Methods and compositions for multiplex pcr

A method of amplifying a plurality of different target nucleic acid sequences comprising:

• a) contacting a portion of the plurality of different target sequences with a plurality of target-specific primers and a polymerase under amplification conditions,
• b) producing a plurality of different amplified target sequences by extending one or more of the plurality of target-specific primers, wherein a plurality of the target-specific primers include a cleavable group and at least one of the plurality of the amplified target sequences includes a primer-derived sequence containing the cleavable group;
• c) cleaving the cleavable group of the primer-derived sequence of the at least one amplified target sequence,
• d) forming a cleaved end of the at least one amplified target sequence;
• and
• e) ligating at least one adapter to the cleaved end of the at least one amplified target sequence, wherein the at least one adapter is not complementary to 20 contiguous nucleotides of the cleaved end of the at least one amplified target sequence.