Hitting the spot

In the post genomic era new techniques seemed to appear overnight and many disappeared just as quickly. Here we discover how microarray spotting robots have survived – just.

MOST commentators believed that, due to the excitement created by the Human Genome Project, there would be huge demand created for all things associated with microarray. However, while a very significant global market has resulted, it has fallen short of expectations particularly with regard to microarray spotting robots.
 
There have been several contributing factors to this shortfall. Time taken for bioinformatics solutions to catch up was an initial problem. Huge quantities of data was being produced in parallel and so software solutions had to catch up in order for researchers to draw valid scientific conclusions before moving forward with their research.

In addition, early attempts at printing microarrays proved difficult. Printing extremely small quantities of material in a way that ensures good spot morphology, desired densities, with excellent reproducibility while guaranteeing biological attachment is extremely challenging. Consequently the number of laboratories printing their own arrays declined and core laboratories were formed as a means of pooling expertise in order to address what were significant technical challenges.

A further blow to spotting sales was when companies like Affymetrix and Agilent began to offer ready to use DNA microarrays and there has been widespread adoption. Many researchers are prepared to accept the high cost in order to avoid the difficulties of printing their own arrays. Sales of microarray hybridisation stations and scanners have increased, while sales of spotters and substrates have fallen behind, which is consistent with uptake of ready made chips. 

While new market entrants have resulted in some moderation of prices it is clear that the economies offered by own printing solutions cannot be reached. It follows then that a higher cost per test, in a world where research funding is becoming tighter, must be limiting the number of tests that researchers would like to do.

With so many mixed experiences being reported, against a backdrop of off the shelf chips coming along, it became very difficult to justify a replacement for a robot which had only ever made do. Groups then held on to old instruments while focussing spending on more sophisticated scanners and software.

Poor performance of non contact array printers also proved to be a stumbling block. It is widely appreciated that non contact/inkjet based printing systems offer significant advantages over contact/pin based robots. However early systems proved fragile, unreliable and slow adding an unwelcome level of complexity to what was already a very difficult task. 

The world of diagnostics is extremely active with many alternative assay systems being investigated including those utilising bead based technologies but microarray is still regarded as offering huge potential in this area. Microarray printing is about being able to print small and therefore economical quantities of material into a small area which in turn allows one sample to be exposed to a number of markers. Many tests can be performed on one sample allowing a profile of the ‘patient’ to be generated. This potential to multiplex is seen as a fundamental requirement for future diagnostic tests.

The transition from research to research diagnostics is clearly under way, and with it a desire for flexibility in sample and substrate type which can not be addressed by off the shelf arrays or pin based printing robots. Array CGH is just one example of where significant potential has been identified and while that particular microarray utilises DNA, other work is being done looking at printing proteins, RNA, whole blood, cells and cell lysates. All are samples which present more complex printing challenges which are more readily addressed through non contact printing.

It is no longer enough to simply consider glass based slides as the preferred substrate in microarray experiments as today the microarray could just as easily end up at the heart of instrument printed on a CMOS chip.

Commercial diagnostics usually means large numbers of devices produced in a tightly controlled environment and so anyone developing an array for such purposes needs to consider how it can be manufactured in greater numbers when the time comes. There can often be a great deal of effort required to optimise a particular sample, substrate and printing combination and so it is in the developer’s interest to ensure that the chosen spotting approach is scaleable.

As mentioned earlier non-contact microarray has a number of advantages over pin spotting and in the case of manufacturing none more so that avoidance of the ‘z’ or ‘zee’ issue. Pin spotters must move down then up and then take a step to side in order  to print a block of array elements whereas instruments like Arrayjets’ Super Marathon dispense ‘on the fly’ sweeping from side to side and printing up to 100 slides at a time.

The consequence is that the printing process is much faster which is important considering production demands and concerns over leaving costly biological content exposed and subject to evaporation.

The drive to research and then ultimately towards clinical diagnostic microarrays has created a need for flexible robotics solutions. There are compelling commercial and technical reasons as to why inkjet technology is best suited to this purpose.

Table 1. Benefits of inkjet technology

It is worth considering the last two items in table 1 from a commercial perspective in more detail. 

As has been seen, one of the main reasons for the slower than anticipated adoption of spotting robots was the advent of off the shelf broad content chips. Such chips have been developed for DNA applications and do not address other applications which are coming along at pace such as antibody arrays. Formats of such chips are determined by the manufacturing process used and so developers lack the freedom to choose the format and substrate which ensure optimum performance of the final array.

In losing this flexibility the opportunity to generate novel, well protected and therefore lucrative intellectual property (IP) could be lost. Whilst off the shelf chips are undoubtedly convenient for certain applications it is likely that most manufacturers will prefer to keep control of their costs, and the value of their business which is in their IP closer to home.

There are certainly steps that will need to be taken to ensure that the current non-contact systems better address the needs of larger scale chip manufacturers but it is to be hoped that such producers will see the clear commercial and technical benefits of such an approach and that they will seek to work with companies to that common end.

Graham Milller. Graham is chief executive of Arrayjet. Previously he was at Smiths Detection, an FTSE 100 company where he was Vice President responsible for building the European market for the HazMatID, a portable chemical identifier.