High-level multiplex amplification

A method for amplifying one or more target nucleic acids, the method comprising:

• contacting sample nucleic acids with a forward primer and a reverse primer for each target nucleic acid, wherein each primer comprises a target-specific portion, a common sequence 5′ of the target-specific portion, a DNA sequencing primer binding site 5′ of the common sequence, and a first or second nucleotide tag 5′ of the DNA sequencing primer binding site, wherein the first and second nucleotide tags in the forward and reverse primers are different, wherein the common sequence is at least 8 nucleotides in length, and wherein the forward primer or the reverse primer additionally comprises a first flow cell attachment site 5′ of the first nucleotide tag;
• and
• amplifying the target nucleic acid(s) to produce at least one target amplicon wherein a target nucleotide sequence is flanked by the common sequence on one end and its reverse complement on the other end, whereby a single strand of the target amplicon can form a stem loop structure, wherein the amplification is carried out using a third primer, wherein the third primer comprises a portion specific for the second nucleotide tag, a barcode nucleotide sequence 5′ of the tag-specific portion, and a second flow cell attachment site 5′ of the barcode nucleotide sequence, wherein the amplification produces target amplicons comprising the structure:
• 5′-first flow cell attachment site-first nucleotide tag-first DNA sequencing primer binding site-common sequence-target nucleotide sequence-reverse complement of common sequence-second DNA sequencing primer binding site-second nucleotide tag-barcode nucleotide sequence-second flow cell attachment site-3′.