Targeted Sequencing - Capture Oligos

Customer Publications -  Targeted Sequencing Applications

Recently, researchers from the National Human Genome Research Institute conducted a systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing¹. They report the testing, optimizing, and rigorous comparing of three genomic enrichment methods: Solution Hybrid Selection, Microarray-based Genomic Selection, and Molecular Inversion Probes (MIP). Oligonucleotides for MIP were obtained from both Agilent and LC Sciences and tested as separate pools. HapMap DNA samples were used for testing and they found that that all three genomic enrichment methods are highly accurate (>99.998%) and practical, with sensitivities comparable to that of 30-fold coverage whole-genome shotgun data.

1. Teer JK, Bonnycastle LL, Chines PS, Hansen NF, Aoyama N, Swift AJ, Abaan HO, Albert TJ; NISC Comparative Sequencing Program, Margulies EH, Green ED, Collins FS, Mullikin JC, Biesecker LG. (2010) Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res 20(10), 1420-31. [abstract]

Customer Publications -  Other Capture Oligo Applications

1. DNA Capture for Methylation Analysis
   Nautiyal S, Carlton VE, Lu Y, Ireland JS, Flaucher D, Moorhead M, Gray JW, Spellman P, Mindrinos M, Berg P, Faham M. High-throughput method for analyzing methylation of CpGs in targeted genomic regions. Proc Natl Acad Sci 107(28), 12587-92. [abstract]
2. DNA Capture  for Synthetic Gene Applications
   Tian, J., Gong, H., Sheng, N., Zhou, X., Gulari, E., Gao, X., and Church, G. (2004) Accurate multiplex gene synthesis from programmable DNA chips. Nature 432, 1050-54. [abstract]
3. ncRNA Capture for Functional Discoveries
   Vagin VV, Sigova A, Li C, Seitz H, Gvozdev V, Zamore PD. (2006) A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313(5785), 320-24.  [abstract]
4. Protein Capture for Studies of Transcription Activation
   Anbanandam A, Albarado DC, Nguyen CT, Halder G, Gao X, Veeraraghavan S. 2006) Insights into transcription enhancer factor 1 (TEF-1) activity from the solution structure of the TEA domain. Proc Natl Acad Sci USA 103(46), 17225-30. [abstract]

Review Publications -  Microarray Synthesized Oligos for Sequence Capture.

1. Zhang J, Chiodini R, Badr A, Zhang G. (2011) The impact of next-generation sequencing on genomics. J Genet Genomics 38(3), 95-109. [abstract]
2. Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ. (2010) Target-enrichment strategies for next-generation sequencing. Nat Methods 7(2), 111-8. [abstract]
3. Baker M. (2011) Microarrays, megasynthesis. Nat Methods 8(6), 457-60. [article]
4. Biocompare – Feature Article: Sequence Capture. [article]

OligoMix^® Synthesis Technology Publications

1. Zhou, X., Cai, S., Hong, A., Yu, P., Sheng, N., Srivannavit, O., Yong, Q., Muranjan, S., Rouillard, J. M., Xia, Y., Zhang, X., Xiang, Q., Ganesh, R., Zhu, Q., Makejko, A., Gulari, E., and Gao, X. (2004) Microfluidic picoarray synthesis of oligodeoxynucleotides and simultaneously assembling of multiple DNA sequences. Nucleic Acids Res 32, 5409-5417.  [ abstract]  [ article]
2. Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596.  [ abstract]
3. Srivannavit, O., Gulari, M., Gulari, E., LeProust, E., Pellois, J. P., Gao, X., Zhou, X. (2004) Design and fabrication of microwell array chips for a solution-based, photogenerated acid-catalyzed parallel oligonucleotide DNA synthesis. Sensors and Actuators A. 116, 150-160.  [article]
4. Gao, X., LeProust, E., Zhang, H., Srivannavit, O., Gulari, E., Yu, P., Nishiguchi, C., Xiang, Q., Zhou, X. (2001) Flexible DNA chip synthesis gated by deprotection using solution photogenerated acids. Nucleic Acids Res 29, 4744-4750.  [ abstract]  [ article]
5. Leproust, E., Zhang, H., Yu, P., Zhou, X., Gao, X. (2001) Characterization of oligodeoxyribonucleotide synthesis on glass plates. Nucleic Acids Res 29, 2171-2180.  [ abstract] [article]
6. LeProust, E., Pellois, J. P, Yu, P., Zhang, H., Srivannavit, O., Gulari, E., Zhou, X., and Gao, X. (2000) Combinatorial screening method for synthesis optimization on a digital light-controlled microarray platform. J Comb Chem 2, 349-354.  [ abstract]
7. Gao, X., Yu, P. Y., LeProust, E., Sonigo, L., Pellois, J. P., and Zhang, H. (1998) Oligonucleotide synthesis using solution photogenerated acids. J Am Chem Soc 120, 12698-12699.