Here we present an adaptation of NimbleGen 2.1M-probe array sequence capture for 
whole exome sequencing using the Illumina Genome Analyzer (GA) platform. The 
protocol involves two-stage library construction. The specificity of exome 
enrichment was approximately 80% with 95.6% even coverage of the 34 Mb target 
region at an average sequencing depth of 33-fold. Comparison of our results with 
whole genome shot-gun resequencing results showed that the exome SNP calls gave 
only 0.97% false positive and 6.27% false negative variants. Our protocol is 
also well suited for use with whole genome amplified DNA. The results presented 
here indicate that there is a promising future for large-scale population 
genomics and medical studies using a whole exome sequencing approach.