Comparative genomic hybridization on encoded multiplex particles

A method of evaluating genomic DNA using a single detectable moiety, the method comprising:

• providing at least one reference DNA sample and a plurality of genomic DNA samples, wherein each sample is labeled with the same detectable moiety;
• providing a particle mixture, the mixture comprising particles from different particle sets, wherein each particle set contains numerous encoded particles and a nucleic acid hybridization probe for a particular genomic locus, such that the mixture collectively includes probes for a plurality of different genomic loci;
• contacting each of the samples to a portion of the particle mixture under hybridization conditions, wherein each sample is contacted to the particle mixture in a separate vessel;
• and
• evaluating hybridization of each sample to particles in the respective portion of the mixture by monitoring the detectable moiety, wherein signals from the monitoring are indicative of the number of copies of each interrogated genomic locus.

A method of evaluating nucleic acid using a single detectable label, the method comprising:

• providing at least one reference nucleic acid sample that is labeled with a first indirect label and a plurality of test nucleic acid samples, wherein each test sample is labeled with a second indirect label;
• providing a particle mixture, the mixture comprising particles from different particle sets, wherein each particle set contains numerous encoded particles and a nucleic acid hybridization probe for a particular target, such that the mixture collectively includes probes for a plurality of different targets;
• contacting each of the test samples and the reference sample to a portion of the particle mixture under hybridization conditions, wherein each test sample is contacted to the particle mixture and the reference sample in a separate vessel;
• binding, to a first portion of each test sample, a first moiety that comprises the single label and an agent that binds the first indirect label;
• binding, to a second portion of each test sample, a second moiety that comprises the single label and an agent that binds the second indirect label;
• evaluating each test sample by monitoring the single label in the first portion of the sample and by monitoring the single label in the second portion of the sample, wherein signals from the monitoring are indicative of the number of copies of each target;
• and
• for each test sample, comparing signals from the single label in the first portion to signals from the single label in the second portion, to obtain an indication of the number of copies of a probe in the test sample relative to the reference sample.