Novel Low Cost, High Throughput DNA Sequencing Platform

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DESCRIPTION (provided by applicant): We aim to commercialize a new technology to rapidly sequence DNA. This technology can be applied (with proper preprocessing steps) to whole genome sequencing, and other assays including transcriptomics, transcription factor activity, miRNA expression, DNA methylation, and SNP analysis. The present STTR Phase I proposal requests one year of support to complete initial proof of principle studies. Current DNA sequencing technologies are too slow (i.e. 12-15 Megabases/hour) and expensive (i.e. $7- $70/Megabases) to be widely applied to whole genome sequencing or other aforementioned applications. The present proposal is to develop and provide new technology to the biomedical research community that can more fully realize the promise of DNA sequencing through a new venture, PerfectExpression, that will develop and offer a product, DNACount, that will provide a cheaper and better alternative to existing sequencing technologies. In particular, DNACount will replace qualitative and noisy microarray, ChIP, and miRNA high throughput assays with digital readouts of gene sequences. In certain circumstances, it may even be cost effective to replace qPCR assays. DNACount measures the actual concentration of each gene by isolating, amplifying, and sequencing each individual molecule in a high throughput manner. Our approach differs from other approaches by providing higher quality (i.e. length) and quantity reads. We use sequencing by synthesis using endogenous dNTP's to produce long reads (i.e. > 250 bp) while using flow cells and glass immobilization technologies to maximize the number of parallel reads (i.e. ~40 million). DNACount uses off-the-shelf optics and microfluidics to minimize capital (< $100,000) and operational (<$1000/run) costs of sequencing. Our goal is to provide a bench-top solution at a low cost such that DNA sequencing becomes as pervasive as PCR. This will open new avenues to basic and clinical researchers. PUBLIC HEALTH RELEVANCE: We aim to commercialize a new technology to rapidly sequence DNA. This technology can be applied (with proper preprocessing steps) to whole genome sequencing, and other assays including transcriptomics, transcription factor activity, miRNA expression, DNA methylation, and SNP analysis. The present STTR Phase I proposal requests one year of support to complete initial proof of principle studies. Current DNA sequencing technologies are too slow (i.e. 12-15 Megabases/hour) and expensive (i.e. $7- $70/Megabases) to be widely applied to whole genome sequencing or other aforementioned applications. The present proposal is to develop and provide new technology to the biomedical research community that can more fully realize the promise of DNA sequencing through a new venture, PerfectExpression, that will develop and offer a product, DNACount, that will provide a cheaper and better alternative to existing sequencing technologies. In particular, DNACount will replace qualitative and noisy microarray, ChIP, and miRNA high throughput assays with digital readouts of gene sequences. In certain circumstances, it may even be cost effective to replace qPCR assays. DNACount measures the actual concentration of each gene by isolating, amplifying, and sequencing each individual molecule in a high throughput manner. Our approach differs from other approaches by providing higher quality (i.e. length) and quantity reads. We use sequencing by synthesis using endogenous dNTP's to produce long reads (i.e. > 250 bp) while using flow cells and glass immobilization technologies to maximize the number of parallel reads (i.e. ~40 million). DNACount uses off-the-shelf optics and microfluidics to minimize capital (< $100,000) and operational (<$1000/run) costs of sequencing. Our goal is to provide a bench-top solution at a low cost such that DNA sequencing becomes as pervasive as PCR. This will open new avenues to basic and clinical researchers.