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Understanding the significance of genetic mutations for the diagnosis and treatment of human disease requires the analysis of sequence regions within large sample populations. However, the current generation of target enrichment technologies focus on the capture of regions of interest for a single sample. Furthermore, most of the methods require significant amounts of sample and suffer from uneven representation of targeted regions. We have developed a novel microfluidic platform, the Access Array™ system, which enables the robust, simultaneous amplification of 48 PCR products from 48 samples using only 50ng input DNA per sample. The Access Array system is an open platform, and can be used to generate amplicons of varying sizes, up to 5Kb in length, using primers designed and validated for plate-based PCR. Additionally, PCR reactions can be multiplexed within Access Array chips, providing flexibility in the number of amplicons used for enrichment. PCR products generated on the Access Array system can be used for sequencing on all next-generation sequencing platforms, including 454 and Illumina GAII. We have successfully demonstrated the enrichment of 12.5 Mb sequence per chip (240Kb per sample) using long-range PCR, and will also present data on the use of 10-plex PCR reactions (480 amplicons per sample) to generate sequencer-ready libraries for 48 samples in parallel.