SBIR-STTR Award

The long-term goal of the proposed research is the design and construction of a DNA sequencing system that can sequence the whole human genome for under $100 including sample preparation and with the cost of goods of the system well under $5,000. The system developed under the proposed research is at least an order of magnitude in cost better than the target of the solicitation while maintaining all performance metrics. In that respect it will break the barrier towards genomic medicine. The overall system is based on sequencing DNA on a carbon nanotube CMOS array via motion of enzymes attached to each nanotube while transcribing or polymerizing the sample DNA. The enzyme motion at each transcription step translates to conductivity changes. When one of the nucleotides is reduced in concentration compared to the other three a pause will be detected in a series of faster steps. Iterating between all nucleotides will lead to decoding of all base positions with respect to each other. This assay has successfully sequenced in an alternate optical-based system, but with limited read length at the 5kb order. The current system can achieve >50kb read length. Preliminary data shows that enzymes can be loaded at a single molecule fashion on a nanotube. Furthermore, other groups have shown that motion of enzymes can be monitored while on nanotubes. While this is a great start, Phase I work will investigate the most optimal attachment of enzymes to nanotubes and show sequencing using Eve Biomedical's assay; investigating accuracy, read length and throughput limits of this sequencing approach. If successful, the main goal is to completely sequence a microbial DNA (Ecoli) at the end of Phase I using a prototype system, and thus completely benchmark the proposed architecture. Beyond Phase I, a low cost bench top system will be constructed to perform sequencing of Whole Human Genome with the target cost defined as goal of this grant solicitation.

Thesaurus Terms:
Address;Architecture;Base;Benchmarking;Biological Assay;Carbon Nanotubes;Cells;Claw;Clinical;Color;Commercialization;Complex;Cost;Data;Design;Design And Construction;Detection;Development;Devices;Diagnostic;Dna;Dna Sequence;Dna-Directed Rna Polymerase;Electronics;Ensure;Enzyme Kinetics;Enzymes;Escherichia Coli;Fluorescence;Genes;Genetic Transcription;Genome;Genome Sequencing;Genomics;Goals;Grant;Housing;Human Genome;Individual;Label;Lead;Length;Measurement;Medicine;Methods;Metric;Microbial;Molecular Conformation;Monitor;Motion;Mutant;Nanopore;Nanotubes;Nucleotides;Optics;Performance;Phase;Point-Of-Care Diagnostics;Positioning Attribute;Preparation;Prevent;Programs;Promotor (Genetics);Prototype;Public Health Relevance;Reading;Research;Resolution;Reverse Transcription;Rna;Sampling;Screening;Series;Signal Transduction;Single Molecule;Staging;Statistics;Surface;System;Technology;Time;Transistors;Translating;Work;

The long-term goal of the proposed research is the design and construction of a DNA sequencing system that can sequence the whole human genome for under $100 including sample preparation and with the cost of goods of the system well under $5,000. The system developed under the proposed research is at least an order of magnitude in cost better than the target of the solicitation while maintaining all performance metrics. In that respect it will break the barrier towards genomic medicine. The overall system is based on sequencing DNA on a carbon nanotube CMOS array via motion of enzymes attached to each nanotube while transcribing or polymerizing the sample DNA. The enzyme motion at each transcription step translates to conductivity changes. When one of the nucleotides is reduced in concentration compared to the other three a pause will be detected in a series of faster steps. Iterating between all nucleotides will lead to decoding of all base positions with respect to each other. This assay has successfully sequenced in an alternate optical-based system, but with limited read length at the 5kb order. The current system can achieve >50kb read length. Preliminary data shows that enzymes can be loaded at a single molecule fashion on a nanotube. Furthermore, other groups have shown that motion of enzymes can be monitored while on nanotubes. While this is a great start, Phase I work will investigate the most optimal attachment of enzymes to nanotubes and show sequencing using Eve Biomedical's assay; investigating accuracy, read length and throughput limits of this sequencing approach. If successful, the main goal is to completely sequence a microbial DNA (Ecoli) at the end of Phase I using a prototype system, and thus completely benchmark the proposed architecture. Beyond Phase I, a low cost bench top system will be constructed to perform sequencing of Whole Human Genome with the target cost defined as goal of this grant solicitation.

Public Health Relevance Statement:


Public Health Relevance:
Currently there are several commercial and under development DNA sequencing systems and although improvements in cost per base and cost for whole human genome have been tremendous, the goal of doing this with appropriate accuracy under $1,000 has not yet been achieved. To address this, Eve Biomedical proposes to develop a compact DNA sequencing system that will be able to sequence the whole human genome under $100 i.e. an order of magnitude less than the target and including sample preparation and with the cost of goods of the system well under $5,000. It will break the barrier to introducing sequencing in clinical diagnostics and jump start the era of genomic medicine.

NIH Spending Category:
Bioengineering; Biotechnology; Genetics; Human Genome; Nanotechnology

Project Terms:
Address; Architecture; base; Benchmarking; Biological Assay; Carbon Nanotubes; Cells; Claw; Clinical; Color; commercialization; Complex; cost; Data; design; design and construction; Detection; Development; Devices; Diagnostic; DNA; DNA Sequence; DNA-Directed RNA Polymerase; ds-DNA; Electronics; Ensure; Enzyme Kinetics; Enzymes; Escherichia coli; Fluorescence; Genes; Genetic Transcription; Genome; Genomics; Goals; Grant; Health; Housing; Human Genome; human genome sequencing; Individual; Label; Lead; Length; Measurement; Medicine; Methods; microbial; Molecular Conformation; Monitor; Motion; mutant; nanopore; Nanotubes; Nucleotides; Optics; Performance; Phase; point-of-care diagnostics; Positioning Attribute; Preparation; prevent; programs; Promotor (Genetics); prototype; Reading; Research; Resolution; Reverse Transcription; RNA; Sampling; screening; Series; Signal Transduction; single molecule; Staging; statistics; Surface; System; Technology; temporal measurement; Time; Transistors; Translating; Work