Prognostic assay for squamous cell lung carcinoma

Abstract

Methods for predicting clinical outcome for a human subject diagnosed with squamous cell lung carcinoma using a panel of molecular markers that includes CDKN2A and CCND1. The markers are related to the subject's increased likelihood of a negative clinical outcome.

What is claimed is: 
     
         1 . A method of predicting clinical outcome for a human subject diagnosed with squamous cell lung carcinoma comprising:
 a) determining the presence of a loss of function mutation in the cyclin-dependent kinase inhibitor 2A (CDKN2A) or deletion of the gene in a biological sample comprising cancer cells obtained from said human subject;   b) determining the presence of an increase in the copy number of the G1/S-specific cyclin-D1 (CCND1) gene in a biological sample comprising cancer cells obtained from said human subject; and   c) predicting the clinical outcome for said human subject,   
       wherein the presence of a loss of function mutation in the CDKN2A gene or deletion of the gene and increase in the copy number of the CCND1 gene positively correlates with an increased likelihood of a negative clinical outcome, and wherein the absence of a loss of function mutation in the CDKN2A gene or deletion of the gene or absence of an increase in the copy number of the CCND1 gene positively correlates with an increased likelihood of a positive clinical outcome. 
     
     
         2 . The method of  claim 1 , wherein the loss of function mutation is a missense mutation, nonsense mutation, or frameshift mutation, or any combination thereof. 
     
     
         3 . The method of  claim 2 , wherein the missense mutation is a D108G, D108N, D108Y, G125R, P114L mutation, or any combination thereof. 
     
     
         4 . The method of  claim 1 , wherein the increase in copy number is greater than or equal to 4. 
     
     
         5 . The method of  claim 1 , wherein the determining the presence of a loss of function mutation in the CDKN2A gene comprises contacting the biological sample with reagents to:
 a) amplify the gene or a portion thereof comprising said mutation to provide an amplification product of the gene or portion thereof, or   b) reverse transcribe a RNA transcript encoded by the CDKN2A gene comprising said mutation and amplify the reverse transcription product to provide an amplification product of the gene or portion thereof.   
     
     
         6 . The method of  claim 5 , wherein the presence of said mutation in the amplification product is determined by next generation sequencing. 
     
     
         7 . The method of  claim 5 , wherein the presence of said mutation in the amplification product is determined by qPCR. 
     
     
         8 . The method of  claim 5 , wherein the reagents are oligonucleotides. 
     
     
         9 . The method of  claim 5 , wherein the reagents are PCR primer sets. 
     
     
         10 . The method of  claim 5 , wherein the reagents are RT-PCR primer sets. 
     
     
         11 . The method of  claim 1 , wherein the squamous cell lung carcinoma is stage I. 
     
     
         12 . The method of  claim 1 , wherein the squamous cell lung carcinoma is stage II. 
     
     
         13 . The method of  claim 1 , wherein the biological sample is obtained from a surgically resected tumor. 
     
     
         14 . The method of  claim 1 , wherein the predicting of clinical outcome provides a 5 year mortality risk assessment. 
     
     
         15 . A kit comprising reagents to amplify the CDKN2A gene comprising a loss of function mutation, or portion of the gene comprising the loss of function mutation. 
     
     
         16 . The kit of  claim 15 , wherein the reagents are PCR primer sets. 
     
     
         17 . A kit comprising reagents to reverse transcribe a RNA transcript encoded by the CDKN2A gene comprising a loss of function mutation. 
     
     
         18 . The kit of  claim 17 , wherein the reagents are RT-PCR sets. 
     
     
         19 . A method of determining a treatment plan for a human subject having squamous cell lung cancer, the method comprising:
 a) determining the presence of a loss of function mutation in the cyclin-dependent kinase inhibitor 2A (CDKN2A) gene or deletion of the gene in a biological sample comprising cancer cells obtained from said human subject;   b) determining the presence of an increase in the copy number of the G1/S-specific cyclin-D1 (CCND1) gene in a biological sample comprising cancer cells obtained from said human subject;   c) predicting the clinical outcome for said human subject,   wherein the presence of a loss of function mutation in the CDKN2A gene or deletion of the gene and increase in the copy number of the CCND1 gene positively correlates with an increased likelihood of a negative clinical outcome, and wherein the absence of a loss of function mutation in the CDKN2A gene or deletion of the gene or absence of an increase in the copy number of the CCND1 gene positively correlates with an increased likelihood of a positive clinical outcome;   d) determining a risk assessment for 5-year mortality based on the prediction; and   e) devising a treatment plan based on the risk assessment.   
     
     
         20 . A system for determining a treatment for a patient diagnosed with squamous cell lung carcinoma comprising:
 a) a processor;   b) a patient database that receives patient data from a treating provider, wherein the patient data includes:
 i) identification of a loss of function mutation in the cyclin-dependent kinase inhibitor 2A (CDKN2A) gene or deletion of the gene in a biological sample comprising cancer cells obtained from said patient; 
 ii) identification of an increase in the copy number of the G1/S-specific cyclin-D1 (CCND1) gene in a biological sample comprising cancer cells obtained from said patient; 
 iii) a correlation of the presence of a loss of function mutation in the CDKN2A gene or deletion of the gene with an increase in the copy number of the CCND1 gene, wherein the correlation is indicative of increased likelihood of a negative clinical outcome; and 
   c) a treatment protocol database that is populated with one or more treatment protocols that provide guidelines for treating patients with the correlation of b), iii); and   d) determining a treatment protocol.   
     
     
         21 . A method of identifying a human subject diagnosed with squamous cell lung carcinoma as a candidate for post-surgical adjuvant therapy, the method comprising:
 a) determining the presence of a loss of function mutation in the cyclin-dependent kinase inhibitor 2A (CDKN2A) gene or deletion of the gene in a biological sample comprising cancer cells obtained from said human subject; and   b) determining the presence of an increase in the copy number of the G1/S-specific cyclin-D1 (CCND1) gene in a biological sample comprising cancer cells obtained from said human subject;   
       wherein the presence of a loss of function mutation in the CDKN2A gene or deletion of the gene and increase in the copy number of the CCND1 gene positively correlates with an increased likelihood of a negative clinical outcome and identifies the human subject as a candidate for post-surgical adjuvant therapy. 
     
     
         22 . The method of  claim 21 , wherein the post-surgical adjuvant therapy is chemotherapy, radiation therapy, or a combination thereof. 
     
     
         23 . A method of treating squamous cell lung carcinoma in a patient comprising;
 a) obtaining a biological sample from the patient containing squamous cell lung carcinoma cells obtained from surgical resection of the cancer;   b) determining the presence of a loss of function mutation in the cyclin-dependent kinase inhibitor 2A (CDKN2A) gene or deletion of the gene in the biological sample;   c) determining the presence of an increase in the copy number of the G1/S-specific cyclin-D1 (CCND1) gene in the biological sample;   d) identifying a patient having squamous cell lung carcinoma cells comprising a loss of function mutation in the CDKN2A gene or deletion of the gene and increase in the copy number of the CCND1 gene; and   e) treating the patient with post-surgical adjuvant therapy.   
     
     
         24 . The method of  claim 23 , wherein the post-surgical adjuvant therapy is chemotherapy, radiation therapy, or a combination thereof.