Monday, September 10, 2007

Microarray Platforms...How "Open" is your Microarray Platform


An open microarray biochip technology platform can be defined in several different ways, but fundamentally the platform itself consists of the equipment that is included to manufacture, process, read and report results from microarray biochip experiments. In some recent written communications I have defined an open platform is one that is supported by multiple vendors and a closed platform is one that is supported by a single vendor. Given the complexity of the microarray experimental life cycle, it is rare that a single vendor provides all 4 phases of the platform. One reason for this is the growing number of microarray applications and the complexity of the microarray experimental life cycle. DNA, protein, peptide, carbohydrate, small molecule and other types of microarrays are being used. That means the tool set that makes up a platform is more complex, with end users having many more choices to make...and the choices get harder as our microarray tool set and applications increase. This is my job....to guide end users within our product line and products complimentary to that line to get end users to their goal (see www.arrayit.com).

In general the more applications your microarray equipment can meet, the smarter the purchasing decision. The more flexible the platform, the more likely some protocol optimizations will need to be done. Microarray equipment has increased in sophistication over the years and it is generally understood in the field that the biological variability of any microarray system is much higher than the variability provided by any closed or open platform tool set (see papers from the FDA's MAQC study).

Let's take one of the most famous companies in our field, Affymetrix. By our definition, Affymetrix provides a closed platform. They do not provide end users the ability to make their own microarrays (they do provide custom microarrays). They have a nice processing station and detection instrument that only works with the microarrays that they produce. Their platform is not currently sold for use with protein or peptide microarrays. Additionally unlike other DNA microarray platforms, the oligonucleotides on their microarrays are shorter than their competitors. This make the analysis of Affymetrix microarrays very different than most other microarrays. What we have witnessed over the years is that Affymetrix 's platform as evolved and many protocol optimizations have been done by various kit vendors....so even this closed platform from a hardware standpoint has many sample preparation kit choices.

Let's consider the Nimblegen Roche platform. Like Affymetrix, Nimblegen Roche does not currently provide equipment for end users to manufacture their own microarrays. However, both the catalog and custom microarrays that they manufacture are built on a microscope slide size glass format. That means that there are choices for the end user for processing and reading the microarrays, both manual and with various levels of automation. Like most vendors, Nimblegen has a tool set that they know works well and can recommend specific equipment...that being said Nimblegen Roche microarrays can be read on any slide based fluorescent microarray scanner with sufficient resolution and can be processed using hybridization equipment made by multiple vendors. For information on our 1 micron resolution microarray scanner, please click here.

What Affymetrix and Nimblegen Roche have in common is that both DNA microarray types are manufactured using an in-situ synthesis process. That means that the DNA bases are built base by base directly on the microarray. The advantage of their technologies is that arrays of oligos can be made at very high densities without pre-synthesizing the oligonucleotides . At ArrayIt we provide a fundamentally different platform (and in some ways superior) that falls under the category of ex-situ microarrays. Ex-situ takes advantage of previously prepared biomolecules and nano fluidics spotting technology to manufacture miniaturized arrays on microscope size slide glass, microplates, plate size glass, membrane slides and other types of biochip devices. The ex-situ format empowers end users to make their own microarray of any biomolecule type, which is compatible with all types of detection techniques.
The format is standardized to a microscope slide size, which means multi-vendor support for many phases of the experimental life cycle exist..but the printing technology can work on many different types of substrates including microfluidic devices. These fundamental characteristics makes spotted microarrays a universal biochemistry platform, not just nucleic acid testing platform.

In summary, implementing the the right tool set to perform a microarray experiment takes a lot of consideration. Care must be taken to choose a platform that will allow microarray data to be reported in such a manner to meet the needs of the experimental design. Choices include manufacturing technique, microarray type, surface chemistry, sample type, throughput, detection resolution, detection type, level of quantitation and so on...
In essence many vendors support an open system and a single vendor supports a closed system. Just like individual components of a computer can be purchased to make a complete system, so can various microarray tools, kits and reagents be used complete a microarray experiment. On the most basic level microarray platforms (not just those for DNA microarrays) considered open are the size and shape of glass microscope slides and those that are closed are not. In general closed systems come with specific microarray processing automation and detection hardware, whereas microscope slide size microarrays have many manufacturing, processing, detection and analysis options. Selecting an open system will benefit the end user through providing hardware selection for processing and detection compatible with microarrays and reagents from many vendors. However, closed platforms may be preferred for the ease of use, optimized protocols and simplified choices. If you have an application and are not sure what you need to purchase please contact me at todd@arrayit.com.