Inkjet spotting of arrays Agilent

Agilent (Palo Alto, CA) is building on its long history of highly engineered ink-jet delivery systems. It has licensed technology from Rosetta Inpharmatics (Kirkland, WA) so that it can synthesize and "spray" onto a glass slide oligonucleotide molecules in a highly localized fashion (see figure 7.3). That is, the nucleotides are "sprayed" separately by the ink-jet heads and linked in situ on the glass slide into oligonucleotides. At present, this technology permits up to 25,000 features per glass slide using volumes only in the picoliter range per feature. Because the features are built using longer nucleotides, there is typically only one feature per gene. This is in contrast to the 40 different features that are used in each probe set on Affymetrix oligonucleotide microarrays, using shorter and therefore individually less specific oligonucleotides.

Figure 7.3: Flexibility of on-the-fly ink-jet arrays. On the right is a comparison of morphology of ink-jet versus pin arrays. Ink-jet printing produces uniform and consistent features. An artifact of on-the-fly printing is formation of oblong spots at maximum print speed (full fires) that can be made into circles upon slowing down. This underscores the theoretical flexibility of this system. In theory, the contact-free nature of the ink-jet process could result in fewer spatial artifacts than the robotically spotted technique. Also, the synthesis technique used allows oligomers with a length up to 60 nucleotides to be constructed. Again, in theory, this could provide more specificity than the shorter oligonucleotides used by Affymetrix, and better normalization by GC content and correction for cross hybridization than longer cDNA molecules. The nature of this technology allows for a very rapid design and test cycle for these microarrays. Although it remains to be seen (at the time of this writing) whether Agilent does deliver on the promise of this technology, it has an opportunity to create a high-quality platform with manufacturing costs orders of magnitude less than others.

Figure 7.3: Flexibility of on-the-fly ink-jet arrays. On the right is a comparison of morphology of ink-jet versus pin arrays. Ink-jet printing produces uniform and consistent features. An artifact of on-the-fly printing is formation of oblong spots at maximum print speed (full fires) that can be made into circles upon slowing down. This underscores the theoretical flexibility of this system. In theory, the contact-free nature of the ink-jet process could result in fewer spatial artifacts than the robotically spotted technique. Also, the synthesis technique used allows oligomers with a length up to 60 nucleotides to be constructed. Again, in theory, this could provide more specificity than the shorter oligonucleotides used by Affymetrix, and better normalization by GC content and correction for cross hybridization than longer cDNA molecules. The nature of this technology allows for a very rapid design and test cycle for these microarrays. Although it remains to be seen (at the time of this writing) whether Agilent does deliver on the promise of this technology, it has an opportunity to create a high-quality platform with manufacturing costs orders of magnitude less than others.

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