ArrayTrack is a free toxicoinformatics software from FDA/NCTR for microarray data management, analysis, visualization, and biological interpretation.

 

www.Gene-Chips.com

DNA Microarray (Genome Chip)
--- Monitoring the Genome on a Chip
(c) 1998-2002 by Leming Shi, Ph.D.

 

Welcome to the DNA Microarray (Genome Chip) Web site! This simple, printer-friendly site has been created and maintained by Leming Shi, Ph.D. You'll find the basics on DNA microarray technology and a list of academic and industrial links related to this exciting new technology. Your comments, corrections, and suggestions are welcome. Please help me make this site more useful to you and many other visitors. 
Last updated on January 7, 2002. CreditDisclaimerWarning: This Web site has NO association with Affymetrix, Inc. or its GeneChip® arrays.

This site was featured in Science magazine, ScienceGenomics.org, BioMedNet, etc.

 

DNA Microarrays - A technology that is reshaping molecular biology

It is widely believed that thousands of genes and their products (i.e., RNA and proteins) in a given living organism function in a complicated and orchestrated way that creates the mystery of life. However, traditional methods in molecular biology generally work on a "one gene in one experiment" basis, which means that the throughput is very limited and the "whole picture" of gene function is hard to obtain. In the past several years, a new technology, called DNA microarray, has attracted tremendous interests among biologists. This technology promises to monitor the whole genome on a single chip so that researchers can have a better picture of the interactions among thousands of genes simultaneously.

Terminologies that have been used in the literature to describe this technology include, but not limited to: biochip, DNA chip, DNA microarray, and gene array. Affymetrix, Inc. owns a registered trademark, GeneChip®, which refers to its high density, oligonucleotide-based DNA arrays. However, in some articles appeared in professional journals, popular magazines, and the WWW the term "gene chip(s)" has been used as a general terminology that refers to the microarray technology. Affymetrix strongly opposes such usage of the term "gene chip(s)". More recently, I prefer the term "genome chip", indicating that this technology is meant to monitor the whole genome on a single chip. GenomeChip would also include the increasingly important and feasible protein chip technology.

Base-pairing (i.e., A-T and G-C for DNA; A-U and G-C for RNA) or hybridization is the underlining principle of DNA microarray.

An array is an orderly arrangement of samples. It provides a medium for matching known and unknown DNA samples based on base-pairing rules and automating the process of identifying the unknowns. An array experiment can make use of common assay systems such as microplates or standard blotting membranes, and can be created by hand or make use of robotics to deposit the sample. In general, arrays are described as macroarrays or microarrays, the difference being the size of the sample spots. Macroarrays contain sample spot sizes of about 300 microns or larger and can be easily imaged by existing gel and blot scanners. The sample spot sizes in microarray are typically less than 200 microns in diameter and these arrays usually contains thousands of spots. Microarrays require specialized robotics and imaging equipment that generally are not commercially available as a complete system.

DNA microarray, or DNA chips are fabricated by high-speed robotics, generally on glass but sometimes on nylon substrates, for which probes* with known identity are used to determine complementary binding, thus allowing massively parallel gene expression and gene discovery studies. An experiment with a single DNA chip can provide researchers information on thousands of genes simultaneously - a dramatic increase in throughput. (*Note: In the literature there exist at least two confusing nomenclature systems for referring to hybridization partners. Both use common terms: "probes" and "targets". According to the nomenclature recommended by B. Phimister of Nature Genetics, a "probe" is the tethered nucleic acid with known sequence, whereas a "target" is the free nucleic acid sample whose identity/abundance is being detected. This site follows that recommendation. See Nature Genetics volume 21 supplement pp 1 - 60, 1999, which is freely accessable.

There are two major application forms for the DNA microarray technology: 1) Identification of sequence (gene / gene mutation); and 2) Determination of expression level (abundance) of genes.

There are two variants* of the DNA microarray technology, in terms of the property of arrayed DNA sequence with known identity:

Format I: probe cDNA (500~5,000 bases long) is immobilized to a solid surface such as glass using robot spotting and exposed to a set of targets either separately or in a mixture. This method, "traditionally" called DNA microarray, is widely considered as developed at Stanford University. A recent article by R. Ekins and F.W. Chu (Microarrays: their origins and applications. Trends in Biotechnology, 1999, 17, 217-218) seems to provide some generally forgotten facts.

Format II: an array of oligonucleotide (20~80-mer oligos) or peptide nucleic acid (PNA) probes is synthesized either in situ (on-chip) or by conventional synthesis followed by on-chip immobilization. The array is exposed to labeled sample DNA, hybridized, and the identity/abundance of complementary sequences are determined. This method, "historically" called DNA chips, was developed at Affymetrix, Inc. , which sells its photolithographically fabricated products under the GeneChip® trademark. Many companies are manufacturing oligonucleotide based chips using alternative in-situ synthesis or depositioning technologies.

In the preparation of this Web site, "DNA microarray(s)" and "DNA chip(s)" are used interchangeably. But viewers should aware this technical difference.

* In addition, microfluidics-based chip or laboratory-on-a-chip systems are also listed in this Web site.

The microarray (DNA chip) technology is having a significant impact on genomics study. Many fields, including drug discovery and toxicological research, will certainly benefit from the use of DNA microarray technology. View an example of the microarray image (38K).

For a very well-written introduction on the steps involved in a microarray experiment, visit Jeremy Buhler's Anatomy of a Comparative Gene Expression Study

An excellent collection of Genomics Glossaries (including a Microarrays Glossary) is being maintained by Mary Chitty of Cambridge Healthtech Institute.

Design of a DNA Microarray System

There are several steps in the design and implementation of a DNA microarray experiment. Many strategies have been investigated at each of these steps. 1) DNA types; 2) Chip fabrication; 3) Sample preparation; 4) Assay; 5) Readout; and 6) Software (informatics)

Table 1. Steps in the design and implementation of a DNA microarray experiment

 

1) Probe (cDNA/oligo with known identity) 

2) Chip fabrication
(Putting probes on the chip)

3) Target (fluorecently labeled sample)

4) Assay

5) Readout

6) Informatics

Small oligos, 
cDNAs, 
chromosome, 
... 
(whole organism on a chip?)

Photolithography, pipette, drop-touch, piezoelectric (ink-jet), electric, ...

RNA, (mRNA==>) 
cDNA

Hybridization, long, short, ligase, base addition, electric, MS, electrophoresis, fluocytometry, PCR-DIRECT, TaqMan, ...

Fluorescence, probeless (conductance, MS, electrophoresis), electronic, ...

Robotics control, Image processing, DBMS, WWW, bioinformatics, data mining and visualization

There are so many options and combinations, as can been seen from the number of companies involved in this business. It seems too early to judge who will be the winner(s) in this game. The forecast is further complicated by recent fights among companies on intellectual property issues.

Applications of DNA Microarray Technology

Gene discovery

(Many, many applications, to be listed)

Disease diagnosis

(Many, many applications, to be listed).
Many "microfluidics" devices (Chemical & Engineering News, February 22, 1999, 77(8):27-36; password required) fall in this category. Although they are not the "traditional" gene chip or microarray, I decided to list related links at this site because of their close connection and integration to the gene chip (microarray) technology.

Drug discovery: Pharmacogenomics

Why some drugs work better in some patients than in others? And why some drugs may even be highly toxic to certain patients? My favorite definition (modified): Pharmacogenomics is the hybridization of functional genomics and molecular pharmacology. The goal of pharmacogenomics is to find correlations between therapeutic responses to drugs and the genetic profiles of patients.

Toxicological research: Toxicogenomics

Have you seen anybody using this terminology? Now let's try to give it a definition: Toxicogenomics is the hybridization of functional genomics and molecular toxicology. The goal of toxicogenomics is to find correlations between toxic responses to toxicants and changes in the genetic profiles of the objects exposed to such toxicants. First Preclinical Toxicity Application (Toxicology EXPRESS™ database using Gene Logic's Flow-thru Chip™ technology) between Wyeth-Ayerst Research and Gene Logic
An interesting article: Nuwaysir, E.F., Bittner, M., Trent, J., Barrett, J.C., and Afshari, C.A. Microarray and Toxicology: The Advent of Toxicogenomics. Molecular Carcinogenesis, 24:153-159(1999).
NIEHS sponsored a meeting on the application of DNA microarray in toxicology (EHP 1999).
NIEHS established the National Center for Toxicogenomics (NCT) in June 2000.

Articles on DNA Microarray Technology

  1. Jenkins RE, Pennington SR. Arrays for protein expression profiling: towards a viable alternative to two-dimensional gel electrophoresis?


Proteomics. 2001 Jan;1(1):13-29. Review.

  1. D. D. Shoemaker, E. E. Schadt, C. D. Armour, Y. D., He, P. Garrett-Engele, P. D. McDonagh, P. M. Loer ..., Experimental annotation of the human genome using microarray technology, Nature Volume 409 Number 6822 Page 922 - 927 (2001)
  2. Kane MD, Jatkoe TA, Stumpf CR, Lu J, Thomas JD, Madore SJ, Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res 2000 Nov 15;28(22):4552-7. Abstract
  3. G. MacBeath and S.L. Schreiber, Printing Proteins as Microarrays for High-Throughput Function Determination, Science 2000 September 8; 289(5485): p. 1760-1763. Abstract (New! Protein chip)
  4. Taton TA, Mirkin CA, Letsinger RL.[Northwestern U.] Scanometric DNA array detection with nanoparticle probes.  Science. 2000 Sep 8; 289(5485):1757-60. Seem to offer great selectivity and sensitivity. Abstract
  5. Jörg Reichert et al., Chip-Based Optical Detection of DNA Hybridization by Means of Nanobead Labeling, Anal. Chem., 72 (24), 6025 -6029, 2000. Abstract
  6. Reinke V, Smith HE, Nance J, Wang J, Van Doren C, Begley R, Jones SJ, Davis EB, Scherer S, Ward S, Kim SK [Stanford] A global profile of germline gene expression in C. elegans. Mol Cell 2000 Sep;6(3):605-16. URL
  7. Marx J. DNA Arrays Reveal Cancer in Its Many Forms. Science2000 September 8; 289: 1670-1672. (in News Focus)
  8. DJ Lockhart and EA Winzeler. Genomics, gene expression and DNA arrays. Nature, 2000, 405(6788):827-836.
  9. Cortese JD, The Array of Today: Biomolecule arrays become the 21st century's test tube, The Scientist 14[17]:25, Sep. 4, 2000 URL
  10. Cortese JD, Array of Options: Instrumentation to exploint the DNA microarray explosion, The Scientist 14[11]:26, May. 29, 2000 URL
  11. Fritz J, Baller MK, Lang HP, Rothuizen H, Vettiger P, Meyer E, Guntherodt H, Gerber C, Gimzewski JK. Translating biomolecular recognition into nanomechanics. Science. 2000 Apr 14;288(5464):316-8. [Medline]
  12. Mark Schena (Ed.),  Microarray Biochip Technology, $49.95, Eaton Publishing Company, Distributed by TeleChem / arrayit.com
  13. Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, Eisen MB, Sausville EA, Pommier Y, Botstein D, Brown PO, Weinstein JN. A gene expression database for the molecular pharmacology of cancer. Nat Genet. 2000 Mar;24(3):236-44. [Medline] [Authors' Web site]
  14. Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van De Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO.  Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet. 2000 Mar;24(3):227-35. [Medline] [Authors' Web site]
  15. Walt DR. Bead-based Fiber-Optic Arrays. Science, 2000 January 21; 287: 451-452. (in Tech.Sight)
  16. Afshari CA, Nuwaysir EF, Barrett JC [NIEHS] Application of complementary DNA microarray technology to carcinogen identification, toxicology, and drug safety evaluation. Cancer Res 1999 Oct 1;59(19):4759-60
  17. Gwynne P. and Page G. Microarray analysis: the next revolution in molecular biology. Science, 1999 August 6. (special advertising supplement; has a list of microarray-related companies)
  18. Baldwin D, Crane V, Rice D. A comparison of gel-based, nylon filter and microarray techniques to detect differential RNA expression in plants. Curr Opin Plant Biol1999 Apr;2(2):96-103
  19. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO [Stanford] Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 1999 Sep;23(1):41-6
  20. Khan J, Saal LH, Bittner ML, Chen Y, Trent JM, Meltzer PS. Expression profiling in cancer using cDNA microarrays. Electrophoresis 1999 Feb;20(2):223-9
  21. Gerhold D, Rushmore T, Caskey CT [Merck]. DNA chips: promising toys have become powerful tools. Trends Biochem Sci 1999 May;24(5):168-73
  22. Ekins R. and Chu F.W. Microarrays: their origins and applications. Trends in Biotechnology, 1999, 17, 217-218.
  23. Nuwaysir, E.F., Bittner, M., Trent, J., Barrett, J.C., and Afshari, C.A. Microarray and Toxicology: The Advent of Toxicogenomics. Molecular Carcinogenesis, 1999, 24:153-159.
  24. Sinclair, B. Everything's Great When It Sits on a Chip - A bright future for DNA arrays, The Scientist, 1999 May 24, 13(11), 18-20.
  25. Nature Genetics published a special issue (January 1999 Supplement), The Chipping Forecast. It's a collection of more than 10 reviews (60 pages) on different aspects of microarray analysis. All the reviews are freely available online.
  26. Biochips: From Technologies to Markets, 2nd Edition, (IBC's D&MD Report , March 1999, 200+ Pages, 25+ Exhibits, 20+ Companies Profiled, $4,950!)
  27. Schena, M. and Davis, R.W. Genes, Genomes and Chips. In DNA Microarrays: A Practical Approach (ed. M. Schena), Oxford University Press, Oxford, UK, 1999.
  28. Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett DE Jr, Hartwell LH, Brown PO, Friend SH [Rosetta/Stanford]. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med. 1998 Nov;4(11):1293-301. [Medline] (convincing results on the utility of microarray technology for drug target validation and identification.)
  29. Wang DG, Fan JB, ..., Lander ES, et al [MIT] Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 1998 May 15;280(5366):1077-82
  30. Schena, M. and R.W. Davis. Parallel Analysis with Biological Chips. in PCR Methods Manual (eds. M. Innis, D. Gelfand, J. Sninsky), Academic Press, San Diego, 1998. (Sorry, I haven't seen it yet.)
  31. Lemieux, B., Aharoni, A., and M. Schena. Overview of DNA Chip Technology.  Molecular Breeding 1998, 4, 277-289.
  32. Schena, M., Heller, R.A., Theriault, T.P., Konrad, K., Lachenmeier, E., and Davis, R.W. Microarrays: biotechnology's discovery platform for functional genomics. Trends in Biotechnology 1998, 16, 301-306.
  33. Service, R.F. Microchip arrays put DNA on the spot. Science 1998, 282(5388), 396-399.
  34. Service, R.F. Coming soon: the pocket DNA sequencer. Science 1998, 282(5388), 399-401.
  35. Kricka, L. Revolution on a Square Centimeter. Nature Biotechnology 1998, 16, 513.
  36. Housman, D.; Ledley, F. Why pharmacogenomics? Why now? Nature Biotechnology 1998, 16(6), 492-493.
  37. Ramsay, G. DNA chips - states-of-the-art. Nature Biotechnology 1998, 16(1), 40-44.
  38. Marshall, A.; Hodgson, J.  DNA chips - an array of possibilities. Nature Biotechnology 1998, 16(1), 27-31.
  39. Kononen J, Bubendorf L, Kallioniemi A, Barlund M, Schraml P, Leighton S, Torhorst J, Mihatsch MJ, Sauter G, Kallioniemi OP. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med 1998 Jul;4(7):844-847
  40. Blanchard, A.P. (1998) Synthetic DNA Arrays; in Genetic Engineering, Vol. 20, pp. 111-123, edited by J.K. Setlow, Plenum Press, New York.
  41. Proudnikov D, Timofeev E, Mirzabekov A [Argonne]. Immobilization of DNA in polyacrylamide gel for the manufacture of DNA and DNA-oligonucleotide microchips. Anal Biochem 1998 May 15;259(1):34-41
  42. Chen JJ, Wu R, Yang PC, Huang JY, Sher YP, Han MH, Kao WC, Lee PJ, Chiu TF, Chang F, Chu YW, Wu CW, Peck K Profiling expression patterns and isolating differentially expressed genes by cDNA microarray system with colorimetry detection. Genomics 1998 Aug 1;51(3):313-24.
  43. Wallace, R. W.  DNA on a chip - serving up the genome for diagnostics and research. Molecular Medicine Today 1997, 3, 384-389.
  44. Covacci, A.; Kennedy, G. C.; Cormack, B.; Rappuoli, R.; Falkow, S. From microbial genomics to meta-genomics. Drug Development Research 1997, 41, 180-192.
  45. Forozan, F.; Karhu, R.; Kononen, J.; Kallioniemi, A.; Kallioniemi, O. P. Genome screening by comparative genomic hybridization. Trends in Genetics 1997, 13, 405-409.
  46. Sapolsky, Ronald J.;  Winzeler, Elizabeth A. The Functional Analysis Of Genomes: Recent Research In The Laboratory Of Dr. Ronald Davis (at Stanford University)
  47. Blanchard, A.P. &  L. Hood.  Sequence to array: probing the genome's secrets. Nature Biotechnology  14:1649, 1996
  48. Blanchard, A.P., R.J.Kaiser, L.E.Hood.  High-Density Oligonucleotide Arrays. Biosensors & Bioelectronics 11:687-690, 1996
  49. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM [Stanford and NIH] Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 1996 Dec;14(4):457-60
  50. Shalon D, Smith SJ, Brown PO [Stanford] A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 1996 Jul;6(7):639-45
  51. Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW [Stanford] Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci U S A 1996 Oct 1;93(20):10614-9
  52. Schena M, Shalon D, Davis RW, Brown PO [Stanford] Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science1995 Oct 20;270(5235):467-70

        See also Andreas Matern's home page on DNA Microarrays.

Academic Links

  1. Many academic organizations have set up their mciroarray core facilities in order to make this technology accessible to their reserchers.  Dr. Wentian Li of Rockefeller University maintains a list of such core facilities.
  2. DNA Microarray (Genome Chip) homepage (this site, created by Dr. Leming Shi), is a good starting point and contains a lot of useful links and background information. This site was reviewed by Science magazine.
  3. Science magazine maintains an excellent collection of information on functional genomics. (www.sciencegenomics.org)
  4. Dr. Ruth Alscher (ralscher@vt.edu) at Virginia Tech maintains an excellent Web site GRID IT on DNA Microarrays (http://www.bsi.vt.edu/ralscher/gridit).
  5. Gene-Arrays mailing list (maintained by Chandi Griffin at San Francisco General Hospital/UCSF). To subscribe, send a one line e-mail message to listserv@listserv.ucsf.edu; the single line message should be: subscribe Gene-Arrays your-first-name your-last-name. This is a very good place to ask all kinds of questions regarding gene chips and DNA microarrays. To post a question to the whole mailing list, send email to http://www.gene-chips.com/GENE-ARRAYS@ITSSRV1.UCSF.EDU. You may leave the list at any time by sending a "SIGNOFF GENE-ARRAYS" command to listserv@listserv.ucsf.eduFAQ in PDF
  6. PlantArrays Mailing List To subscribe send the word "subscribe" to mailto://plantarrays-request@genome.stanford.edu
  7. Tim Tranbarger maintains the Plant-Array Website in the context of the WWW Virtual Library ( http://www.w3.org/vl/).
  8. A microarrays newsgroup was recently made available at http://www.egroups.com/group/microarray/ (maintained by Philippe Marc).
  9. The Association of Biomolecular Resource Facilities (ABRF)'s Microarray Research Group (MARG) conducted a survey on the current status of the microarray technology.  The results is presented in a poster: "THE STATE OF THE ART OF MICROARRAY ANALYSIS: A PROFILE OF MICROARRAY LABORATORIES."
  10. The Microarray Site of Nature Genetics
  11. Nobel Laureate Martin L. Perl's group at the Stanford Linear Accelerator Center (SLAC) is investigating if their new drop-on-demand inkjet technology originally designed for the searching of certain hypothetical types of elementary particles would be of use in the production of DNA microarrays.
  12. Stanford University's Dr. Patrick Brown, one of the major players in this field. This group has a complete guide for researchers to build their own microarrayer, at a fraction of the price of commercial products
  13. DNA Microarray Protocols of Dr. Mark Schena: very detailed and useful information on performing DNA microarray experiments.
  14. Dr. Mark Schena Home Page
  15. NIST ATP Awards 1998: Tools for DNA Diagnostics (7 of the 29 proposals were awarded)  Check project manager Dr. Stanley Abramowitz's overview talk on this field
  16. CGAP (Cancer Genome Anatomy Project) at the National Cancer Institute (NCI), NIH.
  17. Microarray Project at the National Human Genome Research Institute (NHGRI), NIH
  18. The NIEHS cDNA Microarray Center: Human ToxChip v 1.0, Human Discovery Chip, Yeast Chip, Rat Chip, Xenopus Chip v 1.0, and Mouse Chip.
  19. Dr. John N. Weinstein at the National Cancer Institute (NCI) developed an "information-intensive" anticancer drug discovery approach that integrates chemical structure information and anticancer activity patterns of >70,000 screened compounds with gene expression (microarray) data of the 60 human cancer cell lines
  20. Dr. Alan Robinson's web resource on Gene Expression and Microarray Technologies, at EBI. (highly recommended) links to public sources of expression data, informatics, analysis tools, ...
  21. Andreas Matern's home page on DNA Microarrays
  22. PhRMA's Microarrays and "DNA chips" site
  23. Anatomy of a Comparative Gene Expression Study (by Jeremy Buhle). It's a very nice description of the microarray technology, also includes a Glossary of Microarray-related Biotechnology Terms
  24. Whitehead Institute for Biomedical Research/MIT Center for Genome Research
  25. Dr. Geoffrey Childs, Functional Genomics at AECOM, Department of Molecular Genetics, Albert Einstein College of Medicine
  26. Computational Genomics at Harvard University (Dr. George M. Church, a lot of very useful links)
  27. Human Genome Project Information at the Oak Ridge National Laboratory, U.S. Department of Energy
  28. National Human Genome Research Institute (NHGRI) is developing "Tissue Chip" to Illuminate the Cancer Development Process. NIH Clinical Study: 97-C-0178: Fludarabine Treatment of Chronic Lymphocytic Leukemia: cDNA Microarray Gene Expression Analysis, and Preclinical Bone Marrow Transplant/Immunotherapy Studies
  29. Garner Lab at UTSW - Gene Networks
  30. DNA Microarray Technology to identify genes controlling spermatogenesis, Sam Ward at the University of Arizona
  31. Vivian Cheung's Lab at The Children's Hospital of Philadelphia focuses on the development of Direct Identical-by-Descent (IBD) Mapping, which is a DNA microarray-based mapping technique that allows isolation and mapping of DNA fragments shared IBD between individuals.
  32. University of Washington, Dr. Lee Hood,  Java-based Array Image Spot Finding and Quantification Software (CrazyQuant)
  33. Dr. Bernd Weisshaar's listing of DNA microarray links (plants), Max-Planck-Institut für Züchtungsforschung
  34. Dr. Landers' Group at the University of Pittsburgh is developing microcolumn technology for clinical diagnostics. This capillary-based Integrated Diagnostic (ID) Chip may have great potential in clinical diagnostics.
  35. Dr. Claude Jacq's group at ENS, France. They also maintain a discussion list: pucesadn@ens.fr
  36. Toxicogenomics homepage at the Chemical Industry Institute of Toxicology (CIIT): discusses how the DNA microarray technology is impacting toxicological research.
  37. Dr. Kent Vrana's Gene Expression Technology Group at the Wake Forest University School of Medicine.
  38. The Vanderbilt University Microarray Core Facility (microarrays.com) offers microarray-based products and services.
  39. MRC Toxicology Unit DNA Microarray Pages maintained by Dr Timothy W. Gant.
  40. The Nylon MicroArrays site provides detailed information on the use of nylon microarrays (allowing expression profiling with small amounts of unamplified RNA) and a number of useful utilities for choosing and checking IMAGE clones representing given genes. contact: jordan@ciml.univ-mrs.fr
  41. Arabidopsis Functional Genomics Consortium (AFGC) at Stanford University, funded by NSF: microarrays, knockouts, and plant-specific genes.
  42. Dr. Eiichiro Ichiishi of Kyoto Prefectural Univ. of Medicine maintains a Web site on DNA chip technology (in Japanese).
  43. Dr. Michael C. Pirrung at Duke University is developing novel methods to cleave DNA strands into the shorter fragments for DNA chip analysis and DNA chip computation.
  44. ArrayNL platform©: DNA-chips and microarrays in the Netherlands, maintained at the Department of Human and Clinical Genetics, Leiden University Medical Center.
  45. The Microarray Centre at The Ontario Cancer Institute.
  46. Links to DNA Microarray protocols , maintained by Longcheng Li at UCSF
  47. Biochip Research & Development Center, Tsinghua Univeristy, Beijing, China. Director: Dr. Jing Cheng.
  48. Natl. Lab. of Molecular and Biomolecular Elecctronics, Southeast Univ., Nanjing, China.
  49. Zicai Liang at Karolinska Institutet.
  50. KIChip: Karolinska Institute cDNA Micro-Array Core Facility
  51. Dr. Gerhard M. Kreshach maintains a list of more than 1000 links to to Life Science News, Resources & Databases, including DNA, Oligonucleotide, and Protein Arrays
  52. Fission yeast functional genomics group at The Sanger Centre headed by Dr. Jurg Bahler.
  53. The Xenopus Microarray Project at Rockefeller Univ., includes protocols, software, and links.
  54. The U.S. Environmental Protection Agency Microarray Consortium (EPAMAC) (Great!)
  55. The Center for Bioelectronics, Biosensors and Biochips at Virgnia Commonwealth University and the Medical Colleage of Virginia Health System focuses on next generation microarrays, integrated molecular electronic devices using biologically active molecules and neurochips.
  56. St. George's Hospital Medical School's microarray facility on Bacterial Microarrays.
  57. UCLA Human Genetics DNA Microarray Core Facility
  58. Cornell Weill Medical College DNA Microarray Core Facility (Dr. Jenny Z. Xiang)
  59. Baylor College of Medicine Microarray Core Facility
  60. ORNL's Links to the Genetic World
  61. Scottish Centre for Genomic Technology and Informatics, Scotland University of Edinburgh.
  62. Prof. Andreas Manz of the Imperial College, UK, developed a novel concept for Miniaturized Total Analysis Systems (u-TAS): sampling, any sample pretreatment, separation, and detection steps are all performed in an integrated microsystem.
  63. Dr. Michael Weller's group works on protein chips.
  64. Prof. Dave Stahl's group at the Univ. of Washington is working on the Phylochip project: developing 16S rRNA-based microchips for determinative, phylogenetic and environmental studies.

Industry Links (Companies are listed alphabetically.)

A good summary of available Human arrays can be found at the September 4, 2000 issue of The Scientist. (by Jorge D. Cortese)

  1. ACLARA BioSciences, Inc., (used to be called Soane Biosciences) Hayward, California (Plastic chips and microfluidic systems based on "Lab-On-A-Chip" microfluidics US Patent 5,750,015: "Method and device for moving molecules by the application of a plurality of electrical fields") Wins NIST ATP Award in "Tools for DNA Diagnostics" for Project: Multiplexed Sample Preparation Microsystem for DNA Diagnostics
  2. Advanced Array Technology S.A. (Belgium),  BIO-CD™: compact disc platform for DNA detection
  3. Affymetrix, Inc., Santa Clara, California (The technology leader; manufactures the widely used GeneChip®arrays, including HIV, p450, p53, Rat Toxicology U34 arrays, etc.)
  4. Agilent Technologies, Inc. (Palo Alto, California), a subsidiary of Hewlett-Packard Company, plans to expand its presence in the life science market through the introduction of a new DNA microarray program. It uses inkjet printing technology to manufacture its oligo-based DNA microarrays. Licensed from Ed Southern/OGT. LabChip™-based DNA and RNA bioanalyzer.
  5. Alexion Pharmaceuticals Inc., New Haven, Connecticut
  6. Alpha Innotech Corp., San Leandro, CA. Alpha Innotech provides innovation bioinformatic imaging solutions for genetic discovery designed to acquire, manage, and analyze fluorescence, chemiluminescence, or colorimetric microarray slides, plates, gels, blots, or films.
  7. AlphaGene, Inc., Woburn, Massachusetts (full length cDNA FLEX™ and MicroFLEX library construction; High Throughput Gene Expression Profiling; High Throughput DNA Sequencing; Bioinformatics)
  8. Applied Precision, Inc., Issaquah, Washington. ArrayWoRx is a wide field light source based microarray scanner, combines limitless wavelength possibilities with automation and image processing software.
  9. Asper Ltd.,  Estonia. Arrayed Primer Extension (APEX) and Asper ChipReader 003
  10. AVIVA Biosciences Corp., San Diego, CA. Dedicated to the application of breakthrough multiple-force biochip technology for genomics and proteomics. The company is developing an integrated sample-to-result AVIChip™ system with an emphasis on biological sample preparation and chip-based molecular manipulation. The AVIChip™ system will separate and transport a variety of mRNA, or other molecules from crude biological samples and simultaneously perform a wide range of biological and biochemical analyses. AVIVA's technology allows fast, accurate, automated, and high-throughput biological analysis on integrated biochip systems and provides novel approaches to both drug development and clinical diagnostics.
  11. Axon Instruments, Inc., Foster City, California (GenePix 4000 Integrated Microarray Scanner and Analysis Software, simultaneously scans microarray slides at two wavelengths using a dual laser scanning system, displays images from two wavelengths and a ratio image as they are acquired in real time; US$50,000)
  12. AxyS Pharmaceuticals, La Jolla, California: Wins NIST ATP Award in "Tools for DNA Diagnostics" Project: Liquid Array Technology Development
  13. Beckman-Coulter
  14. Beecher Instruments, Silver Spring, MD. Tissue array technology for high-throughput analysis of tissue specimens.
  15. BioArray Solutions, LLC, Piscataway, NJ. Light-controlled Electrokinetic Assembly of Particles near Surfaces (LEAPS), enables  computer controlled assembly of beads and cells into planar arrays within a miniaturized, enclosed fluid compartment on the surface of a semiconductor wafer.
  16. BioChip Technologies
  17. bioDevice Partners, Cohasset, MA. Provides consulting services to the microarraying community in the area of optics and instrumentation
  18. BioDiscovery, Inc., Los Angeles, California (ImaGene™, special image processing and data extraction software; CloneTracker: Databases clones, plates, and slides, and offers array design tool and interfaces to arrayers; GeneSight: Powerful expression analysis software which features statistical methods as well a visualization tools.
  19. Biodot
  20. Biomedical Photometrics, Inc., (MACROscope™  for reading genetic microarrays, in collaboration with Canadian Genetic Microarray Consortium)
  21. bioMerieux, in vitro diagnostics
  22. BioRobotics Ltd.,  Comberton, Cambridge, UK (MicroGrid, for arraying oligonucleotides or cDNA clones on glass slides and plastic chips)
  23. Brax, Cambridge, UK
  24. Cadus Pharmaceutical Corp., Tarrytown, New York