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 an adrenocortical carcinoma patient, the method comprising:
 adding a first reagent capable of specific binding to a biomarker that includes a sequence selected from the group consisting of SEQ ID NO. 1 and SEQ ID NO. 2 to a mixture comprising a sample from the patient;   subjecting the mixture to conditions that allow detection of the binding of the reagent to the biomarker; and   classifying the subject into one of at least a first cohort based upon the binding of the reagent to the sample; and   wherein the first cohort comprises one or more individuals not likely to survive past a point in time.   
     
     
         2 . The method of  claim 1  wherein the biomarker includes SEQ ID NO. 2 and wherein the sample comprises a protein. 
     
     
         3 . The method of  claim 2  wherein the first reagent comprises a first antibody. 
     
     
         4 . The method of  claim 3  wherein the first antibody comprises a first label. 
     
     
         5 . The method of  claim 4  wherein the first label comprises a fluorescent compound. 
     
     
         6 . The method of  claim 4  wherein the first label comprises an enzyme. 
     
     
         7 . The method of  claim 4  wherein the first label comprises a ligand. 
     
     
         8 . The method of  claim 3  further comprising adding a second antibody capable of binding to the first antibody to the mixture. 
     
     
         9 . The method of  claim 1  wherein the biomarker includes SEQ ID NO. 1, wherein the first reagent comprises a first nucleic acid. 
     
     
         10 . The method of  claim 9  wherein the first nucleic acid comprises a first oligonucleotide. 
     
     
         11 . The method of  claim 11  further comprising adding a second oligonucleotide capable of binding to part of the biomarker to the mixture and subjecting the mixture to nucleic acid amplification; wherein the first oligonucleotide and the second oligonucleotide are capable of binding to different sequences and wherein the first oligonucleotide and the second oligonucleotide are capable of binding to different nucleic acid strands. 
     
     
         12 . The method of  claim 11  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. 
     
     
         13 . The method of  claim 12  wherein the third oligonucleotide comprises a fluorescent label. 
     
     
         14 . The method of  claim 12  wherein the third oligonucleotide comprises a quencher. 
     
     
         15 . The method of  claim 11  wherein the result is selected from the group consisting of: a specifically sized band visualized through gel electrophoresis and a Ct value. 
     
     
         16 . The method of  claim 11  further comprising performing DNA sequencing on a product of the nucleic acid amplification. 
     
     
         17 . The method of  claim 1  wherein the first reagent is affixed to a substrate. 
     
     
         18 . The method of  claim 17  further comprising adding a second reagent to the mixture wherein the second reagent is affixed to the substrate and wherein the first and second reagents are configured to form a microarray. 
     
     
         19 . The method of  claim 1  wherein the sample comprises a tumor sample. 
     
     
         20 . The method of  claim 1  wherein the first cohort comprises at least one patient with a tumor belonging to a first tumor cluster. 
     
     
         21 . A kit used to classify adrenocortical carcinoma tumors, the kit comprising:
 a first reagent capable of specific binding to a biomarker selected from the group consisting of SEQ ID NO. 1 and SEQ ID NO. 2 and   an indication of a level of expression that signifies the classification of the subject into a cohort wherein the cohort comprises individuals unlikely to survive past a point in time.   
     
     
         22 . The kit of  claim 21  wherein the first reagent comprises a first antibody. 
     
     
         23 . The kit of  claim 22  wherein the first antibody comprises a label. 
     
     
         24 . The kit of  claim 23  further comprising a second antibody capable of binding to the first antibody. 
     
     
         25 . The kit of  claim 21  wherein the first reagent comprises a first nucleic acid. 
     
     
         26 . The kit of  claim 25  wherein the first nucleic acid is conjugated to a substrate. 
     
     
         27 . The kit of  claim 25  wherein the first nucleic acid comprises a first oligonucleotide 
     
     
         28 . The kit of  claim 27  further comprising a second oligonucleotide wherein the first oligonucleotide and the second oligonucleotide are capable of binding to different parts of the biomarker and to different nucleic acid strands. 
     
     
         29 . The kit of  claim 21  further comprising an enzyme. 
     
     
         30 . The kit of  claim 29  wherein the enzyme is selected from the group consisting of: a reverse transcriptase, a DNA polymerase, and a thermostable DNA polymerase. 
     
     
         31 . The kit of  claim 21  wherein the indication comprises a positive control. 
     
     
         32 . The kit of  claim 21  wherein the indication comprises a printed result. 
     
     
         33 . The kit of  claim 32  wherein the printed result includes a feature selected from the group consisting of a Ct value, a range of Ct values, an absorbance value, a fluorescence value, and a photograph. 
     
     
         34 . The kit of  claim 33  wherein the printed result is made available on a website. 
     
     
         35 . The kit of  claim 34  wherein the indication comprises software configured to detect binding of the reagent as input and classification of the subject into the cohort as output.