Instrumentation for the genome project.

Much of the recent rapid progress in large-scale genomic sequencing has been driven by the dramatic improvements both in the area of biological protocols and in the availability of improved laboratory instrumentation and automation platforms. We discuss recent developments in the area of bioinstrumentation that are contributing to the current revolution in genetic analysis. Examples of systems for laboratory automation are described together with specific single-purpose instruments. Emphasis is placed on those tools that are contributing significantly to the scale-up of genomic mapping and sequencing efforts. In addition, we present a selection of more advanced measurement techniques and instrumentation developments that are likely to contribute significantly to future advances in sequencing and genome analysis.

[1]  D A Lashkari,et al.  An automated multiplex oligonucleotide synthesizer: development of high-throughput, low-cost DNA synthesis. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[2]  S. P. Fodor,et al.  Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two–colour fluorescence analysis , 1996, Nature Genetics.

[3]  D C Uber,et al.  Application of robotics and image processing to automated colony picking and arraying. , 1991, BioTechniques.

[4]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[5]  H. Weetall,et al.  The sixth international meeting on chemical sensors , 1996 .

[6]  G. Ramsay.  DNA chips: State-of-the art , 1998, Nature Biotechnology.

[7]  S. P. Fodor,et al.  Using oligonucleotide probe arrays to access genetic diversity. , 1995, BioTechniques.

[8]  Lloyd M. Smith,et al.  Fluorescence detection in automated DNA sequence analysis , 1986, Nature.

[9]  Takashi Anazawa,et al.  Multiple Sheath-Flow Gel Capillary-Array Electrophoresis for Multicolor Fluorescent DNA Detection , 1994 .

[10]  Edward S. Yeung,et al.  Simultaneous monitoring of DNA fragments separated by electrophoresis in a multiplexed array of 100 capillaries , 1994 .

[11]  G. Freyer,et al.  DNA science : a first course in recombinant DNA technology , 1990 .

[12]  Joseph M. Jaklevic.  Automation of high-throughput PCR assays , 1996 .

[13]  R. Drmanac,et al.  Processing of cDNA and genomic kilobase-size clones for massive screening, mapping and sequencing by hybridization. , 1994, BioTechniques.

[14]  Jonathan D. Wren,et al.  ASTRAL, a hyperspectral imaging DNA sequencer , 1998 .

[15]  Geoff Waite.  Vision‐guided Robotic Screening of Micro‐organisms , 1993 .

[16]  M. Heller,et al.  Preparation and hybridization analysis of DNA/RNA from E. coli on microfabricated bioelectronic chips , 1998, Nature Biotechnology.

[17]  C Schwager,et al.  Automated DNA sequencing: ultrasensitive detection of fluorescent bands during electrophoresis. , 1987, Nucleic acids research.

[18]  G. Evans,et al.  MerMade: an oligodeoxyribonucleotide synthesizer for high throughput oligonucleotide production in dual 96-well plates. , 1998, Genome research.

[19]  N. Dovichi,et al.  Interaction of capillary zone electrophoresis with a sheath flow cuvette detector , 1990 .

[20]  R. Gesteland,et al.  Multiwavelength fluorescence detection for DNA sequencing using capillary electrophoresis. , 1991, Nucleic acids research.

[21]  James L. Winkler,et al.  Accessing Genetic Information with High-Density DNA Arrays , 1996, Science.

[22]  R A Mathies,et al.  DNA sequencing using capillary array electrophoresis. , 1992, Analytical chemistry.

[23]  R A Mathies,et al.  Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[24]  H. Garner,et al.  High-frequency acoustic interaction of resonant systems using SAWs , 1993, IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control.

[25]  Richard A. Mathies,et al.  Capillary array electrophoresis: an approach to high-speed, high-throughput DNA sequencing , 1992, Nature.

[26]  M. Fitzgerald,et al.  Mass spectrometry of nucleic acids: the promise of matrix-assisted laser desorption-ionization (MALDI) mass spectrometry. , 1995, Annual review of biophysics and biomolecular structure.

[27]  S. P. Fodor,et al.  Light-directed, spatially addressable parallel chemical synthesis. , 1991, Science.

[28]  J. Hodgson.  Light, Angles, Action , 1994, Bio/Technology.

[29]  S. P. Fodor,et al.  Multiplexed biochemical assays with biological chips , 1993, Nature.

[30]  Richard A. Mathies,et al.  Capillary array electrophoresis using laser-excited confocal fluorescence detection , 1992 .

[31]  B. Hames,et al.  Nucleic acid hybridisation : a practical approach , 1985 .

[32]  E. Y. Chen.  CHAPTER ONE – The Efficiency of Automated DNA Sequencing , 1994 .

[33]  Lloyd M. Smith,et al.  Genetic analysis by peptide nucleic acid affinity MALDI-TOF mass spectrometry , 1997, Nature Biotechnology.

[34]  R. Drmanac,et al.  Gene-representing cDNA clusters defined by hybridization of 57,419 clones from infant brain libraries with short oligonucleotide probes. , 1996, Genomics.

[35]  Supriyo Datta,et al.  Surface Acoustic Wave Devices , 1986 .

[36]  M. Metzker,et al.  Electrophoretically Uniform Fluorescent Dyes for Automated DNA Sequencing , 1996, Science.

[37]  Routine DNA sequencing of 1000 bases in less than one hour by capillary electrophoresis with replaceable linear polyacrylamide solutions. , 1998, Analytical chemistry.

[38]  M. Davies,et al.  Integration of image analysis and robotics into a fully automated colony picking and plate handling system. , 1992, Nucleic acids research.

[39]  S. P. Fodor,et al.  Light-generated oligonucleotide arrays for rapid DNA sequence analysis. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[40]  R. Reich,et al.  A microchip for quantitative detection of molecules utilizing luminescent and radioisotope reporter groups. , 1994, BioTechniques.

[41]  N. Shen,et al.  Extensive polymorphisms observed in HIV–1 clade B protease gene using high–density oligonucleotide arrays , 1996, Nature Medicine.

[42]  C. Becker,et al.  High-throughput DNA analysis by time-of-flight mass spectrometry , 1997, Nature Medicine.

[43]  R. Reich,et al.  Direct detection of nucleic acid hybridization on the surface of a charge coupled device. , 1994, Nucleic acids research.

[44]  J. Meléndez,et al.  Detection of DNA hybridization using the TISPR-1 surface plasmon resonance biosensor. , 1999, Analytical biochemistry.

[45]  Clement E. Furlong,et al.  A commercial solution for surface plasmon sensing , 1996 .

[46]  J. M. Prober,et al.  A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. , 1987, Science.

[47]  H. Swerdlow,et al.  Three DNA sequencing methods using capillary gel electrophoresis and laser-induced fluorescence. , 1991, Analytical chemistry.

[48]  M. Schena.  Genome analysis with gene expression microarrays. , 1996, BioEssays : news and reviews in molecular, cellular and developmental biology.

[49]  L. Smith.  High-speed DNA sequencing by capillary gel electrophoresis , 1991, Nature.

[50]  D. Barker,et al.  Implementation of a capillary array electrophoresis instrument. , 1996, Journal of capillary electrophoresis.

[51]  C. Campbell.  Surface Acoustic Wave Devices and Their Signal Processing Applications , 1989 .

[52]  L. Hood,et al.  Large-scale and automated DNA sequence determination. , 1991, Science.

[53]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.

[54]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[55]  Deirdre R. Meldrum,et al.  A biomechatronic fluid-sample-handling system for DNA processing , 1997 .

[56]  H. Swerdlow,et al.  Capillary gel electrophoresis for rapid, high resolution DNA sequencing. , 1990, Nucleic acids research.

[57]  P. Brown,et al.  A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. , 1996, Genome research.

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

[59]  J. Jaklevic,et al.  High-throughput DNA synthesis in a multichannel format. , 1995, Nucleic acids research.

[60]  M. Gait,et al.  Oligonucleotide synthesis : a practical approach , 1984 .

[61]  E. Lander,et al.  A Magnetic Attraction to High-Throughput Genomics , 1997, Science.