Test kits

Abstract

This invention relates to prognostic signatures, and compositions and methods for determining the prognosis of cancer in a patient, particularly for colorectal cancer. Specifically, this invention relates to the use of genetic markers for the prediction of the prognosis of cancer, such as colorectal cancer, based on signatures of genetic markers. In various aspects, the invention relates to a method of predicting the likelihood of long-term survival of a cancer patient, a method of determining a treatment regime for a cancer patient, a method of preparing a treatment modality for a cancer patient, among other methods as well as kits and devices for carrying out these methods.

What is claimed is: 
     
         1 . A prognostic signature for determining progression of CRC, comprising two or more genes selected from Tables 1 and 2. 
     
     
         2 . The signature of  claim 1 , selected from any one of the signatures in any one of Tables 3, 4 or Table 9. 
     
     
         3 . A device for determining prognosis of CRC, comprising:
 a substrate having one or more locations thereon, each location having two or more oligonucleotides thereon, each oligonucleotide selected from the group of genes from Tables 1 and 2.   
     
     
         4 . The device of  claim 3 , wherein said the two or more oligonucleotides are a prognostic signature selected from in any one of Tables 3, 4 or Table 9. 
     
     
         5 . A method for determining the prognosis of CRC in a patient, comprising the steps of;
 (i) determining the expression level of a prognostic signature comprising two or more genes from Tables 1 and 2 in CRC tumour sample from the patient,   (ii) applying a predictive model, established by applying a predictive method to expressions levels of the predictive signature in recurrent and non-recurrent tumour samples,   (iii) establishing a prognosis.   
     
     
         6 . The method of  claim 5 , wherein the signature is selected from any one of Tables 3, 4 or Table 9. 
     
     
         7 . The method of  claim 5 , wherein said predictive method is selected from the group consisting of linear models, support vector machines, neural networks, classification and regression trees, ensemble learning methods, discriminant analysis, nearest neighbor method, bayesian networks, independent components analysis. 
     
     
         8 . The method of any one of  claims 5  to  7 , wherein the step of determining the expression level of a prognostic signature is carried out by detecting the expression level of mRNA of each gene. 
     
     
         9 . The method of any one of  claims 5  to  7 , wherein the step of determining the expression level of a prognostic signature is carried out by detecting the expression level of cDNA of each gene. 
     
     
         10 . The method of  claim 9 , wherein the step of determining the expression level of a prognostic signature is carried out using a nucleotide complementary to at least a portion of said cDNA. 
     
     
         11 . The method of  claim 8 , wherein the step of determining the expression level of a prognostic signature is carried out using qPCR method using a forward primer and a reverse primer. 
     
     
         12 . The method of  claim 8 , wherein the step of determining the expression level of a prognostic signature is carried out using a device according to  claim 3  or  claim 4 . 
     
     
         13 . The method of any one of  claims 5  to  7 , wherein the step of determining the expression level of a prognostic signature is carried out by detecting the expression level of the protein of each marker. 
     
     
         14 . The method of any one of  claims 5  to  7 , wherein the step of determining the expression level of a prognostic signature is carried out by detecting the expression level of the peptide of each marker. 
     
     
         15 . The method of  claim 12  or  claim 13 , wherein said step of detecting is carried out using an antibody directed against each marker. 
     
     
         16 . The method of any one of  claims 12  to  14 , wherein said step of detecting is carried out using a sandwich-type immunoassay method. 
     
     
         17 . The method of any one of  claims 12  to  15 , wherein said antibody is a monoclonal antibody. 
     
     
         18 . The method of any one of  claims 12  to  15 , wherein said antibody is a polyclonal antiserum.