INTRODUCTIONPCR-based whole-genome amplification (WGA) has the goal of generating microgram quantities of genome-representative DNA from picogram or nanogram amounts of starting material. This amplification should introduce little, or ideally no, representational bias. In contrast to other techniques for WGA, PCR-based methods are generally less affected by DNA quality and are more applicable to DNA extracted from various sources (fixed and fresh tissues). GenomePlex WGA, described in this protocol, is a proprietary amplification technology based on nonenzymatic random fragmentation of genomic DNA. The protocol involves conversion of the genome into an in vitro molecular library of DNA fragments, followed by incubation at various temperatures to add adaptor sequences with specific PCR priming sites to both ends of every fragment. The fragment library can then be amplified several 1000-fold to generate milligram quantities of DNA starting with as little as 10-100 ng.