Coming soon to a lab near you: Light-based oligonucleotide synthesis for microarrays.
At least two companies, febit in Germany and NimbleGen in the US, are currently developing fully-automated desktop instruments that will allow researchers to make their own high density DNA microarrays using light projection technology that performs in situ synthesis of oligonucleotides.
Febit, a three-year old venture stage company in Mannheim, Germany, is taking an all-in-one approach, combining DNA synthesis, microfluidics-based hybridization and CCD detection in one benchtop instrument.
We tend to compare it with a fax-scanner-copy-machine, said febit chief scientific officer Peer Staehler.
The machine, Geniom One, is being designed to eventually produce chips that each have 48,000 features, and are subdivided into eight separate arrays that can be used in parallel experiments. Febit is planning chips with 34 micron pixels (each made up of four 16 micron pixels) that will use 30 mer oligos , although the company has been able to make oligos up to 60 mers long. Synthesis of each microarray with 30 mer oligos will take about 10 hours, the company said.
The machines built-in CCD detector is intended not only to collect experimental data, but also for quality control during array synthesis and for online detection, for example, to do melting curves.
This all-in-one approach is intended to allow microarray technicians to make arrays without moving them between different machines. We hope to avoid a lot of handling mistakes and therefore increase quality, Staehler said. However, the machine could also be used with an adapter to connect to an outside scanner, he added.
The German Cancer Research Institute (DKFZ) in Heidelberg is testing a prototype of febits instrument in a lymphoma genotyping study. (This prototype, which is not fully scaled up, makes chips with 30,000 features in four subunits.) Febit plans to launch its product in Europe as an early technology access program during the second quarter of 2002, and plans to involve about 20 customer sites. The company would like to expand these marketing efforts to the U.S. in late 2002, targeting not only research and development laboratories at academic institutes, but also in the biotechnology and pharmaceutical industries.
NimbleGen Proposes Maskless Array Synthesizer
When febit takes its product to the US, however, it may soon face home-grown competition. Microarray startup NimbleGen of Madison, Wis., which recently raised $9 million in additional funding, is developing what it calls the MAS Maskless Array Synthesizer) System. Unlike febits instrument, however, NimbleGens does not include a hybridization system. That way, We can remain flexible for the development of better scanners and other systems such as hybridization chambers, said NimbleGen CEO Mike Treble.
But what the instrument lacks in add-ons, it makes up in density. NimbleGen claims the microarrays synthesized using its instrument will have up to 195,000 features of 16 microns each, but can include smaller numbers of larger features; synthesis of a chip with 25 mer oligonucleotides currently takes under three hours. So far NimbleGen said it has been able to build up to 90 mer oligonucleotides.
The company, which also sells custom arrays, plans to deliver its first units to beta testers, among them the University of Wisconsin and Cambridge University in the UK, in about 12 months, and to launch a product in spring 2003.
NimbleGen will target core labs as well as biopharmaceutical customers that are currently using chips. We see it as a replacement for spotters, said Treble.
Gregory Khitrov, director of the gene array core facility at Rockefeller University, believes that laboratory-based in situ array synthesizers would be very useful. However, he is not sure they would work for every researcher. For those who know the sequences and genes they want to screen, that is great, but for the ones that do not and who want to start out, it is going to be a really hard process, he cautioned.
For this reason, febit also plans to offer researchers digital gene libraries containing oligonucleotide sequences. NimbleGen will offer online design tools for the arrays.