Stanford Human OligoExome Resource

Stanford Human OligoExome is a scalable oligonucleotide management system for genomic analysis and high-throughput resequencing.
This set of capture oligonucleotides will cover the CCDS exon space and a high proportion of related regulatory regions from the human genome.

The Stanford Human OligoExome management system has been made publicly available at

These capture oligonucleotides utilize a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using an in-solution method. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets.


  • Georges Natsoulis
  • Nancy Zhang
  • John M. Bell
  • Hua Xu
  • Jason D. Buenrostro
  • Heather Ordonez
  • Sue Grimes
  • Michael Jensen
  • Daniel E. Newburger
  • Jacob M. Zahn
  • Jochen Kumm
  • Hanlee P. Ji


Funded by NHGRI / NI

Technology Approach

For the selective circularization capture assay, genomic DNA is initially subject to restriction enzyme digestion in separate tubes. Pooled capture oligonucleotides with end regions homologous to the genomic targets (two capture arms) are then hybridized to the restriction digested DNA, forcing the genomic DNA of the target into a circular conformation.Addition of a second backbone vector with universal homology to the interior of all oligonucleotides completes the double-stranded DNA circle, after which blunt-end ligation takes place. Uracil-DNA excision mix is added to digest the selector oligonucleotides and linearize the DNA containing the targeted genomic regions. Universal PCR primers specific to the vector oligonucleotides are added and PCR amplification of the captured genomic region is carried out and then sequenced using next-generation DNA sequencers. Two different molecular mechanisms mediate the target-specific circularization. In the first case, the oligonucleotide’s capture arms 1 and 2 recognize the complementary termini of the genomic DNA fragment created by both restriction sites. In the second case, capture arm 1 of the target complementary end-sequence recognizes one fragment terminus and capture arm 2 specifically anneals to the target sequence anywhere within the restriction enzyme fragment. For capture arm 2, the oligonucleotide -genomic DNA hybrid forms a branched structure, referred to as a flap in the absence of a restriction site. This specific DNA flap structure is cleaved by the Taq polymerase, forming ends suitable for ligation of the universal vector and complete genomic circularization as in the first case. This second case provides substantial design flexibility in regards to place capture sequences for any given target.

The website at is provided by the Ji Lab and the Genome Technology Center at Stanford University, and funded by National Institute of Human Genome Research ( NHGRI) / National Institutes of Health.
The information contained in this website is for general information purposes only. While we endeavor to keep the information up to date and correct, we make no representations or warranties of any kind, express or implied, about the completeness, accuracy, reliability, suitability or availability with respect to the website or the information, or related graphics contained on the website for any purpose. Any reliance you place on such information is therefore strictly at your own risk. In no event will we be liable for any loss or damage including without limitation, indirect or consequential loss or damage, or any loss or damage whatsoever arising from loss of data or profits arising out of, or in connection with, the use of this website. Every effort is made to keep the website up and running smoothly. However, we take no responsibility for, and will not be liable for, the website being temporarily unavailable due to technical issues beyond our control.