Microfluidic devices for DNA sequencing: sample preparation and electrophoretic analysis.

Modern DNA sequencing 'factories' have revolutionized biology by completing the human genome sequence, but in the race to completion we are left with inefficient, cumbersome, and costly macroscale processes and supporting facilities. During the same period, microfabricated DNA sequencing, sample processing and analysis devices have advanced rapidly toward the goal of a 'sequencing lab-on-a-chip'. Integrated microfluidic processing dramatically reduces analysis time and reagent consumption, and eliminates costly and unreliable macroscale robotics and laboratory apparatus. A microfabricated device for high-throughput DNA sequencing that couples clone isolation, template amplification, Sanger extension, purification, and electrophoretic analysis in a single microfluidic circuit is now attainable.

[1]  F. Collins,et al.  New goals for the U.S. Human Genome Project: 1998-2003. , 1998, Science.

[2]  S. Quake,et al.  Monolithic microfabricated valves and pumps by multilayer soft lithography. , 2000, Science.

[3]  R. Mathies,et al.  Polymorphism ratio sequencing: a new approach for single nucleotide polymorphism discovery and genotyping. , 2003, Genome research.

[4]  L. Kotler,et al.  A sample purification method for rugged and high-performance DNA sequencing by capillary electrophoresis using replaceable polymer solutions. A. Development of the cleanup protocol. , 1998, Analytical chemistry.

[5]  J. W. Simpson,et al.  A transmission imaging spectrograph and microfabricated channel system for DNA analysis , 2000, Electrophoresis.

[6]  J. Michael Ramsey,et al.  Dispersion Sources for Compact Geometries on Microchips , 1998 .

[7]  J. Landers,et al.  Evaluation of silica resins for direct and efficient extraction of DNA from complex biological matrices in a miniaturized format. , 2000, Analytical biochemistry.

[8]  P. McEwan,et al.  Eight hundred-base sequencing in a microfabricated electrophoretic device. , 2000, Analytical chemistry.

[9]  Martin J. Pollard,et al.  Magnetic bead purification of labeled DNA fragments for high-throughput capillary electrophoresis sequencing. , 2001, BioTechniques.

[10]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[11]  Igor L. Medintz,et al.  Microfabricated 384-lane capillary array electrophoresis bioanalyzer for ultrahigh-throughput genetic analysis. , 2002, Analytical chemistry.

[12]  R A Mathies,et al.  Optimization of high-speed DNA sequencing on microfabricated capillary electrophoresis channels. , 1999, Analytical chemistry.

[13]  L. Linton,et al.  Toward real-world sequencing by microdevice electrophoresis. , 1999, Genome research.

[14]  Richard A Mathies,et al.  High throughput DNA sequencing with a microfabricated 96-lane capillary array electrophoresis bioprocessor , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[15]  J. Zahn,et al.  Microchannel DNA sequencing matrices with a thermally controlled "viscosity switch". , 2001, Analytical chemistry.

[16]  L. Kotler,et al.  Characterization of high molecular mass linear polyacrylamide powder prepared by emulsion polymerization as a replaceable polymer matrix for DNA sequencing by capillary electrophoresis , 1998, Electrophoresis.

[17]  D. Ehrlich,et al.  Optimization of high-performance DNA sequencing on short microfabricated electrophoretic devices. , 2000, Analytical chemistry.

[18]  Paramvir S. Dehal,et al.  Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes , 2002, Science.

[19]  K. A. Wolfe,et al.  Toward a microchip‐based solid‐phase extraction method for isolation of nucleic acids , 2002, Electrophoresis.

[20]  P. Boček,et al.  Injection bias of DNA fragments in capillary electrophoresis with sieving. , 1995, Journal of chromatography. A.

[21]  R. Mathies,et al.  Fully integrated PCR-capillary electrophoresis microsystem for DNA analysis. , 2001, Lab on a chip.

[22]  On-line nanoliter cycle sequencing reaction with capillary zone electrophoresis purification for DNA sequencing. , 2001, Journal of chromatography. A.

[23]  S. Quake,et al.  An Integrated Microfabricated Cell Sorter , 2022 .

[24]  R A Mathies,et al.  Turn geometry for minimizing band broadening in microfabricated capillary electrophoresis channels. , 2000, Analytical chemistry.

[25]  Richard A Mathies,et al.  Microchip bioprocessor for integrated nanovolume sample purification and DNA sequencing. , 2002, Analytical chemistry.

[26]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[27]  D. Rank,et al.  Sub-microliter DNA sequencing for capillary array electrophoresis. , 2000, Journal of chromatography. A.

[28]  Stephen Quake,et al.  A nanoliter rotary device for polymerase chain reaction , 2002, Electrophoresis.

[29]  Satyam Nampalli,et al.  Fluorescence resonance energy transfer terminators for DNA sequencing , 2000 .

[30]  Igor L. Medintz,et al.  High-pressure gel loader for capillary array electrophoresis microchannel plates. , 2001, BioTechniques.

[31]  Paul Richardson,et al.  Human Chromosome 19 and Related Regions in Mouse: Conservative and Lineage-Specific Evolution , 2001, Science.

[32]  A. Woolley,et al.  Ultra-high-speed DNA sequencing using capillary electrophoresis chips. , 1995, Analytical chemistry.

[33]  K. G. Olsen,et al.  Immobilization of DNA hydrogel plugs in microfluidic channels. , 2002, Analytical chemistry.

[34]  T Kitamori,et al.  Photothermal temperature control of a chemical reaction on a microchip using an infrared diode laser. , 2001, Analytical chemistry.

[35]  L. Locascio,et al.  Microfluidic temperature gradient focusing. , 2002, Analytical chemistry.

[36]  R. Mathies,et al.  Monolithic integrated microfluidic DNA amplification and capillary electrophoresis analysis system , 2000 .

[37]  Igor L. Medintz,et al.  Single-molecule DNA amplification and analysis in an integrated microfluidic device. , 2001, Analytical chemistry.

[38]  E. Yeung,et al.  Integrated on-line system for DNA sequencing by capillary electrophoresis: From template to called bases , 1997 .

[39]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[40]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[41]  Eric S. Nordman,et al.  DNA sequencing in a monolithic microchannel device , 2000, Electrophoresis.

[42]  R A Mathies,et al.  High-throughput genetic analysis using microfabricated 96-sample capillary array electrophoresis microplates. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[43]  E. Yeung,et al.  Integrated electroosmotically-driven on-line sample purification system for nanoliter DNA sequencing by capillary electrophoresis. , 2000, Journal of chromatography. A.

[44]  R. Mathies,et al.  Radial capillary array electrophoresis microplate and scanner for high-performance nucleic acid analysis. , 1999, Analytical chemistry.

[45]  L. Kotler,et al.  A sample purification method for rugged and high-performance DNA sequencing by capillary electrophoresis using replaceable polymer solutions. B. Quantitative determination of the role of sample matrix components on sequencing analysis. , 1998, Analytical chemistry.

[46]  Iuliu I. Blaga,et al.  Automated parallel DNA sequencing on multiple channel microchips. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[47]  C. Fuller,et al.  TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing. , 2002, BioTechniques.

[48]  B. Mohammadi,et al.  Optimization of turn geometries for microchip electrophoresis , 2001 .

[49]  William H. Grover,et al.  Monolithic membrane valves and diaphragm pumps for practical large-scale integration into glass microfluidic devices , 2003 .

[50]  J. Khandurina,et al.  Micropreparative fraction collection in microfluidic devices. , 2002, Analytical chemistry.

[51]  S. Quake,et al.  A microfabricated fluorescence-activated cell sorter , 1999, Nature Biotechnology.

[52]  S. Lassiter,et al.  Sanger DNA-sequencing reactions performed in a solid-phase nanoreactor directly coupled to capillary gel electrophoresis. , 1998, Analytical chemistry.