DNA Microarray (Genome Chip)
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.
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.
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.
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.
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).
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)
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.
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.
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.
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.
Genicon Sciences Corp, San Diego, CA. Developed an ultra-sensitive signal generation and detection platform technology based on Resonance Light Scattering (RLS) for the simple and efficient detection, measurement and analysis of biological interactions.
Expression profiling, novel gene identification, and large-scale sequencing (Gene Discovery array), polymorphism analysis and diagnostics (HyGnostics/HyChip arrays), and large-sample sequencing (HyChip array)
Michael P. S. Brown, William Noble Grundy, David Lin, Nello Cristianini, Charles Sugnet, Terrence S. Furey, Manuel Ares, Jr., David Haussler [UCSC]. Knowledge-based Analysis of Microarray Gene Expression Data Using Support Vector Machines. (SVMs are considered a supervised computer learning method.)
The Nature of GED (Gene Expression data); Experimental Variables (Dimensionality); Quality (Reproducibility) of GED; Extracting Signal from Noise; Statistical Approach; Artificial Intelligence-Based Approach; Interpretation of Results; Publicly Available GED (GEO, EBI, SAGE, ...)
The idea of protein microarray is not new. In fact, the basics and theoretical considerations of protein microarrays were done in the 1980's by Roger Ekins and coleagues. See, e.g., Ekins R.P., J Pharm Biomed Anal 1989. 7: 155; Ekins R.P. and Chu F.W., Clin Chem 1991. 37: 1955; Ekins R.P. and Chu F.W, Trends in Biotechnology, 1999, 17, 217-218.
The are two main objectives for proteomic research: 1. quantification of all the proteins expressed in a cell; 2. functional study of thousands of proteins in parallel. For quantification purpose, the standard method is 2D gel separation followed by MS identification. For protein function study, microarray-based assays are being used to study protein-protein and protein-ligand interations.
News: Gavin MacBeath and Stuart L. Schreiber of Harvard University just published a paper on protein microarray - more than 10,000 protein spots were printed on a glass slide. The chip was used to identify protein-protein and protein-drug interactions. I believe it's a truly breakthrough for proteomics and for drug discovery. 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 The question is how to get thousands of pure proteins and keep them in their natural conformation.
In addition to the numerous inqueries I received on the technical part of DNA microarray I also received many requests from my visitors for investment advices. Unfortunately, I am not a financial adviser. However, I list here some of the stocks that are related to the DNA microarracy technology in one way or another. Warning: This is FYI only and I shall not be held responsible for your investment outcome. If you think this site helped you make a good investment decision you are welcome to make a donation to maintain it and/or send my little kids some Pokemon toys :)- Good luck!
Shoko Kawamoto, Tadashi Ohnishi, Hiroko Kita, Osamu Chisaka, and Kousaku Okubo [Osaka/Kyoto]. Expression Profiling by iAFLP: A PCR-Based Method for Genome-Wide Gene Expression Profiling. Genome Res 1999 Dec;9(12):1305-1312
Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA. Database resources of the National Center for Biotechnology Information, Nucleic Acids Res. 2000 Jan 1;28(1):10-4.