Patent Document ID: 8392127
Application ID: 12933936
Patent Flag: 1

Claim One:
1. A method for identifying a subject harboring a tumor who is predicted to respond to an agent that modulates a PI3K growth factor signaling pathway, said method comprising: (a) isolating a tumor cell sample from a subject; (b) calculating a signature score which represents the regulation status of PI3K growth factor pathway signaling of the tumor by a method comprising: (i) measuring the a) expression level of each of a first plurality of genes and each of a second plurality of genes in an isolated tumor cell sample, wherein first plurality of genes has at least 3 or more of the genes for which biomarkers are listed in Table 5a, wherein the at least 3 genes include TRIP13, TOMM40 and CTPS, and said second plurality of genes has at least 3 or more of the genes for which biomarkers are listed in Table 5b, wherein the at least 3 genes include MST1, CTDSP2 and FANK1; (ii) measuring the expression level of each of said first plurality of genes and each of said second plurality of genes in a control cell sample; (iii) calculating the differential expression values of each of said first plurality of genes in (i) relative to each of said first plurality of genes in (ii), and calculating the mean differential expression value for said first plurality of genes; (iv) calculating the differential expression value of each of said second plurality of genes in (i) relative to each of said second plurality of genes in (ii), and calculating the mean differential expression value for said second plurality of genes; and, (v) calculating the signature score by subtracting said mean differential expression value of said second plurality of genes from said mean differential expression value of said first plurality of genes; and (c) classifying said tumor as having a deregulated growth factor signaling pathway if said obtained signature score is above a predetermined threshold, and ii) if said signature score is statistically significant; wherein a subject harboring a tumor classified as having a deregulated growth factor signaling pathway is identified as a subject who is predicted to respond to an agent that modulates a PI3K growth factor signaling pathway, and wherein steps (b) and (c) are displayed or outputted to a user interface device, a computer readable storage medium, or a local or remote computer system.