Mitochondrial DNA deletion between about residues 12317-16254 for use in the detection of cancer

Abstract

The present invention relates to methods for predicting, diagnosing and monitoring cancer. The methods comprise obtaining biological samples, extracting mitochondrial DNA (mtDNA) from the samples, quantifying a mtDNA mutation in the sample and comparing the level of the mtDNA mutation present in the sample with a reference value The methods of the invention may also be effective in screening for new therapeutic agents and treatment regimes Further, said methods may be also be useful for monitoring the response of a subject to a preventative or therapeutic treatment.

1 . A method of detecting a cancer in a subject, the method comprising:
 a) quantifying, in a biological sample obtained from the subject, the amount of mtDNA having a deletion in the mtDNA sequence spanning approximately nucleotides 12317 and 16254 of the human mtDNA genome;   b) comparing the amount of mtDNA in the sample having the deletion to at least one known reference value; and,   c) detecting said cancer based on the results of step (b).   
     
     
         2 . The method of  claim 1  wherein the deletion has a sequence as set forth in SEQ ID NO: 1 or SEQ ID NO: 2. 
     
     
         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, and wherein an elevated amount of the deletion in the biological sample compared to the reference sample is indicative of cancer. 
     
     
         4 . (canceled) 
     
     
         5 . The method of  claim 3  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. 
     
     
         6 . 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, wherein a similar level of the deletion in the biological sample compared to the reference sample is indicative of cancer. 
     
     
         7 . (canceled) 
     
     
         8 . The method of  claim 7  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. 
     
     
         9 . (canceled) 
     
     
         10 . The method of  claim 1  wherein the step of quantifying includes first amplifying a target region of mtDNA that is indicative of the deletion, and quantifying the amount of the amplified target region. 
     
     
         11 . The method of  claim 10  wherein a primer having ID NO: 4 is used as part of a pair of amplification primers for amplifying the target region. 
     
     
         12 . The method of  claim 1  wherein the cancer is prostate cancer or breast cancer. 
     
     
         13 - 27 . (canceled) 
     
     
         28 . A method of detecting a cancer in a subject, the method comprising:
 a) quantifying, in a biological sample obtained from the subject, the amount of mtDNA in the sample having a deletion set forth in SEQ ID NO: 1 or SEQ ID NO: 2; and   b) comparing the amount of mtDNA from step a) to at least one known reference value; and   c) detecting said cancer based on the results of step (b).   
     
     
         29 . The method of  claim 28  wherein the at least one known reference value is the amount of SEQ ID NO: 1 or SEQ ID NO: 2 in a reference sample of mtDNA from known non-cancerous tissue or body fluid. 
     
     
         30 . The method of  claim 28  wherein the at least one known reference value is the amount of SEQ ID NO: 1 or SEQ ID NO: 2 in a reference sample of mtDNA from known cancerous tissue or body fluid. 
     
     
         31 . (canceled) 
     
     
         32 . The method of  claim 31  wherein the step of quantifying includes first amplifying a target region of mtDNA that is indicative of the deletion, and quantifying the amount of the amplified target region. 
     
     
         33 . The method of  claim 32  wherein one of a pair of primers used in the amplifying of the target region overlaps a rejoining site of SEQ ID NO: 1 or SEQ ID NO: 2, after the sequence has re-circularized. 
     
     
         34 . The method of  claim 28  wherein the cancer is prostate cancer or breast cancer. 
     
     
         35 - 38 . (canceled) 
     
     
         39 . A diagnostic kit for carrying out the method of  claim 1  comprising:
 (a) at least one of material for collecting one or more biological samples, material for extracting mtDNA from one or more biological sample or reagent for conducting the method; and 
 (b) at least one suitable primer for detecting the mtDNA deletion. 
 
     
     
         40 . The kit of  claim 39 , wherein the at least one suitable primer overlaps a spliced region of mtDNA having the deletion. 
     
     
         41 . The kit of  claim 40 , therein the at least one suitable primer is SEQ ID NO: 4, SEQ ID NO: 5 or SEQ ID NO: 6. 
     
     
         42 . A diagnostic kit for carrying out the method of  claim 28  comprising:
 (a) at least one of material for collecting one or more biological samples, material for extracting mtDNA from one or more biological sample or reagent for conducting the method; and 
 (b) at least one suitable primer for detecting the deletion set forth in SEQ ID NO: 1 or SEQ ID NO: 2. 
 
     
     
         43 . The kit of  claim 43 , wherein the at least one suitable primer overlaps a rejoining site of SEQ ID NO: 1 or SEQ ID NO: 2.