Methods for detecting and identifying genomic nucleic acids

A method of multiplexing the identification of a plurality of target genomic nucleic acid sequences within genomic DNA comprising:

• hybridizing the genomic DNA with a plurality of probe sets corresponding to the plurality of target genomic nucleic acid sequences, wherein each probe set has a unique associated barcode sequence for identification of the corresponding target genomic nucleic acid sequence, wherein each probe of each probe set includes:
• (1) a complementary sequence complementary to a first strand or a second strand of the target genomic nucleic acid sequence,
• (2) the unique associated barcode sequence or a portion of the associated barcode sequence, and
• (3) one or more additional barcode sequences;
• sequencing the unique associated barcode sequence from probes hybridized to the plurality of target genomic nucleic acid sequence using a fluorescence-based sequencing method,
• identifying the target genomic nucleic acid sequence by the sequenced unique barcode sequence.