDNA comprises PCR analysis using a primer that bridges the mtDNA junction formed by the deletion spanning approximately nucleotides 10744 to 14124. 
     
     
         33 . A method of detecting a mtDNA deletion spanning approximately nucleotides 10744 to 14124 of the human mtDNA genome as a biomarker for prostate cancer, the method comprising:
 a) providing a biological sample from the subject;   b) detecting the presence of the deletion in the mtDNA;   c) comparing the amount of mtDNA in the sample having the deletion to the amount of the deletion in a reference sample of mtDNA wherein the reference sample is from a known non-cancerous tissue or body fluid or from a known cancerous tissue or body fluid;   wherein if the reference sample is from a known non-cancerous tissue or body fluid, then an elevated level of the deletion in the biological sample compared to the non-cancerous reference sample is a biomarker indicative of cancer and if the reference sample is from a known cancerous tissue or body fluid sample then an equivalent or elevated level of the deletion in the biological sample compared to the cancerous reference sample is a biomarker indicative of cancer.   
     
     
         34 . The method of  claim 33 , wherein the deletion is approximately 3379 bp. 
     
     
         35 . A method for confirming or refuting a prostate cancer biopsy test from a biopsy sample, comprising:
 a) obtaining a normal tissue from a biopsy sample;   b) detecting the absence or presence of a human mtDNA deletion at approximately nucleotides 10744 to 14124 of the human mtDNA genome in the normal tissue; and   c) comparing the amount of the mtDNA deletion in the normal tissue to the amount of the deletion in a reference sample of mtDNA wherein the reference sample is from a known non-cancerous tissue or body fluid or from a known cancerous tissue or body fluid;   
       wherein if the reference sample is from a known non-cancerous tissue or body fluid, then an elevated level of the deletion in the normal tissue compared to the non-cancerous reference sample is indicative of a cancerous biopsy and if the reference sample is from a known cancerous tissue or body fluid sample then an equivalent or elevated level of the deletion in the biological sample compared to the cancerous reference sample is indicative of a cancerous biopsy.