Patent ID: 7378236

Claim:
A method of constructing a subarray of distinct gene sequences whose expression levels are specifically related to differences between test cells relative to control cells, comprising: (a) obtaining and preparing reporter-labeled copies of messenger nucleic acid from said control cells in a population of control individuals, and from said test cells in a population of test individuals having a shared phenotype that is not present in control individuals, wherein the reporter is compatible with a fluorescence detection system, (b) applying the reporter-labeled nucleic acids from test and control cells to a microarray of distinct gene sequences, under conditions effective to hybridize the reporter-labeled nucleic acids to complementary genes sequences on the microarray, wherein the microarray comprises at least 1000 distinct gene sequences per cm 2 and the distinct gene sequences at each position in the microarray correspond to a single nucleic acid molecule of interest and are at least 50 subunits in length, wherein the microarray has a hydrophobic surface formed by the support material or by a coating applied to the support, wherein each said position in the microarray is formed by applying a volume of aqueous reagent solution comprising a distinct gene sequence and wherein said hydrophobic surface prevents spreading of aqueous reagents applied to said surface via reagent bead formation, (c) comparing the pattern of reporter levels for nucleic acids from the test cells with that of nucleic acids from the control cells, (d) identifying those test-cell distinct gene sequences on the microarray which show a significant elevation or reduction in reporter levels, when compared with control reporter levels, and (e) forming a subarray of said test-cell distinct gene sequences.