product review
Spotting a microarray system A broader array of commercial products edges out home-built systems. Elizabeth Zubritsky
T
rying to keep up with the latest DNA microarrays means running oneself ragged. Fortunately, the instruments for making and reading those arrays are being developed at a saner pace. But that should not imply that the instrumentation is lagging. Over the past few years, instrument performance has improved, additional vendors have entered the market, and new high-performance ($100,000 or more) and “lite” products (as low as ~$30,000) are bringing microarray instrumentation within reach of well-heeled companies and individual users. Instruments are also becoming more automated and easier to use. Microarrays are best known for measuring differential expression; that is, comparing the relative levels of gene expression between two populations of cells. DNA probes are attached to microscope slides (or other substrates) in a gridlike pattern, and when the sample is added, a complementary piece of target mRNA hybridizes to each probe. Another popular application is to use microarrays to resequence—that is, to test for the presence of a DNA sequence; they can also be used to sequence de novo, although this is not often done. Although some integrated systems are available, most microarray instrumentation is modular. The arrayers for depositing the DNA probes in gridlike patterns on microscope slides (also called “chips”) and the readers for scanning the slides are sold separately and can be mixed and matched. A selection of arrayers is provided in Table 1, and Table 2 lists some available scanners.
Home-built versus commercial Perhaps the most noticeable change is that building one’s own microarray system from scratch is not considered necessary anymore. “Three-and-a-half years ago, there was not much choice in terms of [commercial] instrumentation,” says
Aldo Massimi, who designed and built a system for the Albert Einstein College of Medicine. “Building was the only real solution.” But recently, impressed with the improvements in scanners, Massimi purchased a commercial product as part of an upgrade.
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product review
Table 1. Selected instruments for making DNA microarraysa. Model
Model 417
Array Spotter
MicroGrid II
ProSys 5510
Manufacturer
Affymetrix 3380 Central Expwy. Santa Clara, CA 95051 800-834-5244 www.affymetrix.com
Amersham Pharmacia Biotech P.O. Box 1327 Piscataway, NJ 08855 732-457-8000 www.apbiotech.com
BioRobotics 12 Walnut Hill Park Woburn, MA 01801 877-246-7626 www.biorobotics.com
Cartesian Technologies 17851 Sky Park Cir., Ste. C Irvine, CA 92614 800-935-8007 www.cartesiantech.com
User-defined up to 18,000
≥100,000 features/slide
>80,000 spots/slide
Spot density Number of pins
4 standard; single pin optional
12 spring-loaded pens
Up to 64
Up to 48
xy positional resolution (µm)
10
1
10
10
Types of pins and/or dispensing technologies
Proprietary Pin-and-Ring design
Patented stainless steel capillary design
Compatible with a variety of pins
Capillary quill pins
Plate capacity
3 microplates with up to 384 wells; unlimited number of changes
12 microplate with up to 384 wells
24 microplates with up to 1536 wells
3 microplates with up to 384 wells; up to 50 plates with loader
Slide capacityb
42
36
108
100
Full-density spotting session in 400 samples/h on 108 slides
48 spots/s; full yeast genome (6200 genes) in
