This was a long good read, Schena our boy putting us out front.
Brown, Shalon, and Smith [29], and Davis and [color=red]Schena [30] have argued that spotted microarrays have several advantages over the in situ chips designed by Affymetrix and Edwin Southerland[/color]. As we have seen in the case of GeneChip® design, in situ synthesis methods work with oligonucleotides, libraries of nucleic acid sequences of between 2–25 base pairs. On a GeneChip® a given gene might be represented by 15–20 different 25-mer oligonucleotides that serve as unique sequence-specific detectors. To be effective, the Affymetrix arrays require gene sequence information for specifying the de novo synthesis of the oligomers on the array. Spotted microarrays by contrast represent genes by single DNA fragments greater than several hundred base pairs in length, and virtually any length or origin. Moreover, spotted arrays do not require prior sequence knowledge but can be produced from both known and unknown cDNA and PCR fragments. Spotted microarrays, it is argued, are more flexible and more easily adaptable to a variety of research problems in genomics. Also to the point, spotted microarrays are inexpensive by comparison to Affymetrix chips [31]. Indeed, microarrayers based on the Brown-Shalon design could basically be constructed in-house by most major university research labs at a complete cost (in 1999) of around $60,000 [32]. Brown in fact has been so committed to the low cost production of microarrayers and an open source approach as a means to expedite the production of knowledge in genomics that he posted on his Stanford website all the details of manufacture for his microarray system, including all the software updates for operation of the scanning system, details on manufacturing and servicing the printing tips, and other fine points of the system.
