Method and apparatus for determining a probability of colorectal cancer in a subject

Abstract

A method of determining a probability that a human test subject has colorectal cancer as opposed to not having colorectal cancer is disclosed. The method comprises, for each gene of a set of one or more genes selected from the group consisting of ANXA3, CLEC4D, IL2RB, LMNB1, PRRG4, TNFAIP6 and VNN1: determining a level of RNA encoded by the gene in blood of the test subject, thereby generating test data; providing positive control data representing levels of RNA encoded by the gene in blood of human control subjects having colorectal cancer, and providing negative control data representing levels of RNA encoded by the gene in blood of human control subjects not having colorectal cancer; and determining a probability that the test data corresponds to the positive control data and not to the negative control data, where the probability that the test data corresponds to the positive control data and not to the negative control data represents the probability that the test subject has colorectal cancer as opposed to not having colorectal cancer.

What is claimed is: 
     
         1 . A kit comprising packaging and containing, for each gene of a set of two or more genes selected from the group consisting of ACTB, ANXA3, CLEC4D, IL2RB, LMNB1, PRRG4, TNFAIP6 and VNN1, a primer set capable of generating an amplification product of DNA complementary to RNA encoded, in a human subject, only by the gene. 
     
     
         2 . The kit of  claim 1 , further containing two or more components selected from the group consisting of a thermostable polymerase, a reverse transcriptase, deoxynucleotide triphosphates, nucleotide triphosphates and enzyme buffer. 
     
     
         3 . The kit of  claim 1 , further containing at least one labeled probe capable of selectively hybridizing to either a sense or an antisense strand of the amplification product. 
     
     
         4 . The kit of  claim 1 , further containing a computer-readable medium having instructions stored thereon that are operable when executed by a computer for applying a mathematical model to test data representing a level of RNA encoded by the gene in blood of a human test subject, wherein the mathematical model is derived from positive control data representing levels of RNA encoded by the gene in blood of human control subjects having colorectal cancer, and from negative control data representing levels of RNA encoded by the gene in blood of human control subjects not having colorectal cancer, wherein the mathematical model is for determining a probability that data representing a level of RNA encoded by the gene corresponds to the positive control data and not to the negative control data, and wherein the probability that the test data corresponds to the positive control data and not to the negative control data represents the probability that the test subject has colorectal cancer as opposed to not having colorectal cancer. 
     
     
         5 . The kit of  claim 1 , further containing a computer-readable medium having instructions stored thereon that are operable when executed by a computer for applying, to test data representing a level of RNA encoded by the gene in blood of a human test subject and to negative control data representing a level of RNA encoded by the gene in blood of human control subjects not having colorectal cancer, a mathematical formula for generating a value indicating, for ANXA3, CLEC4D, LMNB1, PRRG4, TNFAIP6 and VNN1, whether the level of RNA encoded by the gene in blood of the test subject is higher than the level of RNA encoded by the gene in blood of human control subjects not having colorectal cancer, and, for IL2RB, whether the level of RNA encoded by the gene in blood of the test subject is lower than the level of RNA encoded by the gene in blood of human control subjects not having colorectal cancer, wherein, for ANXA3, CLEC4D, LMNB1, PRRG4, TNFAIP6 and VNN1, an indication by the value that the level of RNA encoded by the gene in blood of the test subject is higher than the level of RNA encoded by the gene in blood of human control subjects not having colorectal cancer classifies the test subject as more likely to have colorectal cancer than to not have colorectal cancer, and wherein, for IL2RB, an indication by the value that the level of RNA encoded by the gene in blood of the test subject is lower than the level of RNA encoded by the gene in blood of human control subjects not having colorectal cancer classifies the test subject as more likely to have colorectal cancer than to not have colorectal cancer. 
     
     
         6 . The primer set of  claim 1 , wherein the set of genes consists of IL2RB and PRRG4. 
     
     
         7 . The primer set of  claim 1 , wherein the set of genes consists of ANXA3, CLEC4D, IL2RB, LMNB1, PRRG4, TNFAIP6 and VNN1. 
     
     
         8 . A method of determining a probability that a human test subject has colorectal cancer as opposed to not having colorectal cancer, the method comprising, for each gene of a set of one or more genes selected from the group consisting of ANXA3, CLEC4D, IL2RB, LMNB1, PRRG4, TNFAIP6 and VNN1:
 (a) determining a level of RNA encoded by the gene in blood of the test subject, thereby generating test data;   (b) providing positive control data representing levels of RNA encoded by the gene in blood of human control subjects having colorectal cancer, and providing negative control data representing levels of RNA encoded by the gene in blood of human control subjects not having colorectal cancer; and   (c) determining a probability that the test data corresponds to the positive control data and not to the negative control data,   
       wherein the probability that the test data corresponds to the positive control data and not to the negative control data represents the probability that the test subject has colorectal cancer as opposed to not having colorectal cancer. 
     
     
         9 . The method of  claim 8 , further comprising determining levels of RNA encoded by the gene in blood of a population of human subjects having colorectal cancer, thereby providing the positive control data representing the levels of RNA encoded by the gene in blood of human control subjects having colorectal cancer, and determining levels of RNA encoded by the gene in blood of a population of human subjects not having colorectal cancer, thereby providing the negative control data representing the levels of RNA encoded by the gene in blood of human control subjects not having colorectal cancer. 
     
     
         10 . The method of  claim 8 , wherein the determining of the probability that the test data corresponds to the positive control data and not to the negative control data is effected by applying to the test data a mathematical model derived from the positive control data and from the negative control data, and wherein the mathematical model is for determining the probability that data representing a level of RNA encoded by the gene corresponds to the positive control data and not to the negative control data. 
     
     
         11 . A method of classifying a human test subject as more likely to have colorectal cancer than to not have colorectal cancer, the method comprising, for each gene of a set of one or more genes selected from the group consisting of ANXA3, CLEC4D, IL2RB, LMNB1, PRRG4, TNFAIP6 and VNN1:
 (a) determining a level of RNA encoded by a CLEC4D gene in blood of the test subject, thereby generating test data;   (b) providing negative control data representing a level of RNA encoded by the gene in blood of human control subjects not having colorectal cancer; and   (c) applying to the test data and to the negative control data a mathematical formula for generating a value indicating whether the level of RNA encoded by the gene in blood of the test subject is higher than the level of RNA encoded by the gene in blood of human control subjects not having colorectal cancer,   
       wherein an indication by the value that the level of RNA encoded by the gene in blood of the test subject is higher than the level of RNA encoded by the gene in blood of human control subjects not having colorectal cancer classifies the test subject as more likely to have colorectal cancer than to not have colorectal cancer. 
     
     
         12 . The method of  claim 11 , further comprising determining levels of RNA encoded by the gene in blood of a population of human subjects not having colorectal cancer, thereby providing the negative control data representing the levels of RNA encoded by the gene in blood of human control subjects not having colorectal cancer. 
     
     
         13 . The method of  claim 8 , wherein the set of genes consists of IL2RB and PRRG4. 
     
     
         14 . The method of  claim 8 , wherein the set of genes consists of ANXA3, CLEC4D, IL2RB, LMNB1, PRRG4, TNFAIP6 and VNN1. 
     
     
         15 . The method of  claim 8 , wherein the determining of the level of RNA encoded by the gene in blood of the test subject is effected by determining the level of RNA encoded by the gene in a blood sample isolated from the test subject. 
     
     
         16 . The method of  claim 8 , wherein the level of RNA encoded by the gene in blood of the test subject is determined as a ratio to a level of RNA encoded by IL2RB in blood of the test subject. 
     
     
         17 . The method of  claim 11 , wherein the set of genes consists of IL2RB and PRRG4. 
     
     
         18 . The method of  claim 11 , wherein the set of genes consists of ANXA3, CLEC4D, IL2RB, LMNB1, PRRG4, TNFAIP6 and VNN1. 
     
     
         19 . The method of  claim 11 , wherein the determining of the level of RNA encoded by the gene in blood of the test subject is effected by determining the level of RNA encoded by the gene in a blood sample isolated from the test subject. 
     
     
         20 . The method of  claim 11 , wherein the level of RNA encoded by the gene in blood of the test subject is determined as a ratio to a level of RNA encoded by IL2RB in blood of the test subject.