SlipChip for Target Enrichment for Next-Gen Sequencing by Multiplexed PCR

DESCRIPTION (provided by applicant): 1. For the past 30 years, Sanger sequencing has enabled the determination of a sequence of nucleotide 2 bases on a small segment of DNA, with the crowning achievement of the technology being the complete 3 elucidationof the human genome at a cost of several hundreds of millions of dollars. Recently, next- 4 generation sequencing technologies have been developed capable of processing millions of DNA templates in 5 parallel. Compared to the astronomical cost of theoriginal human genome project, the current cost to 6 sequence a complete human genome using next-generation sequencing technology is currently under 7 50,000. However, even this relatively lower cost is still too high for the majority of scientific inquiry or clinical 8 studies that require deep sequencing of focused regions of the genome. Thus, targeted enrichment strategies 9 that enrich only desired segments of the genome for subsequent sequencing are necessary. And, there is 10 currently no solutionfor targeted enrichment exists that is simple, affordable to individual research or clinical 11 laboratories, and that incorporates quality control. 12 SlipChip is an attractive and innovative technology that can potentially solve this problem. SlipChip has 13 already been applied to complex protocols such as enzyme assays, immunoassays, and PCR assays. The PIs 14 have demonstrated that SlipChips fabricated in glass can be used to perform multiplexed PCR and digital PCR. 15 The goal of this Phase I proposal is to establish the feasibility and applicability of this innovation in the area of 16 multiplexed PCR for targeted enrichment and subsequent sequencing, while testing the feasibility of upstream 17 and downstream steps in the sequencing workflow: from Aim 1) where we will test and verify the robustness of 18 multiplexed PCR in the SlipChip using human DNA, Aim 2) where we will optimize the density of SlipChip and 19 finally, Aim 3) where We will verify that on-chip quality control of PCR before committing a sample is feasible. 20 Reaching these specific aims would firmly establish feasibility and viability of SlipChip technology as a 21 sample processing tool for targeted enrichment for next generation sequencing by multiplexed PCR, and would 22 reduce the technical risk of Phase II work in this area, which would include sequencing experiments in the 23 context of biomedical problems of high significance, and will allow for the study of the validated SlipChip 24 system for complete integration in the workflow of an existing next-generation sequencing tool, specifically the 25 Illumina GA IIe. PUBLIC HEALTH RELEVANCE: 1 Technologies for the targeted enrichment of specific genomic regions are urgently needed to bring the 2 power of next-generation sequencing to fundamental and applied biomedical research. However, no solution 3 for targeted enrichment exists that is simple and affordable to individual research or clinical laboratories. This 4 proposal describes a SlipChip technology to address this unmet need.