Methods for high level multiplexed polymerase chain reactions and homogeneous mass extension reactions

A method for performing multiplexed amplification of target nucleic acid, comprising:

• (a) forming a mixture containing 7 or more pairs of primary and secondary primers and one or more target nucleic acids, wherein each primer pair amplifies a nucleic acid-target region of a target nucleic acid and a sequence tag is attached to one or both of the primary and secondary primers of one or more primer pairs;
• and
• (b) amplifying a plurality of nucleic acid-target regions of (a) under amplification conditions, whereby at least 60% of the 7 or more nucleic acid-target regions attempted are amplified by the 7 or more amplification primer pairs to produce an amplified mixture of nucleic acid-target regions, wherein the amplification conditions comprise a multiplicity of thermocycles and amplification reactants comprising a polymerase, dNTPs and MgCl2, wherein the ratio of the concentration of MgCl2 to the concentration of each one of the dNTPs is less than or equal to 10:1 and only a single primer pair is used to amplify each particular nucleic acid target-region.