Methods for identifying cross-contamination among sequential nucleic acid amplification reactions

A method of analyzing nucleic acid with a group of primer sets, the method comprising sequentially amplifying template nucleic acid with each primer set within the group, wherein:

• the group of primer sets comprises two or more primer sets;
• each primer set comprises set-identity primer pairs;
• each set-identity primer pair consists of set-identity primers consisting of a first set-identity primer and a second set-identity primer;
• each set-identity primer comprises a template-annealing segment on a 3′ end of the set-identity primer;
• each set-identity primer comprises a set-identity segment on a 5′ end of the set-identity primer;
• a combination of the set-identity segment on the first set-identity primer and the set-identity segment on the second set-identity primer in each set-identity primer pair defines a set-identity signature;
• and
• each of the set-identity signatures is defined only by set-identity primer pairs in one and only one of the primer sets within the group.