Phase II year
2011
(last award dollars: 2012)
The feasibility of a label-free technology, Millikan Sequencing, will be evaluated for de novo sequencing of mammalian genomes for under $1,000. This novel sequencing-by-synthesis approach measures the increased charge as nucleotides are added to DNA templates attached to a tethered bead. Opposing electrical, hydrodynamic and entropic forces will be used to measure the bead displacement, which is a function of the length of DNA attached to the bead. Simultaneous detection of an array of millions of beads undergoing chain elongation will allow high-throughput sequencing. Model calculations and preliminary results indicate that this method should enable accurate, long read length and label-free DNA sequencing. The lack of labels leads to negligible reagent costs while the relatively simple optics leads to a low-cost instrument. Long read lengths will result in low genome assembly cost. The much lower per-bead copy number required compared to the 454 system should enable amplification options other than emulsion PCR, such as bridge PCR, making initial sample preparation easier and cheaper. Ultimately, the method could be used on single molecules thereby further reducing sample preparation costs. The aims of the proposed two-year exploratory project are: (1) to demonstrate the ability to sequence DNA using a single tethered bead, and (2) to develop a scheme that would allow simultaneous detection of large bead arrays for high throughput analysis.
Public Health Relevance: Nucleic acid sequence information is critical to medical research and to basic biological studies. The goal of this project is to develop a DNA sequencing system based on a label-free detection approach, Millikan Sequencing, which is capable of de novo sequencing of mammalian genomes for under $1,000. Such a platform will allow researchers and clinicians to perform the translational research ultimately required to improve human health.
Public Health Relevance Statement: Nucleic acid sequence information is critical to medical research and to basic biological studies. The goal of this project is to develop a DNA sequencing system based on a label-free detection approach, Millikan Sequencing, which is capable of de novo sequencing of mammalian genomes for under $1,000. Such a platform will allow researchers and clinicians to perform the translational research ultimately required to improve human health.
NIH Spending Category: Bioengineering; Biotechnology; Genetics; Human Genome
Project Terms: base; Base Sequence; Bioinformatics; Biological; Capital; Charge; cost; Dependence; Detection; DNA; DNA Sequence; Drops; Emulsions; Equilibrium; Equipment; Genome; genome sequencing; Goals; Health; high throughput analysis; Human; imaging detector; improved; Individual; instrument; Label; Length; mammalian genome; Measures; Medical Research; Methods; Modeling; Monitor; novel; Nucleic acid sequencing; Nucleotides; Oils; Optics; Phase; Polymers; Preparation; public health relevance; Reading; Reagent; Research Personnel; research study; Sampling; Scheme; single molecule; Small Business Innovation Research Grant; Speed (motion); Surface; System; Technology; Theoretical model; Translational Research
