Accurate variant detection across unamplified and whole genome amplified DNA using targeted next generation sequencing workflow

Many hypothesis driven studies require the ability to comprehensively and efficiently target specific regions of the genome to detect sequence variations. Often, sample availability is limited requiring the use of whole genome amplification (WGA). We evaluated a high-throughput microdroplet-based PCR approach in combination with next generation sequencing to target 384 discrete exons involved in cancer. In our evaluation, we compared the performance of six un-amplified HapMap gDNA samples from two trios. Three of these samples were also evaluated as WGA samples. We tested several multiplexing strategies at different stages of the sequencing workflow.