Methods and kits used in classifying adrenocortical carcinoma

Abstract

The invention encompasses methods and kits used to detect biomarkers that may be used to predict disease outcome in adrenocortical carcinoma patients.

1 . A method of classifying adrenocortical carcinoma in a human patient, the method comprising:
 obtaining a sample of an adrenocortical carcinoma tumor from a human patient;   adding a first oligonucleotide and a second oligonucleotide to a mixture comprising the sample of the adrenocortical carcinoma tumor, wherein the first and second oligonucleotides are capable of binding to a nucleic acid biomarker comprising SEQ ID NO:1;   subjecting the mixture to conditions that allow detection of the binding of the first and second oligonucleotides to the biomarker;   calculating the expression of the biomarker through the level of the binding of the first and second oligonucleotides to the biomarker, wherein the expression of the biomarker in the sample is calculated in comparison to the expression of the biomarker in a control sample; and   classifying the human patient into one of a first cohort of individuals and a second cohort of individuals, wherein individuals in the first cohort are not likely to survive for a greater period of time after diagnosis with adrenocortical carcinoma compared to individuals in the second cohort, and further wherein the human patient is classified into the first cohort of individuals based upon a determination of an at least three fold increase in expression of SEQ ID NO: 1 in the sample of the adrenocortical carcinoma tumor.   
     
     
         2 . The method of  claim 1 , wherein the first oligonucleotide and the second oligonucleotide are capable of binding to different nucleic acid strands. 
     
     
         3 . The method of  claim 2  and further comprising adding a third oligonucleotide to the mixture wherein the third oligonucleotide is capable of binding to a sequence between the sequences to which the first oligonucleotide and the second oligonucleotide are capable of binding. 
     
     
         4 . The method of  claim 3 , wherein the third oligonucleotide comprises a fluorescent label. 
     
     
         5 . The method of  claim 3 , wherein the third oligonucleotide comprises a quencher. 
     
     
         6 . The method of  claim 2 , wherein the nucleic acid amplification is verified by a method selected from the group consisting of a specifically sized band visualized through gel electrophoresis, a Ct value, and DNA sequencing on a product of amplification. 
     
     
         7 . The method of  claim 1 , wherein the first and the second oligonucleotides are affixed to a substrate. 
     
     
         8 . The method of  claim 7 , wherein the first and second oligonucleotides are configured to form a microarray. 
     
     
         9 . The method of  claim 1  and further comprising first diagnosing the human patient as having an adrenocortical carcinoma tumor, wherein diagnosing the human patient comprises obtaining some or all of the adrenocortical carcinoma tumor and evaluating the tumor for the presence of adrenocortical carcinoma. 
     
     
         10 . The method of  claim 1 , wherein the human patient is classified into the first cohort of individuals based upon a determination of a three to five fold increase in expression of the biomarker in the sample of the adrenocortical carcinoma tumor 
     
     
         11 . A method of classifying adrenocortical carcinoma in a human patient, the method comprising:
 obtaining a sample of an adrenocortical carcinoma tumor from a human patient;   adding a first antibody that is capable of binding to a biomarker comprising SEQ ID NO: 2 to a mixture comprising the sample of the adrenocortical carcinoma tumor from the human patient;   subjecting the mixture to conditions that allow detection of the binding of the first antibody to the biomarker;   calculating the expression of the biomarker through the level of the binding of the first antibody to the biomarker, wherein the expression of the biomarker in the sample is calculated in comparison to the expression of the biomarker in a control sample; and   classifying the human patient into one of a first cohort of individuals and a second cohort of individuals, wherein individuals in the first cohort are not likely to survive for a greater period of time after diagnosis with adrenocortical carcinoma compared to individuals in the second cohort, and further wherein the human patient is classified into the first cohort of individuals based upon a determination of an at least three fold increase in expression of the biomarker in the sample of the adrenocortical carcinoma tumor.   
     
     
         12 . The method of  claim 11 , wherein the first antibody comprises a label. 
     
     
         13 . The method of  claim 12 , wherein the label is selected from a grouping consisting of a fluorescent compound, an enzyme, and a ligand. 
     
     
         14 . The method of  claim 11 , and further comprising adding a second antibody to the mixture, wherein the second antibody binds to the first antibody. 
     
     
         15 . The method of  claim 11  and further comprising first diagnosing the human patient as having an adrenocortical carcinoma tumor, wherein diagnosing the human patient comprises obtaining some or all of the adrenocortical carcinoma tumor and evaluating the tumor for the presence of adrenocortical carcinoma. 
     
     
         16 . The method of  claim 11 , wherein the human patient is classified into the first cohort of individuals based upon a determination of a three to five fold increase in expression of the biomarker in the sample of the adrenocortical carcinoma tumor. 
     
     
         17 . A method of determining a likelihood of survival of a human patient with adrenocortical carcinoma, the method comprising the steps of:
 diagnosing the human patient as having an adrenocortical carcinoma tumor, wherein diagnosing the human patient comprises obtaining at least a portion of the adrenocortical carcinoma tumor from the human patient and evaluating the tumor for the presence of adrenocortical carcinoma;   adding a first oligonucleotide, a second oligonucleotide, and third oligonucleotide to a mixture comprising a sample of the adrenocortical carcinoma tumor in the human patient, wherein the first, second, and third oligonucleotides are capable of binding to a nucleotide acid biomarker comprising SEQ ID NO: 1;   subjecting the mixture to conditions that allow detection of the binding of the first, second, and third oligonucleotides to the biomarker; and   classifying the human patient as having a decreased likelihood for survival when there is an at least three fold increase in expression of the biomarker in the sample as compared to a control.   
     
     
         18 . The method of  claim 17 , wherein the human patient is classified as having a decreased likelihood for survival wherein there is a three to five fold increase in expression of the biomarker in the sample compared to the control. 
     
     
         19 . The method of  claim 17 , wherein the third oligonucleotide comprises a fluorescent label. 
     
     
         20 . The method of  claim 19 , wherein the third oligonucleotide comprises a quencher.