Recent major advances in DNA sequencing technologies have resulted in next-gen sequencing platforms capable of generating massive amounts of reads very quickly and relatively inexpensively. The new technologies are being effectively utilized for systematic study of genetic variation in certain targeted regions (subsets) of complex genomes1. By targeting specific regions, one can take better advantage of next-gen sequencing capability; essentially, more coverage is achieved by focusing reads on your area of interest.
LC Sciences’ µParaflo® technology is particularly well suited to provide sequence capture oligonucleotides through massively parallel synthesis of high quality DNA on biochips. Thousands of customer specified oligonucleotide sequences are in situ synthesized on a programmable high density microfluidics chip. Standard DMT-phosphoramidite chemistry and advance microfluidics design ensure high quality synthesis. The oligonucleotides are cleaved from the chip and delivered as a pool of thousands of capture sequences.
LC Sciences has been synthesizing oligonucleotide libraries for use in capture applications since 20042. Our OligoMix® product is a pooled library of thousands of oligonucleotides with customer specified sequences. The product was developed in response to the need for pooled oligonucleotides used in multiplexing reactions and we now have several customers that are using OligoMix® in sequence capture applications that they have developed in their own labs.
- Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM, Shendure J. (2007) Multiplex amplification of large sets of human exons. Nat Methods 4(11), 931-36. [abstract]
- 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]
Next-Gen Sequencing Applications
- Sequence Capture of Specific Gene Sets – Enrich genomic samples for targeted next-gen sequencing (Pathway specific gene sets, Cancer specific gene sets, etc.).
- Target-specific selection of a defined genomic region (such as Mbp region at a specific location, suspected cancer regions, SNP regions, regions for genomic comparisons).
- Sequence Capture for Gene Expression – Capture RNA sequences, such as sets of transcriptome sequences known from previous screening experiments, mRNAs, and miRNAs.
- General use of the capture probes for enrichment or depletion of certain sequences, such as depletion of those which interfere with sequencing reactions or high abundance repeating sequences.
- Sequence Capture for Methylation Analysis – selective enrichment sets for methylation analysis by deep sequencing.
- Multiplex Amplification – Generate custom primer sets to cover missing areas of unknown regions or for variation analysis
- Purification of the sequences to enable multiplexing, high coverage, and high dynamic range sequencing.
Advantages of µParaflo® technology
- Take full advantage of new “next-generation” sequencing technologies
- Target only customer defined genetic elements
- Totally custom sequences – not limited to “exome” sequencing
- Hundreds of reactions per tube
LC Sciences now extends its proven custom microarray synthesis technology to sequencing applications. This technology has been repeatedly demonstrated as very effective for various applications since 2004. Examples – DNA Capture on Chip for Synthetic Gene Applications, ncRNA Capture for Functional Discoveries, and Protein Capture for Studies of Transcription Activation. See the publications page.