Diagnostic tests using gene expression ratios

Abstract

The invention provides methods for diagnosing biological states or conditions based on ratios of gene expression data from cell or tissue samples, such as cancer cell or tissue samples. The invention also provides sets of genes that are expressed differentially in normal and cancer lung cells and tissues. These sets of genes can be used to discriminate between normal and malignant cells or tissues, and between classes of malignant cells or tissues. Accordingly, diagnostic assays for classification of tumors, prediction of tumor outcome, selecting and monitoring treatment regimens and monitoring tumor progression/regression also are provided.

We claim: 
     
         1 .- 69 . (canceled) 
     
     
         70 . A lung cancer diagnostic system comprising
 a measurement device that measures gene expression level data of a set of two or more genes disclosed in Table 1, 4, 5, 6, or 7, wherein the set comprises at least one upregulated gene that is expressed in greater amounts in a first type of lung cell or tissue than in a second type of lung cell or tissue and at least one downregulated gene that is expressed in lesser amounts in the first type of lung cell or tissue than in the second type of lung cell or tissue,   a data transformation device the acquires the gene expression data from the measurement device and performs data transformation to calculate a ratio of the gene expression levels of the upregulated and downregulated genes.   
     
     
         71 . The lung cancer diagnostic system of  claim 70 , wherein data transformation device selects gene expression data of a selected set of genes from the measurement device for calculating the ratio of the selected set of genes, wherein the ratio calculated from the gene expression data of the selected set of genes is diagnostic for a selected lung cancer. 
     
     
         72 . The lung cancer diagnostic system of  claim 70 , further comprising a user interface output device to output the ratio to a user. 
     
     
         73 . The lung cancer diagnostic system of  claim 72 , further comprising a database of ratios of gene expression that are diagnostic for lung cancers, and a comparison device that compares the ratio calculated from the measured gene expression to the diagnostic ratios stored in the database and outputs the comparison to the user interface output device. 
     
     
         74 . The lung cancer diagnostic system of  claim 72 , further comprising a database of treatment information for specific lung cancers, wherein the comparison device identifies treatment information in the database for the specific cancer for which the diagnostic ratio matches the calculated ratio, and wherein the comparison outputs the treatment information to the user interface output device. 
     
     
         75 .- 123 . (canceled)