Methods And Marker Combinations For Screening For Predisposition To Lung Cancer

Abstract

The present invention relates to rapid, sensitive methods for determining whether a subject has or is at risk of developing lung cancer based on certain combinations of biomarkers, or biomarkers and biometric parameters. The methods consist of: a) quantifying in a test sample obtained from a subject, the amount of two or more biomarkers in a panel, the panel comprising at least one antibody and at least one antigen: b) comparing the amount of each biomarker quantified in the panel to a predetermined cutoff for said biomarker and assigning a score for each biomarker based on said comparison: c) combining the assigned score for each biomarker quantified in step b to obtain a total score for said subject: d) comparing the total score in step c with a predetermined total score and e) determining whether said subject has a risk of lung cancer based on the comparison in step d.

1 . A method of aiding in a diagnosis of a subject suspected of lung cancer, the method comprising the steps of:
 a. quantifying in a test sample obtained from a subject, the amount of two or more biomarkers in a panel, the panel comprising at least one antibody and at least one antigen;   b. comparing the amount of each biomarker quantified in the panel to a predetermined cutoff for said biomarker and assigning a score for each biomarker based on said comparison;   c. combining the assigned score for each biomarker quantified in step b to obtain a total score for said subject;   d. comparing the total score determined in step c with a predetermined total score; and   e. determining whether said subject has a risk of lung cancer based on the comparison of the total score in step d.   
     
     
         2 . The method of  claim 1 , wherein the panel comprises at least one antibody selected from the group consisting of: anti-p53, anti-TMP21, anti-NY-ESO-1, anti-HDJ1, anti-NPC1 L1C-domain, anti-TMOD1, anti-CAMK1, anti-RGS1, anti-PACSIN1, anti-RCV1, anti-MAPKAPK3 and anti-Cyclin E2. 
     
     
         3 . The method of  claim 1 , wherein the panel comprises at least one antigen selected from the group consisting of: cytokeratin 8, cytokeratin 19, cytokeratin 18, CEA, CA125, CA19-9, CA15-3, SCC, proGRP, serum amyloid A, alpha-1-anti-trypsin, apolipoprotein CIII and thymosin β4. 
     
     
         4 . The method of  claim 1 , wherein the panel further comprises at least one region of interest selected from the group consisting of: Acn6399, Acn9459, Pub11597, Pub4789, TFA2759, TFA9133, Pub3743, Pub8606, Pub4487, Pub4861, Pub6798, Pub6453, Pub2951, Pub2433, Pub17338, TFA6453 and HIC3959. 
     
     
         5 . The method of  claim 1 , wherein the DFI of the biomarkers relative to lung cancer is less than about 0.4. 
     
     
         6 . The method of  claim 1 , wherein step b comprises comparing the amount of each biomarker in the panel to a number of predetermined cutoffs for said biomarker and assigning a score for each biomarker based on said comparison, step c comprises combining the assigned score for each biomarker quantified in step b to obtain a total score for said subject, step d comprises comparing the total score determined in step c with a predetermined total score and step e comprises determining whether said subject has lung cancer based on the comparison of the total score in step d. 
     
     
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         21 . (canceled) 
     
     
         22 . (canceled) 
     
     
         23 . A kit comprising:
 a peptide selected from the group consisting of: SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5 or combinations thereof.   
     
     
         24 . (canceled) 
     
     
         25 . A kit comprising:
 a. reagents containing at least one antibody for quantifying one or more antigens in a test sample, wherein said antigens are: cytokeratin 8, cytokeratin 19, cytokeratin 18, CEA, CA125, CA15-3, SCC, CA19-9, proGRP, serum amyloid A, alpha-1-anti-trypsin, apolipoprotein CIII or thymosin β4;   b. reagents containing one or more antigens for quantifying at least one antibody in a test sample; wherein said antibodies are: anti-p53, anti-TMP21, anti-NPC1L1C-domain, anti-TMOD1, anti-NY-ESO-1, anti-HDJ1, anti-CAMK1, anti-RGS1, anti-PACSIN1, anti-RCV1, anti-MAPKAPK3 and anti-Cyclin E2; and optionally,   c. algorithms for combining and comparing the amount of each antigen and antibody quantified in the test sample against a predetermined cutoff and assigning a score for each antigen and antibody quantified based on said comparison, combining the assigned score for each antigen and antibody quantified to obtain a total score, comparing the total score with a predetermined total score and using said comparison as an aid in determining whether a subject has lung cancer.   
     
     
         26 . The kit of  claim 25 , further comprising reagents for quantifying one or more regions of interest selected from the group consisting of: ACN9459, Pub11597, Pub4789, TFA2759, TFA9133, Pub3743, Pub8606, Pub4487, Pub4861, Pub6798, Tfa6453 and Hic3959. 
     
     
         27 . The kit of  claim 25 , further comprising:
 a. reagents containing at least one antibody for quantifying one or more antigens in a test sample, wherein said antigens are: cytokeratin 19, CEA, CA 125 and ProGRP;   b. reagents containing one or more antigens for quantifying at least one antibody in a test sample; wherein said antibodies are: anti-p53, anti-NY-ESO-1, anti-MAPKAPK3 and anti-Cyclin E2; and optionally,   c. algorithms for combining and comparing the amount of each antigen and antibody quantified in the test sample against a predetermined cutoff and assigning a score for each antigen and antibody quantified based on said comparison, combining the assigned score for each antigen and antibody quantified to obtain a total score, comparing the total score with a predetermined total score and using said comparison as an aid in determining whether a subject has lung cancer.   
     
     
         28 . The kit of  claim 27 , wherein said kit contains reagents for quantifying each of cytokeratin 19, CEA, CA125 and ProGRP in a test sample. 
     
     
         29 . The kit of  claim 27 , wherein said kit contains reagents for quantifying each of anti-p53, anti-NY-ESO-1, anti-MAPKAPK3 and at least one antibody against immunoreactive Cyclin E2 in a test sample. 
     
     
         30 . The kit of  claim 27 , wherein said kit contains reagents for quantifying each of cytokeratin 19, CEA, CA125 ProGRP, anti-p53, anti-NY-ESO-1, anti-MAPKAPK3 and anti-Cyclin E2 in a test sample. 
     
     
         31 . An isolated polypeptide having an amino acid sequence selected from the group consisting of: SEQ ID NO:3 and a polypeptide having 60% homology to the amino acid sequence of SEQ ID NO:3. 
     
     
         32 . An isolated polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:4 and a polypeptide having 60% homology to the amino acid sequence of SEQ ID NO:4. 
     
     
         33 . An isolated polypeptide having an amino acid sequence selected from the group consisting of: SEQ ID NO:5 and a polypeptide having 60% homology to the amino acid sequence of SEQ ID NO:5. 
     
     
         34 . The method of  claim 1 , wherein the total score from step c further includes the assigned score for one or more biometric parameter, said assigned score determined by obtaining a value for the one or more biometric parameter of a subject and comparing the value of the one or more biometric parameter against a predetermined cutoff for each said biometric parameter and assigning a score for each biometric parameter based on said comparison. 
     
     
         35 . The method of  claim 34  wherein the biometric parameter is selected from the group consisting of: the subject's smoking history, age, carcinogen exposure and gender. 
     
     
         36 . The method of  claim 34  wherein the biometric parameter is pack years of smoking. 
     
     
         37 . The method of  claim 1 , wherein the method involves quantifying the amount of three or more biomarkers in the panel. 
     
     
         38 . The method of  claim 37 , wherein the method involves quantifying the amount of eight biomarkers in the panel. 
     
     
         39 . The method of  claim 1  wherein the panel comprises the amount of two or more biomarkers selected from the group consisting of anti-p53, anti-NY-ESO-1, anti-MAPKAPK3, anti-Cyclin E2, cytokeratin 19, CEA, CA125 and ProGRP anti-p53, anti-NY-ESO-1, anti-MAPKAPK3, anti-Cyclin E2, cytokeratin 19, CEA, CA125 and ProGRP; 
     
     
         40 . The method of  claim 1 , wherein the panel further comprises at least one region of interest selected from the group consisting of: Acn6399, Acn9459, Pub11597, Pub4789, TFA2759, TFA9133, Pub3743, Pub8606, Pub4487, Pub4861, Pub6798, Pub6453, Pub2951, Pub2433, Pub17338, TFA6453 and HIC3959. 
     
     
         41 . The method of  claim 1 , wherein the panel comprises the amount of two or more biomarkers selected from the group consisting of anti-p53, anti-NY-ESO-1, anti-MAPKAPK3, anti-Cyclin E2, cytokeratin 19, CEA, CA125 and ProGRP 
     
     
         42 . The method of  claim 41 , wherein the anti-Cyclin E2 is an antibody against SEQ ID NO:3, SEQ ID NO:4 or SEQ ID NO:5.