Methods and compositions are provided that are useful for detecting and reporting a plurality of different target
polynucleotide sequences in a sample, such as polynucleotides corresponding to a plurality of different genes expressed by a
cell or cells. In particular, the invention provides methods for screening a plurality of candidate
polynucleotide probes to evaluate both the sensitivity and the specificity with which each candidate probe hybridizes to a target polynucleoide sequence. Candidate
polynucleotide probes can then be ranked according to both their sensitivity and specificity, and probes that have optimal sensitivity and specificity for a target polynucleotide sequence can be selected. In one embodiment, polynucleotide probes can be selected according to the methods described herein to prepare “screening chips” wherein a large number of target polynucleotide sequences are detected using a single
microarray have a few (e.g., 1–5) probes for each target polynucleotide sequence. In a particularly preferred embodiment, the invention provides a screening
chip that can detect genetic transcripts from the entire
genome of an
organism. In an alternative embodiment, polynucleotide probes can be selected according to the methods described herein to prepare “signature chips” to more accurately detect certain selected “signature genes” using several polynucleotide probes (e.g., 10–20) for each signature
gene. The invention additionally provides microarrays containing polynucleotide probes for a large number of genes expressed by a
cell or
organism. Further, methods for detecting a plurality of polynucleotide molecules, including a large number of genes expressed by a
cell or
organism, are also provided.