Methods and compositions for analyzing nucleic acids

A method for analyzing nucleic acids in a plurality of samples, which method comprises:

• a) attaching each of target nucleic acids, if there is one in a sample, in a plurality of samples with a signature label separately whereby said target nucleic acid in each of said plurality of samples is attached to a detectably different signature label;
• b) pooling said labeled target nucleic acids in different samples into a single mixture;
• c) hybridizing each of said labeled target nucleic acids in said single mixture with a probe that is hybridizable to each of said labeled target nucleic acids in a single reaction to form a plurality of target nucleic acid/probe duplexes;
• and
• d) determining presence or absence, amount and/or identity of said target nucleic acid in each of said plurality of samples by analyzing presence or absence, amount and/or identity of said signature label in each of said target nucleic acid/probe duplexes.