Multiplexed pcr assay for high throughput genotyping

A method for genotyping one or more target loci in a nucleic acid sample, comprising the steps of:

• a) providing a nucleic acid sample;
• b) adding a first set of primers to said sample to form a first amplification mixture, wherein the primers in said first set comprises a primer tail sequence and is capable of hybridizing to a target sequence within or adjacent to one or more of said target loci;
• c) performing a first amplification reaction on said first amplification mixture to produce a first library of amplicons, wherein said amplicons comprise said primer tail sequence;
• d) adding a second set of primers to said first library to form a second amplification mixture, wherein the primers in the second set are capable of hybridizing to said primer tail sequence;
• and
• e) performing a second amplification reaction on said second amplification mixture to generate a second library of amplicons;
• wherein for at least 90% of said target loci, the number of amplicons in said second library derived from each of said target loci deviates from the average number of amplicons for all target loci by less than one order of magnitude (+ or −10×).