Complementing Next Generation Sequencing Technologies With Agilent’s SureSelect DNA Capture Array

Massively parallel DNA sequencing technologies are of pivotal importance in genome biology and medicine, as they can potentially enable comprehensive and systematic evaluation of genetic variation. Currently, these sequencing technologies are geared toward sequencing whole genomes. A broader adoption of these technologies requires a more cost-effective method with higher throughput and greater versatility than PCR—a method such as target enrichment, the targeted resequencing of multiple discrete genomic regions of interest. To validate the use of Agilent DNA microarrays for target enrichment, Agilent collaborated with the laboratory of Dr. Greg Hannon (Cold Spring Harbor Laboratory) to capture exonic regions relevant to a breast cancer sequencing study. We targeted 0.025% of the human genome, using an Agilent 244K array of 60-mer probes to capture approximately 1,287 discrete genomic regions.
The captured DNA was then released and sequenced. Various hybridization conditions were tested, ultimately obtaining a 2,700-fold enrichment of sequencing reads within targeted regions. The system was seen to be effective, with sequencing reads covering over 99.8% of the targeted regions and 98% of the targeted bases with at least one read and with a normalized average per-base read depth of 27 per million 32-base reads. These results confi rm that Agilent DNA microarrays can provide a rapid and effective solution for targeted sequencing of genomic regions of interest.