Diagnostic methods for determining prognosis of non-small cell lung cancer

Abstract

Disclosed are methods for identifying early-stage non-small-cell lung cancer (NSCLC) patients who will have an unfavorable prognosis for the recurrence of lung cancer after surgical resection. The methods are based in part on the discovery that chromosomal copy number gains at Chr19, 34.7 Mb-35.6 Mb can be used for prognostic classification. The methods preferably use fluorescence in situ hybridization with fluorescently labeled nucleic acid probes to hybridize to patient samples to quantify the chromosomal copy number of this genetic locus.

What is claimed is: 
     
         1 . A method of predicting disease outcome in a patient being treated for lung cancer, the method comprising the steps of:
 a) providing a test sample from a patient;   b) determining a copy number for the cyclin E1 gene in the test sample;   c) comparing the copy number of the cyclin E1 gene in the test sample against a baseline copy number of two, thereby determining the presence or absence of a copy number gain for the cyclin E1 gene in the test sample; and   d) based on the presence or absence of a copy number gain for the cyclin E1 gene in the test sample, identifying the patient as having an increased risk of a poor disease outcome when compared to a baseline measure of disease outcome in patients having no copy number gain in the cyclin E1 gene, wherein the presence of a copy number gain in the cyclin E1 gene is predictive of poor disease outcome.   
     
     
         2 . The method of  claim 1  wherein the poor disease outcome is at least one of a decreased overall survival time when compared to an overall survival time of patients having no copy number gain for the cyclin E1 gene, and a shorter time to recurrence when compared to an overall survival time of patients having no copy number gain for the cyclin E1 gene. 
     
     
         3 . A method of predicting disease outcome in a patient being treated for lung cancer, the method comprising the steps of:
 a) providing a test sample from a patient;   b) determining the presence or absence of a copy number gain for the cyclin E1 gene; and   c) based on the presence or absence of a copy number gain for the cyclin E1 gene, determining whether the patient has a higher risk of a decreased overall survival time or a shorter time to recurrence when compared to an overall survival time of patients having no copy number gain for the cyclin E1 gene.   
     
     
         4 . The method of any of  claims 1 - 3 , wherein the cyclin E1 gene is located at chromosome 19, 34.7 Mb-35.6 Mb. 
     
     
         5 . The method of any of  claims 1 - 3 , wherein the test sample comprises a tissue sample. 
     
     
         6 . The method of  claim 5 , wherein the tissue sample comprises a blood sample, a tumor tissue or a suspected tumor tissue, a thin layer cytological sample, a fine needle aspirate sample, a lung wash sample, a pleural effusion sample, a fresh frozen tissue sample, a paraffin embedded tissue sample or an extract or processed sample produced from any of a peripheral blood sample. 
     
     
         7 . The method of  claim 5 , wherein the tissue sample comprises a lung tissue sample or a peripheral blood sample comprising circulating tumor cells. 
     
     
         8 . The method of any of  claims 1 - 3 , wherein the determining step (b) is performed by in situ hybridization. 
     
     
         9 . The method of  claim 8 , wherein the in situ hybridization is performed with a nucleic acid probe that is fluorescently labeled. 
     
     
         10 . The method of  claim 8 , wherein the in situ hybridization is performed with at least two nucleic acid probes. 
     
     
         11 . The method of  claim 8 , wherein the in situ hybridization is performed with a peptide nucleic acid probe. 
     
     
         12 . The method of any of  claims 1 - 3 , wherein the determining step (b) is performed by polymerase chain reaction. 
     
     
         13 . The method of any of  claims 1 - 3 , wherein the determining step (b) is performed by a nucleic acid sequencing assay. 
     
     
         14 . The method of any of  claims 1 - 3 , wherein the determining step (b) is performed by a nucleic acid microarray assay. 
     
     
         15 . The method of any of  claims 1 - 3 , wherein the lung cancer is non-small-cell lung cancer. 
     
     
         16 . The method of any of  claims 1 - 3 , wherein the cancer is selected form the group consisting of squamous cell carcinoma, large cell carcinoma and adenocarcinoma. 
     
     
         17 . The method of any of  claims 1 - 3 , wherein the patient is being treated with chemotherapy, radiation, surgery or any combination thereof. 
     
     
         18 . A method of selecting a treatment for a patient suffering from lung cancer, the method comprising the steps of:
 a) providing a test sample from the patient wherein treatment with a chemotherapy agent is at least one treatment option for the patient;   b) determining a copy number for the cyclin E1 gene in the test sample;   c) comparing the copy number of the cyclin E1 gene in the test sample against a baseline copy number of two thereby determining the presence or absence of a copy number gain for cyclin E1 in the test sample; and   d) determining a chemotherapy treatment regimen based on the comparison in step c).   
     
     
         19 . The method of claim  68  wherein determining a treatment regimen based on the comparison in step c) comprises selecting a chemotherapy agent and determining a frequency of chemotherapy treatment when a copy number change is present for the cancer outcome marker. 
     
     
         20 . The method of  claim 18 , wherein the test sample comprises a tissue sample. 
     
     
         21 . The method of  claim 20 , wherein the tissue sample comprises a blood sample, a tumor tissue or a suspected tumor tissue, a thin layer cytological sample, a fine needle aspirate sample, a lung wash sample, a pleural effusion sample, a fresh frozen tissue sample, a paraffin embedded tissue sample or an extract or processed sample produced from any of a peripheral blood sample. 
     
     
         22 . The method of  claim 20 , wherein the tissue sample comprises a lung tissue sample or a peripheral blood sample comprising circulating tumor cells. 
     
     
         23 . The method of  claim 18 , wherein the determining step (b) is performed by in situ hybridization. 
     
     
         24 . The method of  claim 23 , wherein the in situ hybridization is performed with a nucleic acid probe that is fluorescently labeled. 
     
     
         25 . The method of  claim 23 , wherein the in situ hybridization is performed with at least two nucleic acid probes. 
     
     
         26 . The method of  claim 23 , wherein the in situ hybridization is performed with a peptide nucleic acid probe. 
     
     
         27 . The method of  claim 18 , wherein the determining step (b) is performed by polymerase chain reaction. 
     
     
         28 . The method of  claim 18 , wherein the determining step (b) is performed by a nucleic acid sequencing assay. 
     
     
         29 . The method of  claim 18 , wherein the determining step (b) is performed by a nucleic acid microarray assay. 
     
     
         30 . The method of  claim 18 , wherein the lung cancer is non-small-cell lung cancer. 
     
     
         31 . The method of  claim 18 , wherein the cancer is selected form the group consisting of squamous cell carcinoma, large cell carcinoma and adenocarcinoma. 
     
     
         32 . The method of  claim 18 , wherein the patient is also being treated with radiation or surgery or a combination thereof. 
     
     
         33 . A method of classifying a patient as having a lung cancer that is resistant to treatment comprising the steps of:
 a) providing a test sample from a patient;   b) determining a copy number for the cyclin E1 gene;   c) comparing the copy number for the cyclin E1 gene in the test sample against a baseline copy number of two for the cyclin E1 gene to determine the presence or absence of a copy number gain in the cyclin E1 gene in the patient; and   d) classifying the patient as having a lung cancer that is resistant to treatment based on the presence of a copy number gain in the cyclin E1 gene.   
     
     
         34 . The method of  claim 33 , wherein the test sample comprises a tissue sample. 
     
     
         35 . The method of  claim 34 , wherein the tissue sample comprises a blood sample, a tumor tissue or a suspected tumor tissue, a thin layer cytological sample, a fine needle aspirate sample, a lung wash sample, a pleural effusion sample, a fresh frozen tissue sample, a paraffin embedded tissue sample or an extract or processed sample produced from any of a peripheral blood sample. 
     
     
         36 . The method of  claim 34 , wherein the tissue sample comprises a lung tissue sample or a peripheral blood sample comprising circulating tumor cells. 
     
     
         37 . The method of  claim 33 , wherein the determining step (b) is performed by in situ hybridization. 
     
     
         38 . The method of  claim 37 , wherein the in situ hybridization is performed with a nucleic acid probe that is fluorescently labeled. 
     
     
         39 . The method of  claim 37 , wherein the in situ hybridization is performed with at least two nucleic acid probes. 
     
     
         40 . The method of  claim 37 , wherein the in situ hybridization is performed with a peptide nucleic acid probe. 
     
     
         41 . The method of  claim 33 , wherein the determining step (b) is performed by polymerase chain reaction. 
     
     
         42 . The method of  claim 33 , wherein the determining step (b) is performed by a nucleic acid sequencing assay. 
     
     
         43 . The method of  claim 33 , wherein the determining step (b) is performed by a nucleic acid microarray assay. 
     
     
         44 . The method of  claim 33 , wherein the lung cancer is non-small-cell lung cancer. 
     
     
         45 . The method of  claim 34 , wherein the cancer is selected form the group consisting of squamous cell carcinoma, large cell carcinoma and adenocarcinoma. 
     
     
         46 . The method of  claim 33 , wherein the patient is being treated with chemotherapy, radiation, surgery or any combination thereof. 
     
     
         47 . A kit comprising:
 a) reagents for determining the presence or absence of a copy number gain for the cyclin E1 gene; and   b) instructions for performing the test.   
     
     
         48 . The kit of  claim 47 , wherein the reagents to determine the presence or absence of a copy number gain comprise detectably-labeled polynucleotides that hybridize to at least a portion of the cyclin E1 gene.