Neoepitope detection of disease using protein arrays

Abstract

A biosensor for use in detecting the presence of diseases, the biosensor comprising a detector for detecting a presence of at least one marker indicative of a specific disease. A method of determining efficacy of a pharmaceutical for treating a disease or staging disease by administering a pharmaceutical to a sample containing markers for a disease, detecting the amount of at least one marker of the disease in the sample, and analyzing the amount of the marker in the sample, whereby the amount of marker correlates to pharmaceutical efficacy or disease stage. Markers for gynecological disease. An immuno-imaging agent comprising labeled antibodies, whereby the labeled antibodies are isolated and reactive to proteins overexpressed in vivo. Informatics software for analyzing the arrays, the software including analyzing means for analyzing the arrays.

What is claimed is: 
     
         1 . A biosensor for use in detecting the presence of diseases, said biosensor comprising detection means for detecting a presence of at least one marker indicative of a specific disease. 
     
     
         2 . The biosensor according to  claim 1 , wherein the disease is a gynecological illness. 
     
     
         3 . The biosensor according to  claim 1 , wherein said detection means is selected from the group consisting essentially of an assay, a microarray, a macroarray, a slide, and a filter containing specific biomarkers of disease. 
     
     
         4 . The biosensor according to  claim 1 , wherein said detection means is an immunoassay. 
     
     
         5 . A diagnostic tool for determining the efficacy of a pharmaceutical for treating a disease, said tool comprising:
 detection means for detecting a presence of at least one marker indicative of a specific disease; and   analyzing means operatively connected to said detection means, said analyzing means for determining fluctuations in amount of marker present in said detection means, whereby fluctuations correlate to pharmaceutical efficacy.   
     
     
         6 . A diagnostic tool for staging the progression of a disease, said tool comprising:
 detection means for detecting a presence of at least one marker indicative of disease recurrence; and   analyzing means operatively connected to said detection means, said analyzing means for determining fluctuations in amount of marker present in said detection means, whereby fluctuations correlate to disease stage.   
     
     
         7 . The biosensor according to  claim 1  for use as detecting means for detecting the efficacy of a pharmaceutical. 
     
     
         8 . The biosensor according to  claim 1  for use as staging means for detecting the disease stage. 
     
     
         9 . A method of determining efficacy of a pharmaceutical for treating a disease by:
 administering a pharmaceutical to a sample containing markers for a disease;   detecting the amount of at least one marker of the disease in the sample;   analyzing the amount of the marker in the sample, whereby the amount of marker correlates to response to therapy.   
     
     
         10 . The method according to  claim 9 , wherein said analyzing step includes automatically analyzing results of said detecting step using software. 
     
     
         11 . A method of staging a disease by:
 administering a therapy to a sample containing markers for a disease;   detecting the amount of at least one marker of the disease in the sample;   analyzing the amount of the marker in the sample, whereby the amount of marker correlates to disease stage.   
     
     
         12 . The method according to  claim 11 , wherein said analyzing step includes automatically analyzing results of said detecting step using software. 
     
     
         13 . An antigen array for use in detecting the presence of disease. 
     
     
         14 . The array according to  claim 13 , wherein said array is selected from the group consisting essentially of a microarray, spinning disk, antigens bound to colored beads, and a macroarray. 
     
     
         15 . The array according to  claim 13 , wherein the disease is a gynecological disease. 
     
     
         16 . The array according to  claim 15 , wherein said gynecological disease is selected from the group consisting essentially of endometriosis, ovarian cancer, breast cancer, cervical cancer, and primary peritoneal carcinoma. 
     
     
         17 . The array according to  claim 13  further including markers of disease selected from the list in Table 6. 
     
     
         18 . The array according to  claim 17  further including markers of disease selected from Table 8. 
     
     
         19 . Therapeutic targets for treating disease, said targets comprising the antigens in the array set forth in  claim 13 . 
     
     
         20 . The targets according to  claim 19 , wherein said targets a personalized to the individual receiving treatment. 
     
     
         21 . A method of treating disease by:
 detecting at least one marker of the disease in a sample;   analyzing the type of the marker in the sample, whereby the type of marker correlates to a specific therapy.   
     
     
         22 . Markers for gynecological disease selected from the list in Table 6. 
     
     
         23 . The markers according to  claim 22  further including markers selected from the list in Table 8. 
     
     
         24 . An immuno-imaging agent comprising labeled antibodies, whereby said labeled antibodies are isolated and reactive to proteins overexpressed in vivo. 
     
     
         25 . The agent according to  claim 24 , wherein said protein is identified by the biosensor of  claim 1 . 
     
     
         26 . Informatics software for analyzing the arrays of  claim 13 , said software comprising analyzing means for analyzing the arrays. 
     
     
         27 . The informatics software according to  claim 26 , further including weighting means for modifying the analyzing means. 
     
     
         28 . Diagnostic or prognostic markers for molecular pathology said markers being overexpressed or mutated proteins in tumor cells.