Methodology article
Solution-based targeted genomic enrichment for precious DNA samples
1 Department of Otolaryngology—Head & Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
2 Department of Molecular Physiology & Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
3 Interdepartmental PhD Program in Genetics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
BMC Biotechnology 2012, 12:20 doi:10.1186/1472-6750-12-20
Published: 4 May 2012Abstract
Background
Solution-based targeted genomic enrichment (TGE) protocols permit selective sequencing of genomic regions of interest on a massively parallel scale. These protocols could be improved by: 1) modifying or eliminating time consuming steps; 2) increasing yield to reduce input DNA and excessive PCR cycling; and 3) enhancing reproducible.
Results
We developed a solution-based TGE method for downstream Illumina sequencing in a non-automated workflow, adding standard Illumina barcode indexes during the post-hybridization amplification to allow for sample pooling prior to sequencing. The method utilizes Agilent SureSelect baits, primers and hybridization reagents for the capture, off-the-shelf reagents for the library preparation steps, and adaptor oligonucleotides for Illumina paired-end sequencing purchased directly from an oligonucleotide manufacturing company.
Conclusions
This solution-based TGE method for Illumina sequencing is optimized for small- or medium-sized laboratories and addresses the weaknesses of standard protocols by reducing the amount of input DNA required, increasing capture yield, optimizing efficiency, and improving reproducibility.
