exomeseq_comparison
Performance comparison of exome DNA sequencing technologies
The same genetic sample was exome enriched using each of three major commercial exome-seq platforms: Agilent SureSelect Human All Exon (50M), Nimblegen SeqCap EZ-Exome Library SR v2.0 (44M), and Illumina TruSeq Exome (62M). These exome enriched samples were then sequenced with the Illumina HiSeq 2000 on one lane each. In addition, seven lanes of whole genome sequencing was performed on the same sample for the sake of comparison.
Whole exome sequencing (exome-seq) by high-throughput sequencing of target-enriched genomic DNA has become increasingly common in basic and translational research as a means of interrogating the interpretable part of the human genome at relatively low cost. Using the same human sample, we performed an unbiased comparison of three major commercial exome-seq platforms from Agilent, Illumina and Nimblegen. These platforms differ significantly in their probe design, targeted genomic regions, on-target bait density and biochemical approach. Platforms with high-density overlapping baits have increased enrichment efficiency and variant detection sensitivity, but cover fewer genomic regions than those with lower density probes. Moreover, the different platforms target distinct exomic features. Comparison to whole genome sequencing demonstrates particular advantages of exome-seq and recommends sequencing levels for each platform. Overall, this study has significant general implications for targeted genomic sequencing and especially for the analysis of human disease and variation.